Running as unit: rb-build-amd64_30-53789.service ==================================================================================== Wed Aug 6 07:21:07 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_30) on jenkins, called using "ionos15-amd64 ionos1-amd64" as arguments. Wed Aug 6 07:21:07 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-uLdYDhuw" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Aug 6 07:21:07 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Aug 6 07:21:07 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-9GowPi' Wed Aug 6 07:21:08 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Wed Aug 6 07:21:08 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-L1HiEt' ok, let's check if peptidebuilder is building anywhere yet… ok, peptidebuilder is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of peptidebuilder in trixie on amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Wed Aug 6 07:21:22 UTC 2025 I: starting to build peptidebuilder/trixie/amd64 on jenkins on '2025-08-06 07:21' Wed Aug 6 07:21:22 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_30/53789/console.log 1754464882 amd64 trixie peptidebuilder Wed Aug 6 07:21:22 UTC 2025 I: Downloading source for trixie/peptidebuilder=1.1.0-3 --2025-08-06 07:21:23-- http://deb.debian.org/debian/pool/main/p/peptidebuilder/peptidebuilder_1.1.0-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2239 (2.2K) [text/prs.lines.tag] Saving to: ‘peptidebuilder_1.1.0-3.dsc’ 0K .. 100% 264M=0s 2025-08-06 07:21:23 (264 MB/s) - ‘peptidebuilder_1.1.0-3.dsc’ saved [2239/2239] --2025-08-06 07:21:23-- http://deb.debian.org/debian/pool/main/p/peptidebuilder/peptidebuilder_1.1.0-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2239 (2.2K) [text/prs.lines.tag] Saving to: ‘peptidebuilder_1.1.0-3.dsc’ 0K .. 100% 264M=0s 2025-08-06 07:21:23 (264 MB/s) - ‘peptidebuilder_1.1.0-3.dsc’ saved [2239/2239] Wed Aug 6 07:21:23 UTC 2025 I: peptidebuilder_1.1.0-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: peptidebuilder Binary: python3-peptidebuilder Architecture: all Version: 1.1.0-3 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Nilesh Patra Homepage: https://github.com/clauswilke/PeptideBuilder/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/peptidebuilder Vcs-Git: https://salsa.debian.org/med-team/peptidebuilder.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: debhelper-compat (= 13), dh-python, python3-setuptools, python3-all, python3-biopython, python3-pytest , python3-pytest-cov Package-List: python3-peptidebuilder deb science optional arch=all Checksums-Sha1: a85fb4c9ed7ec362ae5ec59de54494bea15572a9 467902 peptidebuilder_1.1.0.orig.tar.gz 54117dfe573dcffca22d791cae9fbf5b563258b8 4016 peptidebuilder_1.1.0-3.debian.tar.xz Checksums-Sha256: 382b43fd118a3a7668fb03ecc07d8ffff6b8b522e687e4902d9f854426011e6d 467902 peptidebuilder_1.1.0.orig.tar.gz 8569e090c1ca19012108e18a45636d3189e57a6b124fdd8e70044ea362dde5a3 4016 peptidebuilder_1.1.0-3.debian.tar.xz Files: eee55fc2ed9e7a588483942dce64ae56 467902 peptidebuilder_1.1.0.orig.tar.gz e4fd36c0b9a8d0100c8fb8ff60195bf4 4016 peptidebuilder_1.1.0-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFgr+sRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHIyQ/8D9g/8Not/13uMO1TOddk8yvGW7dFdpwB +r/cSdmppFWWuJoyekscttOzISyaEP4a5cyazgulX3ebgkBeFnYRAe8tim0ZD2wx ikgRhKruaDeW5ACTXqSx19ESlSe51EwFFvUf1YuKsCd8XZ4cFDD3tax3aYr32TLA iiRNkKir2CoFMReen5AYpa/SwiSqm3yuDKYhi/gAOONV6taCG8CqjiufW0bGA6lH iV+k69Ts7WxIK00dB4/HzWscfwDN8hooZRMLu879l07V4fV1aDqwrr6eKpKJdr5M OtMqvQmgOTKJtNVSsBJftafv3GbTvC67I93vqld7N3Y0vDecjNRT4uUgDavFp4HK CZDYrNRwcRqSOlx8RJQl0Yljij0XoZZjvRQqNiOkDGqfcP+G4/6UALvKwGhrDRWC RijwhGr3iM46Qx5wf2stmo/xs1kG/VDbf2pIhHzoZ3Fvla1l+6wDO31lNrawlIln 0xg15HMQENK5LFkFmXiwhJ7RHLuAQGV4YpijEfXXeJEK8JXT1izN75Y62I5rOSRm 1WIHBSmh/PUERW6xBMewZQ+b2cX53oOV89c6yeJxtU6KgWR2V3US6LIc4XBt1z5T F/8FPPSoJC6QM01fJercG9NFMsF29cliIlwWwLRe4Bp+2JW/bcH7HXK0XdP3HpEj 5w0vQ41BRk4= =mUE9 -----END PGP SIGNATURE----- Wed Aug 6 07:21:23 UTC 2025 I: Checking whether the package is not for us Wed Aug 6 07:21:23 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Wed Aug 6 07:21:23 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Wed Aug 6 07:21:23 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Aug 6 07:21:23 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-EqO6KH' ==================================================================================== Tue Sep 8 13:44:23 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 peptidebuilder trixie /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe 1.1.0-3" as arguments. Tue Sep 8 13:44:23 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-Wqf4Olhg" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 8 13:44:23 UTC 2026 I: Downloading source for trixie/peptidebuilder=1.1.0-3 Reading package lists... NOTICE: 'peptidebuilder' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/peptidebuilder.git Please use: git clone https://salsa.debian.org/med-team/peptidebuilder.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 474 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (dsc) [2239 B] Get:2 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (tar) [468 kB] Get:3 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (diff) [4016 B] Fetched 474 kB in 0s (17.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'peptidebuilder' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/peptidebuilder.git Please use: git clone https://salsa.debian.org/med-team/peptidebuilder.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 474 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (dsc) [2239 B] Get:2 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (tar) [468 kB] Get:3 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (diff) [4016 B] Fetched 474 kB in 0s (17.4 MB/s) Download complete and in download only mode ============================================================================= Building peptidebuilder in trixie on amd64 on ionos15-amd64 now. Date: Tue Sep 8 13:44:23 UTC 2026 Date UTC: Tue Sep 8 13:44:23 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 Sep 8 01:44:23 -12 2026 I: pbuilder-time-stamp: 1788875063 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [peptidebuilder_1.1.0-3.dsc] I: copying [./peptidebuilder_1.1.0.orig.tar.gz] I: copying [./peptidebuilder_1.1.0-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./peptidebuilder_1.1.0-3.dsc: no acceptable signature found dpkg-source: info: extracting peptidebuilder in peptidebuilder-1.1.0 dpkg-source: info: unpacking peptidebuilder_1.1.0.orig.tar.gz dpkg-source: info: unpacking peptidebuilder_1.1.0-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-paths-with-os.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4134318/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='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='10d2f77fed4b48e2ba92525f40e313de' 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='4134318' 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.WogjSVQe/pbuilderrc_l9lc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b1 --logfile b1/build.log peptidebuilder_1.1.0-3.dsc' SUDO_GID='111' 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 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4134318/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-python, python3-setuptools, python3-all, python3-biopython, python3-pytest, python3-pytest-cov dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19851 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however: Package python3-pytest-cov 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} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-coverage{a} python3-freetype{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pytest{a} python3-pytest-cov{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra javascript-common libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-olefile python3-pygments shared-mime-info wget xdg-user-dirs 0 packages upgraded, 123 newly installed, 0 to remove and 0 not upgraded. Need to get 54.0 MB of archives. After unpacking 186 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-4 [260 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-4 [160 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-4 [2447 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250414 [116 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.48-1 [282 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 60 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.3-1 [1515 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-hotkeys all 0.2.0-1 [12.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 84 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get: 85 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.5-1 [1048 B] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 103 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.85+dfsg-4 [1672 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 python3-coverage amd64 7.6.0+dfsg1-2+b2 [175 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 114 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 120 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.5-2 [250 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 python3-pytest-cov all 5.0.0-1 [26.8 kB] Fetched 54.0 MB in 1s (77.0 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 ... 19851 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.5-2_amd64.deb ... Unpacking python3.13-minimal (3.13.5-2) ... Setting up libpython3.13-minimal:amd64 (3.13.5-2) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.5-2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20185 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_amd64.deb ... Unpacking python3-minimal (3.13.5-1) ... 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-4_all.deb ... Unpacking tzdata (2025b-4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_amd64.deb ... Unpacking python3.13 (3.13.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.5-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3-minimal (3.13.5-1) ... 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 ... 21200 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.5-1_amd64.deb ... Unpacking python3 (3.13.5-1) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../002-libblas3_3.12.1-4_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../003-libgfortran5_14.2.0-19_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-19) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../004-liblapack3_3.12.1-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-4) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy (1:2.2.4+ds-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../008-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../014-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../021-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../022-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../023-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../024-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../025-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../026-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../027-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../028-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../029-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../030-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../031-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../032-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../033-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../034-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package dh-python. Preparing to unpack .../035-dh-python_6.20250414_all.deb ... Unpacking dh-python (6.20250414) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../036-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../037-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../038-libfontenc1_1%3a1.1.8-1+b2_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.8-1+b2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../039-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../040-libpng16-16t64_1.6.48-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.48-1) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../041-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../042-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../043-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../044-xfonts-utils_1%3a7.7+7_amd64.deb ... Unpacking xfonts-utils (1:7.7+7) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../045-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../046-fontconfig-config_2.15.0-2.3_amd64.deb ... Unpacking fontconfig-config (2.15.0-2.3) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../047-libfontconfig1_2.15.0-2.3_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-2.3) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../048-libpixman-1-0_0.44.0-3_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.44.0-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../049-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../050-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../051-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../052-libx11-data_2%3a1.8.12-1_all.deb ... Unpacking libx11-data (2:1.8.12-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../053-libx11-6_2%3a1.8.12-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.12-1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../054-libxcb-render0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../055-libxcb-shm0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../056-libxext6_2%3a1.3.4-1+b3_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b3) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../057-libxrender1_1%3a0.9.12-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.12-1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../058-libcairo2_1.18.4-1+b1_amd64.deb ... Unpacking libcairo2:amd64 (1.18.4-1+b1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../059-libdeflate0_1.23-2_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-2) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../060-libfribidi0_1.0.16-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.16-1) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../061-libglib2.0-0t64_2.84.3-1_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.84.3-1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../062-libgraphite2-3_1.3.14-2+b1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../063-libharfbuzz0b_10.2.0-1+b1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (10.2.0-1+b1) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../064-libimagequant0_2.18.0-1+b2_amd64.deb ... Unpacking libimagequant0:amd64 (2.18.0-1+b2) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../065-libjbig0_2.1-6.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../066-libjpeg62-turbo_1%3a2.1.5-4_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-4) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../067-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-hotkeys. Preparing to unpack .../068-libjs-jquery-hotkeys_0.2.0-1_all.deb ... Unpacking libjs-jquery-hotkeys (0.2.0-1) ... Selecting previously unselected package libjs-jquery-isonscreen. Preparing to unpack .../069-libjs-jquery-isonscreen_1.2.0-1.1_all.deb ... Unpacking libjs-jquery-isonscreen (1.2.0-1.1) ... Selecting previously unselected package libjs-jquery-metadata. Preparing to unpack .../070-libjs-jquery-metadata_12-4_all.deb ... Unpacking libjs-jquery-metadata (12-4) ... Selecting previously unselected package libjs-jquery-tablesorter. Preparing to unpack .../071-libjs-jquery-tablesorter_1%3a2.31.3+dfsg1-4_all.deb ... Unpacking libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Selecting previously unselected package libjs-jquery-throttle-debounce. Preparing to unpack .../072-libjs-jquery-throttle-debounce_1.1+dfsg.1-2_all.deb ... Unpacking libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../073-liblcms2-2_2.16-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.16-2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../074-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../075-libopenjp2-7_2.5.3-2_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.3-2) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../076-libraqm0_0.10.2-1_amd64.deb ... Unpacking libraqm0:amd64 (0.10.2-1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../077-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../078-libwebp7_1.5.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../079-libtiff6_4.7.0-3_amd64.deb ... Unpacking libtiff6:amd64 (4.7.0-3) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../080-libwebpdemux2_1.5.0-0.1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../081-libwebpmux3_1.5.0-0.1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... Selecting previously unselected package python3-all. Preparing to unpack .../082-python3-all_3.13.5-1_amd64.deb ... Unpacking python3-all (3.13.5-1) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../083-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../084-python3-chardet_5.2.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-2) ... Selecting previously unselected package python3-pil:amd64. Preparing to unpack .../085-python3-pil_11.1.0-5+b1_amd64.deb ... Unpacking python3-pil:amd64 (11.1.0-5+b1) ... Selecting previously unselected package python3-cairo. Preparing to unpack .../086-python3-cairo_1.27.0-2_amd64.deb ... Unpacking python3-cairo (1.27.0-2) ... Selecting previously unselected package python3-freetype. Preparing to unpack .../087-python3-freetype_2.5.1-1_all.deb ... Unpacking python3-freetype (2.5.1-1) ... Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../088-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../089-python3-reportlab_4.3.1-1_all.deb ... Unpacking python3-reportlab (4.3.1-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../090-sgml-base_1.31+nmu1_all.deb ... Unpacking sgml-base (1.31+nmu1) ... Selecting previously unselected package xml-core. Preparing to unpack .../091-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../092-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../093-python3-biopython_1.85+dfsg-4_amd64.deb ... Unpacking python3-biopython (1.85+dfsg-4) ... Selecting previously unselected package python3-coverage. Preparing to unpack .../094-python3-coverage_7.6.0+dfsg1-2+b2_amd64.deb ... Unpacking python3-coverage (7.6.0+dfsg1-2+b2) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../095-python3-more-itertools_10.7.0-1_all.deb ... Unpacking python3-more-itertools (10.7.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../096-python3-typing-extensions_4.13.2-1_all.deb ... Unpacking python3-typing-extensions (4.13.2-1) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../097-python3-typeguard_4.4.2-1_all.deb ... Unpacking python3-typeguard (4.4.2-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../098-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../099-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../100-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 .../101-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 .../102-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 .../103-python3-zipp_3.21.0-1_all.deb ... Unpacking python3-zipp (3.21.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../104-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 .../105-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../106-python3-packaging_25.0-1_all.deb ... Unpacking python3-packaging (25.0-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../107-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../108-python3-pytest_8.3.5-2_all.deb ... Unpacking python3-pytest (8.3.5-2) ... Selecting previously unselected package python3-pytest-cov. Preparing to unpack .../109-python3-pytest-cov_5.0.0-1_all.deb ... Unpacking python3-pytest-cov (5.0.0-1) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up file (1:5.46-5) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Sep 8 13:45:12 UTC 2026. Universal Time is now: Tue Sep 8 13:45:12 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libx11-data (2:1.8.12-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.48-1) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up autopoint (0.23.1-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libtiff6:amd64 (4.7.0-3) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libopenjp2-7:amd64 (2.5.3-2) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libjs-jquery-hotkeys (0.2.0-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libtool (2.5.4-4) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libglib2.0-0t64:amd64 (2.84.3-1) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3.13 (3.13.5-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.5-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... 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 libcairo2:amd64 (1.18.4-1+b1) ... Setting up python3-packaging (25.0-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-pytest (8.3.5-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-all (3.13.5-1) ... Setting up python3-coverage (7.6.0+dfsg1-2+b2) ... Setting up debhelper (13.24.2) ... Setting up python3-pytest-cov (5.0.0-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:amd64 (11.1.0-5+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-reportlab (4.3.1-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-11) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-4) ... 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/peptidebuilder-1.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../peptidebuilder_1.1.0-3_source.changes dpkg-buildpackage: info: source package peptidebuilder dpkg-buildpackage: info: source version 1.1.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from peptidebuilder-1.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p 3.13 I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/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 -rf .pybuild/ find . -name \*.pyc -exec rm {} \; dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-peptidebuilder.substvars debian/files rm -fr -- debian/python3-peptidebuilder/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.13 I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p 3.13 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/peptidebuilder-1.1.0' PYTHONPATH=$(pwd) pytest-3 ============================= test session starts ============================== platform linux -- Python 3.13.5, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /build/reproducible-path/peptidebuilder-1.1.0 configfile: pytest.ini testpaths: tests plugins: cov-5.0.0, typeguard-4.4.2 collecting ... collected 28 items tests/test_Geometry.py::test_geometry_A PASSED [ 3%] tests/test_Geometry.py::test_geometry_C PASSED [ 7%] tests/test_Geometry.py::test_geometry_D PASSED [ 10%] tests/test_Geometry.py::test_geometry_E PASSED [ 14%] tests/test_Geometry.py::test_geometry_F PASSED [ 17%] tests/test_Geometry.py::test_geometry_G PASSED [ 21%] tests/test_Geometry.py::test_geometry_H PASSED [ 25%] tests/test_Geometry.py::test_geometry_I PASSED [ 28%] tests/test_Geometry.py::test_geometry_K PASSED [ 32%] tests/test_Geometry.py::test_geometry_L PASSED [ 35%] tests/test_Geometry.py::test_geometry_M PASSED [ 39%] tests/test_Geometry.py::test_geometry_N PASSED [ 42%] tests/test_Geometry.py::test_geometry_P PASSED [ 46%] tests/test_Geometry.py::test_geometry_Q PASSED [ 50%] tests/test_Geometry.py::test_geometry_R PASSED [ 53%] tests/test_Geometry.py::test_geometry_S PASSED [ 57%] tests/test_Geometry.py::test_geometry_T PASSED [ 60%] tests/test_Geometry.py::test_geometry_V PASSED [ 64%] tests/test_Geometry.py::test_geometry_W PASSED [ 67%] tests/test_Geometry.py::test_geometry_Y PASSED [ 71%] tests/test_PeptideBuilder.py::test_add_residue PASSED [ 75%] tests/test_PeptideBuilder.py::test_add_residue2 PASSED [ 78%] tests/test_PeptideBuilder.py::test_make_structure_from_geos PASSED [ 82%] tests/test_PeptideBuilder.py::test_make_extended_structure PASSED [ 85%] tests/test_PeptideBuilder.py::test_make_structure_from_geos2 PASSED [ 89%] tests/test_PeptideBuilder.py::test_make_structure PASSED [ 92%] tests/test_PeptideBuilder.py::test_make_structure2 PASSED [ 96%] tests/test_PeptideBuilder.py::test_add_terminal_OXT PASSED [100%] =============================== warnings summary =============================== tests/test_PeptideBuilder.py: 10 warnings /usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:384: PDBConstructionWarning: Ignoring unrecognized record 'TER' at line 168 warnings.warn( tests/test_PeptideBuilder.py: 10 warnings /usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:384: PDBConstructionWarning: Ignoring unrecognized record 'END' at line 169 warnings.warn( tests/test_PeptideBuilder.py::test_add_terminal_OXT /usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:384: PDBConstructionWarning: Ignoring unrecognized record 'END' at line 170 warnings.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ---------- coverage: platform linux, python 3.13.5-final-0 ----------- Name Stmts Miss Cover ------------------------------------------------------ PeptideBuilder/Geometry.py 846 204 76% PeptideBuilder/PeptideBuilder.py 869 3 99% PeptideBuilder/__init__.py 3 0 100% ------------------------------------------------------ TOTAL 1718 207 88% ======================= 28 passed, 21 warnings in 2.37s ======================== make[1]: Leaving directory '/build/reproducible-path/peptidebuilder-1.1.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/python3-peptidebuilder.substvars rm -fr -- debian/.debhelper/generated/python3-peptidebuilder/ debian/python3-peptidebuilder/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/peptidebuilder-1.1.0' dh_auto_install install -m0755 -d /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder pybuild --install -i python{version} -p 3.13 --dest-dir=/build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() 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 running install_lib creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/PeptideBuilder.py to PeptideBuilder.cpython-313.pyc byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/Geometry.py to Geometry.cpython-313.pyc byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/__init__.py to __init__.cpython-313.pyc running install_egg_info running egg_info creating PeptideBuilder.egg-info writing PeptideBuilder.egg-info/PKG-INFO writing dependency_links to PeptideBuilder.egg-info/dependency_links.txt writing requirements to PeptideBuilder.egg-info/requires.txt writing top-level names to PeptideBuilder.egg-info/top_level.txt writing manifest file 'PeptideBuilder.egg-info/SOURCES.txt' reading manifest file 'PeptideBuilder.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'PeptideBuilder.egg-info/SOURCES.txt' Copying PeptideBuilder.egg-info to /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder-1.1.0.egg-info Skipping SOURCES.txt running install_scripts find debian/python3-peptidebuilder/usr/lib/ -name .coverage -delete make[1]: Leaving directory '/build/reproducible-path/peptidebuilder-1.1.0' dh_installdocs -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder install -p -m0644 debian/copyright debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder/copyright dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder install -p -m0644 debian/.debhelper/generated/python3-peptidebuilder/dh_installchangelogs.dch.trimmed debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder/changelog.Debian dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:180: version: 6.20250414 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:183: supported Python versions: 3.13 (default=3.13) D: dh_python3 debhelper:174: source=peptidebuilder, binary packages=['python3-peptidebuilder'] D: dh_python3 dh_python3:205: processing package python3-peptidebuilder... D: dh_python3 fs:50: moving files from debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages to debian/python3-peptidebuilder/usr/lib/python3/dist-packages/ D: dh_python3 fs:338: package python3-peptidebuilder details = {'requires.txt': {'debian/python3-peptidebuilder/usr/lib/python3/dist-packages/PeptideBuilder-1.1.0.egg-info/requires.txt'}, 'egg-info': {'debian/python3-peptidebuilder/usr/lib/python3/dist-packages/PeptideBuilder-1.1.0.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-peptidebuilder D: dh_python3 pydist:175: trying to find dependency for Biopython (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 depends:253: D={'python3:any', 'python3-biopython'}; R=[]; S=[]; E=[], B=[]; RT=[] 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 cd debian/python3-peptidebuilder chmod a-x usr/share/doc/python3-peptidebuilder/changelog.Debian gzip -9nf usr/share/doc/python3-peptidebuilder/changelog.Debian cd '/build/reproducible-path/peptidebuilder-1.1.0' dh_fixperms -O--buildsystem=pybuild find debian/python3-peptidebuilder ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-peptidebuilder/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-peptidebuilder/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-peptidebuilder/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-peptidebuilder -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-peptidebuilder/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-peptidebuilder/DEBIAN/postinst cat debian/python3-peptidebuilder.postinst.debhelper >> debian/python3-peptidebuilder/DEBIAN/postinst chmod 0755 -- debian/python3-peptidebuilder/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-peptidebuilder/DEBIAN/prerm cat debian/python3-peptidebuilder.prerm.debhelper >> debian/python3-peptidebuilder/DEBIAN/prerm chmod 0755 -- debian/python3-peptidebuilder/DEBIAN/prerm dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/DEBIAN echo misc:Depends= >> debian/python3-peptidebuilder.substvars echo misc:Pre-Depends= >> debian/python3-peptidebuilder.substvars dpkg-gencontrol -ppython3-peptidebuilder -ldebian/changelog -Tdebian/python3-peptidebuilder.substvars -cdebian/control -Pdebian/python3-peptidebuilder chmod 0644 -- debian/python3-peptidebuilder/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/DEBIAN cd debian/python3-peptidebuilder >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-peptidebuilder/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-peptidebuilder .. dpkg-deb: building package 'python3-peptidebuilder' in '../python3-peptidebuilder_1.1.0-3_all.deb'. dpkg-genbuildinfo --build=binary -O../peptidebuilder_1.1.0-3_amd64.buildinfo dpkg-genchanges --build=binary -O../peptidebuilder_1.1.0-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from peptidebuilder-1.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ 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/4134318 and its subdirectories I: Current time: Tue Sep 8 01:47:10 -12 2026 I: pbuilder-time-stamp: 1788875230 Tue Sep 8 13:47:10 UTC 2026 I: Signing ./b1/peptidebuilder_1.1.0-3_amd64.buildinfo as peptidebuilder_1.1.0-3_amd64.buildinfo.asc Tue Sep 8 13:47:10 UTC 2026 I: Signed ./b1/peptidebuilder_1.1.0-3_amd64.buildinfo as ./b1/peptidebuilder_1.1.0-3_amd64.buildinfo.asc Tue Sep 8 13:47:10 UTC 2026 - build #1 for peptidebuilder/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Tue Sep 8 13:47:10 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-Wqf4Olhg, removing. /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 07:24 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 07:21 b2 -rw-r--r-- 1 jenkins jenkins 2239 Oct 8 2021 peptidebuilder_1.1.0-3.dsc -rw------- 1 jenkins jenkins 3386 Aug 6 07:21 rbuildlog.26OTdsE /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b1: total 120 -rw-r--r-- 1 jenkins jenkins 69137 Aug 6 07:24 build.log -rw-r--r-- 1 jenkins jenkins 4016 Aug 6 07:24 peptidebuilder_1.1.0-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2239 Aug 6 07:24 peptidebuilder_1.1.0-3.dsc -rw-r--r-- 1 jenkins jenkins 7572 Aug 6 07:24 peptidebuilder_1.1.0-3_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8454 Aug 6 07:24 peptidebuilder_1.1.0-3_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1275 Aug 6 07:24 peptidebuilder_1.1.0-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 1398 Aug 6 07:24 peptidebuilder_1.1.0-3_source.changes -rw-r--r-- 1 jenkins jenkins 12844 Aug 6 07:24 python3-peptidebuilder_1.1.0-3_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b2: total 0 Wed Aug 6 07:24:11 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 8 01:44:23 -12 2026 I: pbuilder-time-stamp: 1788875063 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [peptidebuilder_1.1.0-3.dsc] I: copying [./peptidebuilder_1.1.0.orig.tar.gz] I: copying [./peptidebuilder_1.1.0-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./peptidebuilder_1.1.0-3.dsc: no acceptable signature found dpkg-source: info: extracting peptidebuilder in peptidebuilder-1.1.0 dpkg-source: info: unpacking peptidebuilder_1.1.0.orig.tar.gz dpkg-source: info: unpacking peptidebuilder_1.1.0-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-paths-with-os.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4134318/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='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='10d2f77fed4b48e2ba92525f40e313de' 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='4134318' 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.WogjSVQe/pbuilderrc_l9lc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b1 --logfile b1/build.log peptidebuilder_1.1.0-3.dsc' SUDO_GID='111' 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 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4134318/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-python, python3-setuptools, python3-all, python3-biopython, python3-pytest, python3-pytest-cov dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19851 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however: Package python3-pytest-cov 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} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-coverage{a} python3-freetype{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pytest{a} python3-pytest-cov{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra javascript-common libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-olefile python3-pygments shared-mime-info wget xdg-user-dirs 0 packages upgraded, 123 newly installed, 0 to remove and 0 not upgraded. Need to get 54.0 MB of archives. After unpacking 186 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-4 [260 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-4 [160 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-4 [2447 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250414 [116 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.48-1 [282 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 60 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.3-1 [1515 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-hotkeys all 0.2.0-1 [12.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 84 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get: 85 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.5-1 [1048 B] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 103 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.85+dfsg-4 [1672 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 python3-coverage amd64 7.6.0+dfsg1-2+b2 [175 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 114 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 120 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.5-2 [250 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 python3-pytest-cov all 5.0.0-1 [26.8 kB] Fetched 54.0 MB in 1s (77.0 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 ... 19851 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.5-2_amd64.deb ... Unpacking python3.13-minimal (3.13.5-2) ... Setting up libpython3.13-minimal:amd64 (3.13.5-2) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.5-2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20185 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_amd64.deb ... Unpacking python3-minimal (3.13.5-1) ... 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-4_all.deb ... Unpacking tzdata (2025b-4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_amd64.deb ... Unpacking python3.13 (3.13.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.5-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3-minimal (3.13.5-1) ... 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 ... 21200 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.5-1_amd64.deb ... Unpacking python3 (3.13.5-1) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../002-libblas3_3.12.1-4_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../003-libgfortran5_14.2.0-19_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-19) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../004-liblapack3_3.12.1-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-4) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy (1:2.2.4+ds-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../008-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../014-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../021-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../022-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../023-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../024-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../025-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../026-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../027-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../028-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../029-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../030-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../031-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../032-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../033-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../034-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package dh-python. Preparing to unpack .../035-dh-python_6.20250414_all.deb ... Unpacking dh-python (6.20250414) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../036-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../037-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../038-libfontenc1_1%3a1.1.8-1+b2_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.8-1+b2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../039-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../040-libpng16-16t64_1.6.48-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.48-1) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../041-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../042-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../043-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../044-xfonts-utils_1%3a7.7+7_amd64.deb ... Unpacking xfonts-utils (1:7.7+7) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../045-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../046-fontconfig-config_2.15.0-2.3_amd64.deb ... Unpacking fontconfig-config (2.15.0-2.3) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../047-libfontconfig1_2.15.0-2.3_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-2.3) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../048-libpixman-1-0_0.44.0-3_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.44.0-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../049-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../050-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../051-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../052-libx11-data_2%3a1.8.12-1_all.deb ... Unpacking libx11-data (2:1.8.12-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../053-libx11-6_2%3a1.8.12-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.12-1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../054-libxcb-render0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../055-libxcb-shm0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../056-libxext6_2%3a1.3.4-1+b3_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b3) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../057-libxrender1_1%3a0.9.12-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.12-1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../058-libcairo2_1.18.4-1+b1_amd64.deb ... Unpacking libcairo2:amd64 (1.18.4-1+b1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../059-libdeflate0_1.23-2_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-2) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../060-libfribidi0_1.0.16-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.16-1) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../061-libglib2.0-0t64_2.84.3-1_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.84.3-1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../062-libgraphite2-3_1.3.14-2+b1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../063-libharfbuzz0b_10.2.0-1+b1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (10.2.0-1+b1) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../064-libimagequant0_2.18.0-1+b2_amd64.deb ... Unpacking libimagequant0:amd64 (2.18.0-1+b2) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../065-libjbig0_2.1-6.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../066-libjpeg62-turbo_1%3a2.1.5-4_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-4) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../067-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-hotkeys. Preparing to unpack .../068-libjs-jquery-hotkeys_0.2.0-1_all.deb ... Unpacking libjs-jquery-hotkeys (0.2.0-1) ... Selecting previously unselected package libjs-jquery-isonscreen. Preparing to unpack .../069-libjs-jquery-isonscreen_1.2.0-1.1_all.deb ... Unpacking libjs-jquery-isonscreen (1.2.0-1.1) ... Selecting previously unselected package libjs-jquery-metadata. Preparing to unpack .../070-libjs-jquery-metadata_12-4_all.deb ... Unpacking libjs-jquery-metadata (12-4) ... Selecting previously unselected package libjs-jquery-tablesorter. Preparing to unpack .../071-libjs-jquery-tablesorter_1%3a2.31.3+dfsg1-4_all.deb ... Unpacking libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Selecting previously unselected package libjs-jquery-throttle-debounce. Preparing to unpack .../072-libjs-jquery-throttle-debounce_1.1+dfsg.1-2_all.deb ... Unpacking libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../073-liblcms2-2_2.16-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.16-2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../074-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../075-libopenjp2-7_2.5.3-2_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.3-2) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../076-libraqm0_0.10.2-1_amd64.deb ... Unpacking libraqm0:amd64 (0.10.2-1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../077-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../078-libwebp7_1.5.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../079-libtiff6_4.7.0-3_amd64.deb ... Unpacking libtiff6:amd64 (4.7.0-3) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../080-libwebpdemux2_1.5.0-0.1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../081-libwebpmux3_1.5.0-0.1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... Selecting previously unselected package python3-all. Preparing to unpack .../082-python3-all_3.13.5-1_amd64.deb ... Unpacking python3-all (3.13.5-1) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../083-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../084-python3-chardet_5.2.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-2) ... Selecting previously unselected package python3-pil:amd64. Preparing to unpack .../085-python3-pil_11.1.0-5+b1_amd64.deb ... Unpacking python3-pil:amd64 (11.1.0-5+b1) ... Selecting previously unselected package python3-cairo. Preparing to unpack .../086-python3-cairo_1.27.0-2_amd64.deb ... Unpacking python3-cairo (1.27.0-2) ... Selecting previously unselected package python3-freetype. Preparing to unpack .../087-python3-freetype_2.5.1-1_all.deb ... Unpacking python3-freetype (2.5.1-1) ... Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../088-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../089-python3-reportlab_4.3.1-1_all.deb ... Unpacking python3-reportlab (4.3.1-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../090-sgml-base_1.31+nmu1_all.deb ... Unpacking sgml-base (1.31+nmu1) ... Selecting previously unselected package xml-core. Preparing to unpack .../091-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../092-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../093-python3-biopython_1.85+dfsg-4_amd64.deb ... Unpacking python3-biopython (1.85+dfsg-4) ... Selecting previously unselected package python3-coverage. Preparing to unpack .../094-python3-coverage_7.6.0+dfsg1-2+b2_amd64.deb ... Unpacking python3-coverage (7.6.0+dfsg1-2+b2) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../095-python3-more-itertools_10.7.0-1_all.deb ... Unpacking python3-more-itertools (10.7.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../096-python3-typing-extensions_4.13.2-1_all.deb ... Unpacking python3-typing-extensions (4.13.2-1) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../097-python3-typeguard_4.4.2-1_all.deb ... Unpacking python3-typeguard (4.4.2-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../098-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../099-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../100-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 .../101-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 .../102-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 .../103-python3-zipp_3.21.0-1_all.deb ... Unpacking python3-zipp (3.21.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../104-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 .../105-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../106-python3-packaging_25.0-1_all.deb ... Unpacking python3-packaging (25.0-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../107-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../108-python3-pytest_8.3.5-2_all.deb ... Unpacking python3-pytest (8.3.5-2) ... Selecting previously unselected package python3-pytest-cov. Preparing to unpack .../109-python3-pytest-cov_5.0.0-1_all.deb ... Unpacking python3-pytest-cov (5.0.0-1) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up file (1:5.46-5) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Sep 8 13:45:12 UTC 2026. Universal Time is now: Tue Sep 8 13:45:12 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libx11-data (2:1.8.12-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.48-1) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up autopoint (0.23.1-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libtiff6:amd64 (4.7.0-3) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libopenjp2-7:amd64 (2.5.3-2) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libjs-jquery-hotkeys (0.2.0-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libtool (2.5.4-4) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libglib2.0-0t64:amd64 (2.84.3-1) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3.13 (3.13.5-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.5-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... 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 libcairo2:amd64 (1.18.4-1+b1) ... Setting up python3-packaging (25.0-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-pytest (8.3.5-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-all (3.13.5-1) ... Setting up python3-coverage (7.6.0+dfsg1-2+b2) ... Setting up debhelper (13.24.2) ... Setting up python3-pytest-cov (5.0.0-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:amd64 (11.1.0-5+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-reportlab (4.3.1-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-11) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-4) ... 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/peptidebuilder-1.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../peptidebuilder_1.1.0-3_source.changes dpkg-buildpackage: info: source package peptidebuilder dpkg-buildpackage: info: source version 1.1.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from peptidebuilder-1.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p 3.13 I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/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 -rf .pybuild/ find . -name \*.pyc -exec rm {} \; dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-peptidebuilder.substvars debian/files rm -fr -- debian/python3-peptidebuilder/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.13 I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p 3.13 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/peptidebuilder-1.1.0' PYTHONPATH=$(pwd) pytest-3 ============================= test session starts ============================== platform linux -- Python 3.13.5, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /build/reproducible-path/peptidebuilder-1.1.0 configfile: pytest.ini testpaths: tests plugins: cov-5.0.0, typeguard-4.4.2 collecting ... collected 28 items tests/test_Geometry.py::test_geometry_A PASSED [ 3%] tests/test_Geometry.py::test_geometry_C PASSED [ 7%] tests/test_Geometry.py::test_geometry_D PASSED [ 10%] tests/test_Geometry.py::test_geometry_E PASSED [ 14%] tests/test_Geometry.py::test_geometry_F PASSED [ 17%] tests/test_Geometry.py::test_geometry_G PASSED [ 21%] tests/test_Geometry.py::test_geometry_H PASSED [ 25%] tests/test_Geometry.py::test_geometry_I PASSED [ 28%] tests/test_Geometry.py::test_geometry_K PASSED [ 32%] tests/test_Geometry.py::test_geometry_L PASSED [ 35%] tests/test_Geometry.py::test_geometry_M PASSED [ 39%] tests/test_Geometry.py::test_geometry_N PASSED [ 42%] tests/test_Geometry.py::test_geometry_P PASSED [ 46%] tests/test_Geometry.py::test_geometry_Q PASSED [ 50%] tests/test_Geometry.py::test_geometry_R PASSED [ 53%] tests/test_Geometry.py::test_geometry_S PASSED [ 57%] tests/test_Geometry.py::test_geometry_T PASSED [ 60%] tests/test_Geometry.py::test_geometry_V PASSED [ 64%] tests/test_Geometry.py::test_geometry_W PASSED [ 67%] tests/test_Geometry.py::test_geometry_Y PASSED [ 71%] tests/test_PeptideBuilder.py::test_add_residue PASSED [ 75%] tests/test_PeptideBuilder.py::test_add_residue2 PASSED [ 78%] tests/test_PeptideBuilder.py::test_make_structure_from_geos PASSED [ 82%] tests/test_PeptideBuilder.py::test_make_extended_structure PASSED [ 85%] tests/test_PeptideBuilder.py::test_make_structure_from_geos2 PASSED [ 89%] tests/test_PeptideBuilder.py::test_make_structure PASSED [ 92%] tests/test_PeptideBuilder.py::test_make_structure2 PASSED [ 96%] tests/test_PeptideBuilder.py::test_add_terminal_OXT PASSED [100%] =============================== warnings summary =============================== tests/test_PeptideBuilder.py: 10 warnings /usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:384: PDBConstructionWarning: Ignoring unrecognized record 'TER' at line 168 warnings.warn( tests/test_PeptideBuilder.py: 10 warnings /usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:384: PDBConstructionWarning: Ignoring unrecognized record 'END' at line 169 warnings.warn( tests/test_PeptideBuilder.py::test_add_terminal_OXT /usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:384: PDBConstructionWarning: Ignoring unrecognized record 'END' at line 170 warnings.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ---------- coverage: platform linux, python 3.13.5-final-0 ----------- Name Stmts Miss Cover ------------------------------------------------------ PeptideBuilder/Geometry.py 846 204 76% PeptideBuilder/PeptideBuilder.py 869 3 99% PeptideBuilder/__init__.py 3 0 100% ------------------------------------------------------ TOTAL 1718 207 88% ======================= 28 passed, 21 warnings in 2.37s ======================== make[1]: Leaving directory '/build/reproducible-path/peptidebuilder-1.1.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/python3-peptidebuilder.substvars rm -fr -- debian/.debhelper/generated/python3-peptidebuilder/ debian/python3-peptidebuilder/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/peptidebuilder-1.1.0' dh_auto_install install -m0755 -d /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder pybuild --install -i python{version} -p 3.13 --dest-dir=/build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() 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 running install_lib creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/PeptideBuilder.py to PeptideBuilder.cpython-313.pyc byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/Geometry.py to Geometry.cpython-313.pyc byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/__init__.py to __init__.cpython-313.pyc running install_egg_info running egg_info creating PeptideBuilder.egg-info writing PeptideBuilder.egg-info/PKG-INFO writing dependency_links to PeptideBuilder.egg-info/dependency_links.txt writing requirements to PeptideBuilder.egg-info/requires.txt writing top-level names to PeptideBuilder.egg-info/top_level.txt writing manifest file 'PeptideBuilder.egg-info/SOURCES.txt' reading manifest file 'PeptideBuilder.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'PeptideBuilder.egg-info/SOURCES.txt' Copying PeptideBuilder.egg-info to /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder-1.1.0.egg-info Skipping SOURCES.txt running install_scripts find debian/python3-peptidebuilder/usr/lib/ -name .coverage -delete make[1]: Leaving directory '/build/reproducible-path/peptidebuilder-1.1.0' dh_installdocs -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder install -p -m0644 debian/copyright debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder/copyright dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder install -p -m0644 debian/.debhelper/generated/python3-peptidebuilder/dh_installchangelogs.dch.trimmed debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder/changelog.Debian dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:180: version: 6.20250414 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:183: supported Python versions: 3.13 (default=3.13) D: dh_python3 debhelper:174: source=peptidebuilder, binary packages=['python3-peptidebuilder'] D: dh_python3 dh_python3:205: processing package python3-peptidebuilder... D: dh_python3 fs:50: moving files from debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages to debian/python3-peptidebuilder/usr/lib/python3/dist-packages/ D: dh_python3 fs:338: package python3-peptidebuilder details = {'requires.txt': {'debian/python3-peptidebuilder/usr/lib/python3/dist-packages/PeptideBuilder-1.1.0.egg-info/requires.txt'}, 'egg-info': {'debian/python3-peptidebuilder/usr/lib/python3/dist-packages/PeptideBuilder-1.1.0.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-peptidebuilder D: dh_python3 pydist:175: trying to find dependency for Biopython (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 depends:253: D={'python3:any', 'python3-biopython'}; R=[]; S=[]; E=[], B=[]; RT=[] 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 cd debian/python3-peptidebuilder chmod a-x usr/share/doc/python3-peptidebuilder/changelog.Debian gzip -9nf usr/share/doc/python3-peptidebuilder/changelog.Debian cd '/build/reproducible-path/peptidebuilder-1.1.0' dh_fixperms -O--buildsystem=pybuild find debian/python3-peptidebuilder ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-peptidebuilder/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-peptidebuilder/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-peptidebuilder/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-peptidebuilder -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-peptidebuilder/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-peptidebuilder/DEBIAN/postinst cat debian/python3-peptidebuilder.postinst.debhelper >> debian/python3-peptidebuilder/DEBIAN/postinst chmod 0755 -- debian/python3-peptidebuilder/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-peptidebuilder/DEBIAN/prerm cat debian/python3-peptidebuilder.prerm.debhelper >> debian/python3-peptidebuilder/DEBIAN/prerm chmod 0755 -- debian/python3-peptidebuilder/DEBIAN/prerm dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/DEBIAN echo misc:Depends= >> debian/python3-peptidebuilder.substvars echo misc:Pre-Depends= >> debian/python3-peptidebuilder.substvars dpkg-gencontrol -ppython3-peptidebuilder -ldebian/changelog -Tdebian/python3-peptidebuilder.substvars -cdebian/control -Pdebian/python3-peptidebuilder chmod 0644 -- debian/python3-peptidebuilder/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/DEBIAN cd debian/python3-peptidebuilder >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-peptidebuilder/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-peptidebuilder .. dpkg-deb: building package 'python3-peptidebuilder' in '../python3-peptidebuilder_1.1.0-3_all.deb'. dpkg-genbuildinfo --build=binary -O../peptidebuilder_1.1.0-3_amd64.buildinfo dpkg-genchanges --build=binary -O../peptidebuilder_1.1.0-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from peptidebuilder-1.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ 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/4134318 and its subdirectories I: Current time: Tue Sep 8 01:47:10 -12 2026 I: pbuilder-time-stamp: 1788875230 Wed Aug 6 07:24:11 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Wed Aug 6 07:24:11 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Wed Aug 6 07:24:11 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Wed Aug 6 07:24:11 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Wx0Q7t' ==================================================================================== Wed Aug 6 07:24:12 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "2 peptidebuilder trixie /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe 1.1.0-3" as arguments. Wed Aug 6 07:24:12 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-k70d8nZr" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Aug 6 07:24:12 UTC 2025 I: Downloading source for trixie/peptidebuilder=1.1.0-3 Reading package lists... NOTICE: 'peptidebuilder' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/peptidebuilder.git Please use: git clone https://salsa.debian.org/med-team/peptidebuilder.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 474 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (dsc) [2239 B] Get:2 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (tar) [468 kB] Get:3 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (diff) [4016 B] Fetched 474 kB in 0s (14.6 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'peptidebuilder' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/peptidebuilder.git Please use: git clone https://salsa.debian.org/med-team/peptidebuilder.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 474 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (dsc) [2239 B] Get:2 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (tar) [468 kB] Get:3 http://deb.debian.org/debian trixie/main peptidebuilder 1.1.0-3 (diff) [4016 B] Fetched 474 kB in 0s (14.6 MB/s) Download complete and in download only mode ============================================================================= Re-Building peptidebuilder in trixie on amd64 on ionos1-amd64 now. Date: Wed Aug 6 07:24:13 UTC 2025 Date UTC: Wed Aug 6 07:24:13 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/pbuilderrc_Zg3u + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' peptidebuilder = debian-installer -o peptidebuilder = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' peptidebuilder = u-boot ']' + case "${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.WogjSVQe/pbuilderrc_Zg3u --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b2 --logfile b2/build.log peptidebuilder_1.1.0-3.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: Wed Aug 6 21:24:13 +14 2025 I: pbuilder-time-stamp: 1754465053 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [peptidebuilder_1.1.0-3.dsc] I: copying [./peptidebuilder_1.1.0.orig.tar.gz] I: copying [./peptidebuilder_1.1.0-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./peptidebuilder_1.1.0-3.dsc: no acceptable signature found dpkg-source: info: extracting peptidebuilder in peptidebuilder-1.1.0 dpkg-source: info: unpacking peptidebuilder_1.1.0.orig.tar.gz dpkg-source: info: unpacking peptidebuilder_1.1.0-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-paths-with-os.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/580776/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-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 Aug 6 07:24 /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/580776/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/580776/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=7fc4a66d8b2742718b18aa1559874c5c 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=580776 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.WogjSVQe/pbuilderrc_Zg3u --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b2 --logfile b2/build.log peptidebuilder_1.1.0-3.dsc' SUDO_GID=110 SUDO_UID=105 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 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/580776/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-python, python3-setuptools, python3-all, python3-biopython, python3-pytest, python3-pytest-cov dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19851 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however: Package python3-pytest-cov 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} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-coverage{a} python3-freetype{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pytest{a} python3-pytest-cov{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra javascript-common libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-olefile python3-pygments shared-mime-info wget xdg-user-dirs 0 packages upgraded, 123 newly installed, 0 to remove and 0 not upgraded. Need to get 54.0 MB of archives. After unpacking 186 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-4 [260 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-4 [160 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-4 [2447 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250414 [116 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.48-1 [282 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 60 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.3-1 [1515 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-hotkeys all 0.2.0-1 [12.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 84 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get: 85 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.5-1 [1048 B] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 103 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.85+dfsg-4 [1672 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 python3-coverage amd64 7.6.0+dfsg1-2+b2 [175 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 114 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 120 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.5-2 [250 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 python3-pytest-cov all 5.0.0-1 [26.8 kB] Fetched 54.0 MB in 3s (17.3 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 ... 19851 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.5-2_amd64.deb ... Unpacking python3.13-minimal (3.13.5-2) ... Setting up libpython3.13-minimal:amd64 (3.13.5-2) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.5-2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20185 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_amd64.deb ... Unpacking python3-minimal (3.13.5-1) ... 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-4_all.deb ... Unpacking tzdata (2025b-4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_amd64.deb ... Unpacking python3.13 (3.13.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.5-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3-minimal (3.13.5-1) ... 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 ... 21200 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.5-1_amd64.deb ... Unpacking python3 (3.13.5-1) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../002-libblas3_3.12.1-4_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../003-libgfortran5_14.2.0-19_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-19) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../004-liblapack3_3.12.1-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-4) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy (1:2.2.4+ds-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../008-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../014-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../021-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../022-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../023-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../024-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../025-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../026-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../027-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../028-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../029-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../030-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../031-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../032-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../033-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../034-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package dh-python. Preparing to unpack .../035-dh-python_6.20250414_all.deb ... Unpacking dh-python (6.20250414) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../036-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../037-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../038-libfontenc1_1%3a1.1.8-1+b2_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.8-1+b2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../039-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../040-libpng16-16t64_1.6.48-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.48-1) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../041-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../042-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../043-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../044-xfonts-utils_1%3a7.7+7_amd64.deb ... Unpacking xfonts-utils (1:7.7+7) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../045-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../046-fontconfig-config_2.15.0-2.3_amd64.deb ... Unpacking fontconfig-config (2.15.0-2.3) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../047-libfontconfig1_2.15.0-2.3_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-2.3) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../048-libpixman-1-0_0.44.0-3_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.44.0-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../049-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../050-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../051-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../052-libx11-data_2%3a1.8.12-1_all.deb ... Unpacking libx11-data (2:1.8.12-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../053-libx11-6_2%3a1.8.12-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.12-1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../054-libxcb-render0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../055-libxcb-shm0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../056-libxext6_2%3a1.3.4-1+b3_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b3) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../057-libxrender1_1%3a0.9.12-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.12-1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../058-libcairo2_1.18.4-1+b1_amd64.deb ... Unpacking libcairo2:amd64 (1.18.4-1+b1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../059-libdeflate0_1.23-2_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-2) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../060-libfribidi0_1.0.16-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.16-1) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../061-libglib2.0-0t64_2.84.3-1_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.84.3-1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../062-libgraphite2-3_1.3.14-2+b1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../063-libharfbuzz0b_10.2.0-1+b1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (10.2.0-1+b1) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../064-libimagequant0_2.18.0-1+b2_amd64.deb ... Unpacking libimagequant0:amd64 (2.18.0-1+b2) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../065-libjbig0_2.1-6.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../066-libjpeg62-turbo_1%3a2.1.5-4_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-4) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../067-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-hotkeys. Preparing to unpack .../068-libjs-jquery-hotkeys_0.2.0-1_all.deb ... Unpacking libjs-jquery-hotkeys (0.2.0-1) ... Selecting previously unselected package libjs-jquery-isonscreen. Preparing to unpack .../069-libjs-jquery-isonscreen_1.2.0-1.1_all.deb ... Unpacking libjs-jquery-isonscreen (1.2.0-1.1) ... Selecting previously unselected package libjs-jquery-metadata. Preparing to unpack .../070-libjs-jquery-metadata_12-4_all.deb ... Unpacking libjs-jquery-metadata (12-4) ... Selecting previously unselected package libjs-jquery-tablesorter. Preparing to unpack .../071-libjs-jquery-tablesorter_1%3a2.31.3+dfsg1-4_all.deb ... Unpacking libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Selecting previously unselected package libjs-jquery-throttle-debounce. Preparing to unpack .../072-libjs-jquery-throttle-debounce_1.1+dfsg.1-2_all.deb ... Unpacking libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../073-liblcms2-2_2.16-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.16-2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../074-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../075-libopenjp2-7_2.5.3-2_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.3-2) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../076-libraqm0_0.10.2-1_amd64.deb ... Unpacking libraqm0:amd64 (0.10.2-1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../077-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../078-libwebp7_1.5.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../079-libtiff6_4.7.0-3_amd64.deb ... Unpacking libtiff6:amd64 (4.7.0-3) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../080-libwebpdemux2_1.5.0-0.1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../081-libwebpmux3_1.5.0-0.1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... Selecting previously unselected package python3-all. Preparing to unpack .../082-python3-all_3.13.5-1_amd64.deb ... Unpacking python3-all (3.13.5-1) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../083-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../084-python3-chardet_5.2.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-2) ... Selecting previously unselected package python3-pil:amd64. Preparing to unpack .../085-python3-pil_11.1.0-5+b1_amd64.deb ... Unpacking python3-pil:amd64 (11.1.0-5+b1) ... Selecting previously unselected package python3-cairo. Preparing to unpack .../086-python3-cairo_1.27.0-2_amd64.deb ... Unpacking python3-cairo (1.27.0-2) ... Selecting previously unselected package python3-freetype. Preparing to unpack .../087-python3-freetype_2.5.1-1_all.deb ... Unpacking python3-freetype (2.5.1-1) ... Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../088-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../089-python3-reportlab_4.3.1-1_all.deb ... Unpacking python3-reportlab (4.3.1-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../090-sgml-base_1.31+nmu1_all.deb ... Unpacking sgml-base (1.31+nmu1) ... Selecting previously unselected package xml-core. Preparing to unpack .../091-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../092-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../093-python3-biopython_1.85+dfsg-4_amd64.deb ... Unpacking python3-biopython (1.85+dfsg-4) ... Selecting previously unselected package python3-coverage. Preparing to unpack .../094-python3-coverage_7.6.0+dfsg1-2+b2_amd64.deb ... Unpacking python3-coverage (7.6.0+dfsg1-2+b2) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../095-python3-more-itertools_10.7.0-1_all.deb ... Unpacking python3-more-itertools (10.7.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../096-python3-typing-extensions_4.13.2-1_all.deb ... Unpacking python3-typing-extensions (4.13.2-1) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../097-python3-typeguard_4.4.2-1_all.deb ... Unpacking python3-typeguard (4.4.2-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../098-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../099-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../100-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 .../101-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 .../102-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 .../103-python3-zipp_3.21.0-1_all.deb ... Unpacking python3-zipp (3.21.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../104-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 .../105-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../106-python3-packaging_25.0-1_all.deb ... Unpacking python3-packaging (25.0-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../107-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../108-python3-pytest_8.3.5-2_all.deb ... Unpacking python3-pytest (8.3.5-2) ... Selecting previously unselected package python3-pytest-cov. Preparing to unpack .../109-python3-pytest-cov_5.0.0-1_all.deb ... Unpacking python3-pytest-cov (5.0.0-1) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up file (1:5.46-5) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Aug 6 07:25:11 UTC 2025. Universal Time is now: Wed Aug 6 07:25:11 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libx11-data (2:1.8.12-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.48-1) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up autopoint (0.23.1-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libtiff6:amd64 (4.7.0-3) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libopenjp2-7:amd64 (2.5.3-2) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libjs-jquery-hotkeys (0.2.0-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libtool (2.5.4-4) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libglib2.0-0t64:amd64 (2.84.3-1) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3.13 (3.13.5-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.5-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... 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 libcairo2:amd64 (1.18.4-1+b1) ... Setting up python3-packaging (25.0-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-pytest (8.3.5-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-all (3.13.5-1) ... Setting up python3-coverage (7.6.0+dfsg1-2+b2) ... Setting up debhelper (13.24.2) ... Setting up python3-pytest-cov (5.0.0-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:amd64 (11.1.0-5+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-reportlab (4.3.1-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-11) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-4) ... 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/580776/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/580776/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/peptidebuilder-1.1.0/ && 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 > ../peptidebuilder_1.1.0-3_source.changes dpkg-buildpackage: info: source package peptidebuilder dpkg-buildpackage: info: source version 1.1.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from peptidebuilder-1.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p 3.13 I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/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 -rf .pybuild/ find . -name \*.pyc -exec rm {} \; dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-peptidebuilder.substvars debian/files rm -fr -- debian/python3-peptidebuilder/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.13 I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p 3.13 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/peptidebuilder-1.1.0' PYTHONPATH=$(pwd) pytest-3 ============================= test session starts ============================== platform linux -- Python 3.13.5, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /build/reproducible-path/peptidebuilder-1.1.0 configfile: pytest.ini testpaths: tests plugins: typeguard-4.4.2, cov-5.0.0 collecting ... collected 28 items tests/test_Geometry.py::test_geometry_A PASSED [ 3%] tests/test_Geometry.py::test_geometry_C PASSED [ 7%] tests/test_Geometry.py::test_geometry_D PASSED [ 10%] tests/test_Geometry.py::test_geometry_E PASSED [ 14%] tests/test_Geometry.py::test_geometry_F PASSED [ 17%] tests/test_Geometry.py::test_geometry_G PASSED [ 21%] tests/test_Geometry.py::test_geometry_H PASSED [ 25%] tests/test_Geometry.py::test_geometry_I PASSED [ 28%] tests/test_Geometry.py::test_geometry_K PASSED [ 32%] tests/test_Geometry.py::test_geometry_L PASSED [ 35%] tests/test_Geometry.py::test_geometry_M PASSED [ 39%] tests/test_Geometry.py::test_geometry_N PASSED [ 42%] tests/test_Geometry.py::test_geometry_P PASSED [ 46%] tests/test_Geometry.py::test_geometry_Q PASSED [ 50%] tests/test_Geometry.py::test_geometry_R PASSED [ 53%] tests/test_Geometry.py::test_geometry_S PASSED [ 57%] tests/test_Geometry.py::test_geometry_T PASSED [ 60%] tests/test_Geometry.py::test_geometry_V PASSED [ 64%] tests/test_Geometry.py::test_geometry_W PASSED [ 67%] tests/test_Geometry.py::test_geometry_Y PASSED [ 71%] tests/test_PeptideBuilder.py::test_add_residue PASSED [ 75%] tests/test_PeptideBuilder.py::test_add_residue2 PASSED [ 78%] tests/test_PeptideBuilder.py::test_make_structure_from_geos PASSED [ 82%] tests/test_PeptideBuilder.py::test_make_extended_structure PASSED [ 85%] tests/test_PeptideBuilder.py::test_make_structure_from_geos2 PASSED [ 89%] tests/test_PeptideBuilder.py::test_make_structure PASSED [ 92%] tests/test_PeptideBuilder.py::test_make_structure2 PASSED [ 96%] tests/test_PeptideBuilder.py::test_add_terminal_OXT PASSED [100%] =============================== warnings summary =============================== tests/test_PeptideBuilder.py: 10 warnings /usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:384: PDBConstructionWarning: Ignoring unrecognized record 'TER' at line 168 warnings.warn( tests/test_PeptideBuilder.py: 10 warnings /usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:384: PDBConstructionWarning: Ignoring unrecognized record 'END' at line 169 warnings.warn( tests/test_PeptideBuilder.py::test_add_terminal_OXT /usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:384: PDBConstructionWarning: Ignoring unrecognized record 'END' at line 170 warnings.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ---------- coverage: platform linux, python 3.13.5-final-0 ----------- Name Stmts Miss Cover ------------------------------------------------------ PeptideBuilder/Geometry.py 846 204 76% PeptideBuilder/PeptideBuilder.py 869 3 99% PeptideBuilder/__init__.py 3 0 100% ------------------------------------------------------ TOTAL 1718 207 88% ======================= 28 passed, 21 warnings in 1.83s ======================== make[1]: Leaving directory '/build/reproducible-path/peptidebuilder-1.1.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/python3-peptidebuilder.substvars rm -fr -- debian/.debhelper/generated/python3-peptidebuilder/ debian/python3-peptidebuilder/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/peptidebuilder-1.1.0' dh_auto_install install -m0755 -d /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder pybuild --install -i python{version} -p 3.13 --dest-dir=/build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() 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 running install_lib creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/PeptideBuilder.py to PeptideBuilder.cpython-313.pyc byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/Geometry.py to Geometry.cpython-313.pyc running install_egg_info running egg_info creating PeptideBuilder.egg-info writing PeptideBuilder.egg-info/PKG-INFO writing dependency_links to PeptideBuilder.egg-info/dependency_links.txt writing requirements to PeptideBuilder.egg-info/requires.txt writing top-level names to PeptideBuilder.egg-info/top_level.txt writing manifest file 'PeptideBuilder.egg-info/SOURCES.txt' reading manifest file 'PeptideBuilder.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'PeptideBuilder.egg-info/SOURCES.txt' Copying PeptideBuilder.egg-info to /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder-1.1.0.egg-info Skipping SOURCES.txt running install_scripts find debian/python3-peptidebuilder/usr/lib/ -name .coverage -delete make[1]: Leaving directory '/build/reproducible-path/peptidebuilder-1.1.0' dh_installdocs -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder install -p -m0644 debian/copyright debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder/copyright dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder install -p -m0644 debian/.debhelper/generated/python3-peptidebuilder/dh_installchangelogs.dch.trimmed debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder/changelog.Debian dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:180: version: 6.20250414 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:183: supported Python versions: 3.13 (default=3.13) D: dh_python3 debhelper:174: source=peptidebuilder, binary packages=['python3-peptidebuilder'] D: dh_python3 dh_python3:205: processing package python3-peptidebuilder... D: dh_python3 fs:50: moving files from debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages to debian/python3-peptidebuilder/usr/lib/python3/dist-packages/ D: dh_python3 fs:338: package python3-peptidebuilder details = {'requires.txt': {'debian/python3-peptidebuilder/usr/lib/python3/dist-packages/PeptideBuilder-1.1.0.egg-info/requires.txt'}, 'egg-info': {'debian/python3-peptidebuilder/usr/lib/python3/dist-packages/PeptideBuilder-1.1.0.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-peptidebuilder D: dh_python3 pydist:175: trying to find dependency for Biopython (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 depends:253: D={'python3:any', 'python3-biopython'}; R=[]; S=[]; E=[], B=[]; RT=[] 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 cd debian/python3-peptidebuilder chmod a-x usr/share/doc/python3-peptidebuilder/changelog.Debian gzip -9nf usr/share/doc/python3-peptidebuilder/changelog.Debian cd '/build/reproducible-path/peptidebuilder-1.1.0' dh_fixperms -O--buildsystem=pybuild find debian/python3-peptidebuilder ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-peptidebuilder/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-peptidebuilder/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-peptidebuilder/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-peptidebuilder -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-peptidebuilder/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-peptidebuilder/DEBIAN/postinst cat debian/python3-peptidebuilder.postinst.debhelper >> debian/python3-peptidebuilder/DEBIAN/postinst chmod 0755 -- debian/python3-peptidebuilder/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-peptidebuilder/DEBIAN/prerm cat debian/python3-peptidebuilder.prerm.debhelper >> debian/python3-peptidebuilder/DEBIAN/prerm chmod 0755 -- debian/python3-peptidebuilder/DEBIAN/prerm dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/DEBIAN echo misc:Depends= >> debian/python3-peptidebuilder.substvars echo misc:Pre-Depends= >> debian/python3-peptidebuilder.substvars dpkg-gencontrol -ppython3-peptidebuilder -ldebian/changelog -Tdebian/python3-peptidebuilder.substvars -cdebian/control -Pdebian/python3-peptidebuilder chmod 0644 -- debian/python3-peptidebuilder/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/python3-peptidebuilder/DEBIAN cd debian/python3-peptidebuilder >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-peptidebuilder/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-peptidebuilder .. dpkg-deb: building package 'python3-peptidebuilder' in '../python3-peptidebuilder_1.1.0-3_all.deb'. dpkg-genbuildinfo --build=binary -O../peptidebuilder_1.1.0-3_amd64.buildinfo dpkg-genchanges --build=binary -O../peptidebuilder_1.1.0-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from peptidebuilder-1.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ 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/580776/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/580776/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/580776 and its subdirectories I: Current time: Wed Aug 6 21:27:41 +14 2025 I: pbuilder-time-stamp: 1754465261 + false + set +x Wed Aug 6 07:27:41 UTC 2025 I: Signing ./b2/peptidebuilder_1.1.0-3_amd64.buildinfo as peptidebuilder_1.1.0-3_amd64.buildinfo.asc Wed Aug 6 07:27:41 UTC 2025 I: Signed ./b2/peptidebuilder_1.1.0-3_amd64.buildinfo as ./b2/peptidebuilder_1.1.0-3_amd64.buildinfo.asc Wed Aug 6 07:27:42 UTC 2025 - build #2 for peptidebuilder/trixie/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Wed Aug 6 07:27:42 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-k70d8nZr, removing. /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe: total 88 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 07:24 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 07:27 b2 -rw-r--r-- 1 jenkins jenkins 2239 Oct 8 2021 peptidebuilder_1.1.0-3.dsc -rw------- 1 jenkins jenkins 72810 Aug 6 07:24 rbuildlog.26OTdsE /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b1: total 124 -rw-r--r-- 1 jenkins jenkins 69137 Aug 6 07:24 build.log -rw-r--r-- 1 jenkins jenkins 4016 Aug 6 07:24 peptidebuilder_1.1.0-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2239 Aug 6 07:24 peptidebuilder_1.1.0-3.dsc -rw-r--r-- 1 jenkins jenkins 7572 Aug 6 07:24 peptidebuilder_1.1.0-3_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8454 Aug 6 07:24 peptidebuilder_1.1.0-3_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1275 Aug 6 07:24 peptidebuilder_1.1.0-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 1398 Aug 6 07:24 peptidebuilder_1.1.0-3_source.changes -rw-r--r-- 1 jenkins jenkins 12844 Aug 6 07:24 python3-peptidebuilder_1.1.0-3_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b2: total 124 -rw-r--r-- 1 jenkins jenkins 71041 Aug 6 07:27 build.log -rw-r--r-- 1 jenkins jenkins 4016 Aug 6 07:27 peptidebuilder_1.1.0-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2239 Aug 6 07:27 peptidebuilder_1.1.0-3.dsc -rw-r--r-- 1 jenkins jenkins 7559 Aug 6 07:27 peptidebuilder_1.1.0-3_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8441 Aug 6 07:27 peptidebuilder_1.1.0-3_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1275 Aug 6 07:27 peptidebuilder_1.1.0-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 1398 Aug 6 07:27 peptidebuilder_1.1.0-3_source.changes -rw-r--r-- 1 jenkins jenkins 12844 Aug 6 07:27 python3-peptidebuilder_1.1.0-3_all.deb Wed Aug 6 07:27:42 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Wed Aug 6 07:27:42 UTC 2025 I: peptidebuilder_1.1.0-3_amd64.changes: Format: 1.8 Date: Fri, 08 Oct 2021 22:50:43 +0200 Source: peptidebuilder Binary: python3-peptidebuilder Architecture: all Version: 1.1.0-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: python3-peptidebuilder - generate atomic oligopeptide 3D structure from sequence Changes: peptidebuilder (1.1.0-3) unstable; urgency=medium . * Team upload. * Upstream has broken semantic versioning - so mangle upstream version to really get the latest upstream code * Standards-Version: 4.6.0 (routine-update) Checksums-Sha1: 72fe934fb6e1995f58da24964c2c9187931ac548 7572 peptidebuilder_1.1.0-3_amd64.buildinfo 083dd929f27be0d24e8eb37d9da5aef091fde4ac 12844 python3-peptidebuilder_1.1.0-3_all.deb Checksums-Sha256: a77178191e22c89c7962ed1579b46e95c5c93beab200ef2ef698588d70af0760 7572 peptidebuilder_1.1.0-3_amd64.buildinfo 61ed7ef5f319e80c0f71217b57ebb0825f529af90b5645ccfa7525f9493f4283 12844 python3-peptidebuilder_1.1.0-3_all.deb Files: 7ca3ce0606b28a3de9af0699de7ef97b 7572 science optional peptidebuilder_1.1.0-3_amd64.buildinfo 8bc9448b8b8ec6647ea476ebaefdd033 12844 science optional python3-peptidebuilder_1.1.0-3_all.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/peptidebuilder_1.1.0-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/peptidebuilder_1.1.0-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/peptidebuilder_1.1.0-3.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/peptidebuilder_1.1.0-3.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/peptidebuilder_1.1.0-3_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/peptidebuilder_1.1.0-3.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-08-06 07:24:11.524641953 +0000 +++ b2/build.log 2025-08-06 07:27:42.396903561 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 8 01:44:23 -12 2026 -I: pbuilder-time-stamp: 1788875063 +I: Current time: Wed Aug 6 21:24:13 +14 2025 +I: pbuilder-time-stamp: 1754465053 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -24,52 +24,84 @@ dpkg-source: info: applying fix-paths-with-os.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4134318/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/580776/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Aug 6 07:24 /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/580776/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/580776/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='trixie' - 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]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='10d2f77fed4b48e2ba92525f40e313de' - 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='4134318' - PS1='# ' - PS2='> ' + INVOCATION_ID=7fc4a66d8b2742718b18aa1559874c5c + 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=580776 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.WogjSVQe/pbuilderrc_l9lc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b1 --logfile b1/build.log peptidebuilder_1.1.0-3.dsc' - SUDO_GID='111' - 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.WogjSVQe/pbuilderrc_Zg3u --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b2 --logfile b2/build.log peptidebuilder_1.1.0-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + 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 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4134318/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/580776/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -240,7 +272,7 @@ Get: 121 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.5-2 [250 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 python3-pytest-cov all 5.0.0-1 [26.8 kB] -Fetched 54.0 MB in 1s (77.0 MB/s) +Fetched 54.0 MB in 3s (17.3 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 ... 19851 files and directories currently installed.) @@ -653,8 +685,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Sep 8 13:45:12 UTC 2026. -Universal Time is now: Tue Sep 8 13:45:12 UTC 2026. +Local time is now: Wed Aug 6 07:25:11 UTC 2025. +Universal Time is now: Wed Aug 6 07:25:11 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... @@ -765,7 +797,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/peptidebuilder-1.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../peptidebuilder_1.1.0-3_source.changes +I: user script /srv/workspace/pbuilder/580776/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/580776/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/peptidebuilder-1.1.0/ && 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 > ../peptidebuilder_1.1.0-3_source.changes dpkg-buildpackage: info: source package peptidebuilder dpkg-buildpackage: info: source version 1.1.0-3 dpkg-buildpackage: info: source distribution unstable @@ -852,8 +888,8 @@ running build_py creating /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder -copying PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder +copying PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/peptidebuilder-1.1.0' PYTHONPATH=$(pwd) pytest-3 @@ -863,7 +899,7 @@ rootdir: /build/reproducible-path/peptidebuilder-1.1.0 configfile: pytest.ini testpaths: tests -plugins: cov-5.0.0, typeguard-4.4.2 +plugins: typeguard-4.4.2, cov-5.0.0 collecting ... collected 28 items tests/test_Geometry.py::test_geometry_A PASSED [ 3%] @@ -919,7 +955,7 @@ ------------------------------------------------------ TOTAL 1718 207 88% -======================= 28 passed, 21 warnings in 2.37s ======================== +======================= 28 passed, 21 warnings in 1.83s ======================== make[1]: Leaving directory '/build/reproducible-path/peptidebuilder-1.1.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -965,11 +1001,11 @@ creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder -copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder +copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/PeptideBuilder.py to PeptideBuilder.cpython-313.pyc -byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/Geometry.py to Geometry.cpython-313.pyc byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/__init__.py to __init__.cpython-313.pyc +byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/Geometry.py to Geometry.cpython-313.pyc running install_egg_info running egg_info creating PeptideBuilder.egg-info @@ -1051,12 +1087,14 @@ 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/580776/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/580776/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/4134318 and its subdirectories -I: Current time: Tue Sep 8 01:47:10 -12 2026 -I: pbuilder-time-stamp: 1788875230 +I: removing directory /srv/workspace/pbuilder/580776 and its subdirectories +I: Current time: Wed Aug 6 21:27:41 +14 2025 +I: pbuilder-time-stamp: 1754465261 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/peptidebuilder_1.1.0-3.diff: 71.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/peptidebuilder_1.1.0-3.diff.gz b2/build.log: 80.8% -- replaced with stdout Compressing the 1st log... b1/build.log: 81.2% -- replaced with stdout Wed Aug 6 07:27:43 UTC 2025 I: diffoscope 303 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_peptidebuilder_trixie_amd64_1754465263 + touch /var/log/reproducible-builds/diffoscope_stamp_peptidebuilder_trixie_amd64_1754465263 + RESULT=0 + systemd-run '--description=diffoscope on peptidebuilder/1.1.0-3 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_30-53789 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe --run-session -c jenkins-reproducible-trixie-diffoscope-ab4c5f87-1387-49ca-825f-87ba6e1c9f8a -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/dbd-tmp-CDm4Txk ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/peptidebuilder_1.1.0-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/peptidebuilder_1.1.0-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/peptidebuilder_1.1.0-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b1/peptidebuilder_1.1.0-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b2/peptidebuilder_1.1.0-3_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_30-53789.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/peptidebuilder_1.1.0-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/peptidebuilder_1.1.0-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/peptidebuilder_1.1.0-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b1/peptidebuilder_1.1.0-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.WogjSVQe/b2/peptidebuilder_1.1.0-3_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 Service runtime: 156ms CPU time consumed: 158ms _ _ _ _ _ _ _ _ __ ___ _ __ | |_(_) __| | ___| |__ _ _(_) | __| | ___ _ __ | '_ \ / _ \ '_ \| __| |/ _` |/ _ \ '_ \| | | | | |/ _` |/ _ \ '__| | |_) | __/ |_) | |_| | (_| | __/ |_) | |_| | | | (_| | __/ | | .__/ \___| .__/ \__|_|\__,_|\___|_.__/ \__,_|_|_|\__,_|\___|_| |_| |_| Wed Aug 6 07:27:43 UTC 2025 I: diffoscope 303 found no differences in the changes files, and a .buildinfo file also exists. Wed Aug 6 07:27:43 UTC 2025 I: peptidebuilder from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-08-06 07:27:44] INFO: Starting at 2025-08-06 07:27:44.198844 [2025-08-06 07:27:44] INFO: Generating the pages of 1 package(s) [2025-08-06 07:27:44] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/peptidebuilder didn't produce a buildlog, even though it has been built. [2025-08-06 07:27:44] INFO: Finished at 2025-08-06 07:27:44.380013, took: 0:00:00.181172 Wed Aug 6 07:27:44 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/peptidebuilder.html Wed Aug 6 07:27:44 UTC 2025 I: Removing signed peptidebuilder_1.1.0-3_amd64.buildinfo.asc files: removed './b1/peptidebuilder_1.1.0-3_amd64.buildinfo.asc' removed './b2/peptidebuilder_1.1.0-3_amd64.buildinfo.asc' 1754465264 amd64 trixie peptidebuilder Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/peptidebuilder_1.1.0-3.rbuild.log: 79.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/peptidebuilder_1.1.0-3.rbuild.log.gz [2025-08-06 07:27:44] INFO: Starting at 2025-08-06 07:27:44.631193 [2025-08-06 07:27:44] INFO: Generating the pages of 1 package(s) [2025-08-06 07:27:44] INFO: Finished at 2025-08-06 07:27:44.806539, took: 0:00:00.175349 All cleanup done. Wed Aug 6 07:27:44 UTC 2025 - total duration: 0h 6m 36s. Wed Aug 6 07:27:44 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-uLdYDhuw, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 6min 37.111s CPU time consumed: 4.367s