Running as unit: rb-build-arm64_23-76846.service ==================================================================================== Tue Jan 21 12:53:21 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_23) on jenkins, called using "codethink03-arm64 codethink04-arm64" as arguments. Tue Jan 21 12:53:21 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-8JcZCrB6" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 21 12:53:21 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Tue Jan 21 12:53:21 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-ZsC4aY' Tue Jan 21 12:53:22 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Tue Jan 21 12:53:22 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-N59PsV' ok, let's check if python-pyani is building anywhere yet… ok, python-pyani is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of python-pyani in trixie on arm64 on jenkins now. 1st build will be done on codethink03-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Tue Jan 21 12:53:29 UTC 2025 I: starting to build python-pyani/trixie/arm64 on jenkins on '2025-01-21 12:53' Tue Jan 21 12:53:29 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_23/76846/console.log 1737464009 arm64 trixie python-pyani Tue Jan 21 12:53:29 UTC 2025 I: Downloading source for trixie/python-pyani=0.2.12-3 --2025-01-21 12:53:29-- http://deb.debian.org/debian/pool/main/p/python-pyani/python-pyani_0.2.12-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2404 (2.3K) [text/prs.lines.tag] Saving to: ‘python-pyani_0.2.12-3.dsc’ 0K .. 100% 297M=0s 2025-01-21 12:53:29 (297 MB/s) - ‘python-pyani_0.2.12-3.dsc’ saved [2404/2404] --2025-01-21 12:53:29-- http://deb.debian.org/debian/pool/main/p/python-pyani/python-pyani_0.2.12-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2404 (2.3K) [text/prs.lines.tag] Saving to: ‘python-pyani_0.2.12-3.dsc’ 0K .. 100% 297M=0s 2025-01-21 12:53:29 (297 MB/s) - ‘python-pyani_0.2.12-3.dsc’ saved [2404/2404] Tue Jan 21 12:53:29 UTC 2025 I: python-pyani_0.2.12-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-pyani Binary: python3-pyani Architecture: any Version: 0.2.12-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/widdowquinn/pyani Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-pyani Vcs-Git: https://salsa.debian.org/med-team/python-pyani.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: python3-all, python3-pytest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-setuptools, python3-biopython , python3-matplotlib , python3-pandas , python3-scipy , python3-seaborn , mummer , ncbi-blast+ , python3-pytest Package-List: python3-pyani deb python optional arch=any Checksums-Sha1: 5a3411c6f6c3fbc237492c0d756f19b1a6ea4589 49038533 python-pyani_0.2.12.orig.tar.gz 60d43d56d1f100769c150f7b8c87e11e6c92add9 11404 python-pyani_0.2.12-3.debian.tar.xz Checksums-Sha256: 31bac50843d3af54cf273a4388f4f87bffb0688082e4e3179ea1640aa208626d 49038533 python-pyani_0.2.12.orig.tar.gz 811e72aaf7f67bc5f2c6d5538f527ad610ffab339278526ff33cae6826100ea6 11404 python-pyani_0.2.12-3.debian.tar.xz Files: be120c6027f0fb7e14bbefeff7cb9abb 49038533 python-pyani_0.2.12.orig.tar.gz d629542deb83329b306d5d71bdcf7805 11404 python-pyani_0.2.12-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVhBpURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHF/w//YPO8mJUlMjl5j9etCPFv1LFe+v7Z1dZU cWw5oq3j380r9kwJPM5PLuWjXWYVeew2ky46KYi65hjjOUHc3IEo/nfBOjfBAR5G 07ozcQSxJ53ymG6s691QYKz6eL6HtMuSZFqJdRHS/x8/fI9pymQpnLzP6SWNK0xe tKV/6khTAeyxzwMdSRHMGuN9mRPJ3LPhkYhWoPpZ/P+qbE+wOBFENGorpyF04qaN fJ6QdhNzrAr6gkOPo0sqRA8fS5n37364pf15leBzGXs91QATsIEJC3WEymf8g4LV ntUeaas816ex0cfFEU2sOFf2m7IIPJl1ExbPkHF2lvk1USudHwpPeBP3cSHYKMqi PSx11nRB7ksy9eGIbFRnVnXcrqayKctjiZCmFxqCNEPa5Mm4h0PgtKPVZ5EZfw4V NxS/Sm96ECSeZxkvMWDVMPAeiHJE8R+xzZqVSqetOode0On20dzoelw19OmdWWnP OfzeRL50mM62w8pFnTHgxtGHoS/gv8bclRf67ZhPHPziBa6idgSg3P1a4Ax/Lrpa mnnMZCaoWk+nvwkdu2BU0orv5DUMaYtJ4yT+5IbOzmtnfa8+Gt7Lknn3ryYhDXXD 2JRKzITGjlcNWpOd3BGfSfbjbMAJXuhP+MtLNeoMhybg9grQbSKuLP1R2uvTVCH7 e30pLfbRf04= =DsHD -----END PGP SIGNATURE----- Tue Jan 21 12:53:29 UTC 2025 I: Checking whether the package is not for us Tue Jan 21 12:53:29 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Tue Jan 21 12:53:29 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Tue Jan 21 12:53:29 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Tue Jan 21 12:53:29 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-swqwqk' ==================================================================================== Mon Feb 23 19:16:30 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "1 python-pyani trixie /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd 0.2.12-3" as arguments. Mon Feb 23 19:16:30 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-mwsgmnxD" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Feb 23 19:16:30 UTC 2026 I: Downloading source for trixie/python-pyani=0.2.12-3 Reading package lists... NOTICE: 'python-pyani' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-pyani.git Please use: git clone https://salsa.debian.org/med-team/python-pyani.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 49.1 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (dsc) [2404 B] Get:2 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (tar) [49.0 MB] Get:3 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (diff) [11.4 kB] Fetched 49.1 MB in 1s (34.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'python-pyani' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-pyani.git Please use: git clone https://salsa.debian.org/med-team/python-pyani.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 49.1 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (dsc) [2404 B] Get:2 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (tar) [49.0 MB] Get:3 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (diff) [11.4 kB] Fetched 49.1 MB in 1s (34.1 MB/s) Download complete and in download only mode ============================================================================= Building python-pyani in trixie on arm64 on codethink03-arm64 now. Date: Mon Feb 23 19:16:32 GMT 2026 Date UTC: Mon Feb 23 19:16:32 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: Mon Feb 23 07:16:32 -12 2026 I: pbuilder-time-stamp: 1771874192 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 [python-pyani_0.2.12-3.dsc] I: copying [./python-pyani_0.2.12.orig.tar.gz] I: copying [./python-pyani_0.2.12-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-pyani_0.2.12-3.dsc: unsupported subcommand dpkg-source: info: extracting python-pyani in python-pyani-0.2.12 dpkg-source: info: unpacking python-pyani_0.2.12.orig.tar.gz dpkg-source: info: unpacking python-pyani_0.2.12-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying pytest.patch dpkg-source: info: applying dataframe_sort.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2419425/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='fd9d109c59e84ca992f9622bbc954a65' 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='2419425' 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.cDh5QhHd/pbuilderrc_xOOA --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.cDh5QhHd/b1 --logfile b1/build.log python-pyani_0.2.12-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2419425/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-setuptools, python3-biopython, python3-matplotlib, python3-pandas, python3-scipy, python3-seaborn, mummer, ncbi-blast+, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19970 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest 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} blt{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-lyx{a} fonts-urw-base35{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libnghttp2-14{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsigsegv2{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{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} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} m4{a} man-db{a} media-types{a} mummer{a} ncbi-blast+{a} ncbi-data{a} netbase{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-biopython{a} python3-brotli{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pyparsing{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-sympy{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libltdl-dev libmail-sendmail-perl lynx python-biopython-doc python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-pygments python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 195 newly installed, 0 to remove and 0 not upgraded. Need to get 158 MB of archives. After unpacking 742 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libsigsegv2 arm64 2.14-1+b2 [34.3 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 gawk arm64 1:5.2.1-2+b2 [644 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-5 [810 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.8-5 [1934 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.8-1 [26.9 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 17 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-5 [1904 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.8-5 [677 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.8-1 [9788 B] Get: 25 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.8-1 [27.9 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.2 [216 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 55 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b3 [27.2 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b3 [51.6 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7+b1 [538 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 blt arm64 2.5.3+dfsg-7+b1 [6344 B] Get: 69 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 75 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 90 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20250108 [113 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 liblmdb0 arm64 0.9.31-1+b2 [43.5 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libmbedcrypto16 arm64 3.6.2-3 [341 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libmbedx509-7 arm64 3.6.2-3 [146 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libmbedtls21 arm64 3.6.2-3 [222 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.8-5 [1985 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.8-5 [4822 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.12.8-1 [10.1 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libpython3.13 arm64 3.13.1-3 [1971 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libpython3.13-dev arm64 3.13.1-3 [4710 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.12.8-1 [1068 B] Get: 136 http://deb.debian.org/debian trixie/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 mummer arm64 3.23+dfsg-8+b1 [643 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 ncbi-blast+ arm64 2.16.0+ds-6+b1 [13.8 MB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.1-3 [740 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.8-1 [1048 B] Get: 151 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.8-5 [506 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.12.8-1 [26.1 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 python3.13-dev arm64 3.13.1-3 [504 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.12.8-1 [1068 B] Get: 155 http://deb.debian.org/debian trixie/main arm64 python3-attr all 24.3.0-1 [68.8 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 python3.12-tk arm64 3.12.8-5 [111 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 python3.13-tk arm64 3.13.1-3 [101 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 python3-tk arm64 3.13.1-1 [9464 B] Get: 161 http://deb.debian.org/debian trixie/main arm64 python3-pil.imagetk arm64 10.4.0-1.1 [79.7 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.4.0-1.1 [498 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.1-2+b1 [130 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.84+dfsg-4+b1 [1644 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 python3-brotli arm64 1.1.0-2+b6 [306 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-contourpy arm64 1.3.1-1 [237 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.2-1 [31.0 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-fs all 2.4.16-6 [95.1 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-lxml arm64 5.3.0-1+b1 [1433 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-lz4 arm64 4.4.0+dfsg-1 [25.6 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.14.1-3 [18.5 MB] Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-sympy all 1.13.3-1 [4147 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 python3-fonttools arm64 4.55.3-1 [1501 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 187 http://deb.debian.org/debian trixie/main arm64 python3-kiwisolver arm64 1.4.7-2+b1 [71.6 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib arm64 3.8.3-3+b1 [5586 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-seaborn all 0.13.2-4 [215 kB] Fetched 158 MB in 1s (246 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19970 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../libsigsegv2_2.14-1+b2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.14-1+b2) ... Setting up readline-common (8.2-6) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up libsigsegv2:arm64 (2.14-1+b2) ... Selecting previously unselected package gawk. (Reading database ... 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Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.5.0-0.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up mummer (3.23+dfsg-8+b1) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b4) ... Setting up python3.13-minimal (3.13.1-3) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libmbedcrypto16:arm64 (3.6.2-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up libwebpmux3:arm64 (1.5.0-0.1) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-3) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpython3.13:arm64 (3.13.1-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-4) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b3) ... Setting up libtool (2.5.4-2) ... Setting up python3.13 (3.13.1-3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... Setting up libxext6:arm64 (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:arm64 (2.82.4-2) ... No schema files found: doing nothing. Setting up libmbedx509-7:arm64 (3.6.2-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libpython3.13-dev:arm64 (3.13.1-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libjs-sphinxdoc (8.1.3-4) ... Setting up libmbedtls21:arm64 (3.6.2-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:arm64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:arm64 (10.2.0-1) ... Setting up libxss1:arm64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:arm64 (2.15.0-2) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b2) ... Setting up libxft2:arm64 (2.3.6-1+b3) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up python3.13-dev (3.13.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.16-1) ... Setting up python3.12-tk (3.12.8-5) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up python3.13-tk (3.13.1-3) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7+b1) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-5) ... Setting up blt (2.5.3+dfsg-7+b1) ... Setting up python3.12 (3.12.8-5) ... Setting up debhelper (13.23) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3.12t64:arm64 (3.12.8-5) ... Setting up libpython3-stdlib:arm64 (3.12.8-1) ... Setting up python3 (3.12.8-1) ... Setting up libpython3.12-dev:arm64 (3.12.8-5) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-tz (2024.2-1) ... Setting up python3-fs (2.4.16-6) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up python3-pil:arm64 (10.4.0-1.1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-2+b1) ... Setting up python3.12-dev (3.12.8-5) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lxml:arm64 (5.3.0-1+b1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (24.3.0-1) ... Setting up libpython3-dev:arm64 (3.12.8-1) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-lz4 (4.4.0+dfsg-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.8-1) ... Setting up python3-tk:arm64 (3.13.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:arm64 (10.4.0-1.1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up libpython3-all-dev:arm64 (3.12.8-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.8-1) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-all-dev (3.12.8-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-contourpy (1.3.1-1) ... Setting up dh-python (6.20250108) ... Setting up python3-scipy (1.14.1-3) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-fonttools (4.55.3-1) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Setting up python3-seaborn (0.13.2-4) ... Processing triggers for libc-bin (2.40-5) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... 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/python-pyani-0.2.12/ && 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 > ../python-pyani_0.2.12-3_source.changes dpkg-buildpackage: info: source package python-pyani dpkg-buildpackage: info: source version 0.2.12-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pyani-0.2.12' dh_auto_clean I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -f pyani.egg-info/PKG-INFO pyani.egg-info/SOURCES.txt pyani.egg-info/dependency_links.txt pyani.egg-info/requires.txt pyani.egg-info/top_level.txt make[1]: Leaving directory '/build/reproducible-path/python-pyani-0.2.12' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani running egg_info creating pyani.egg-info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt writing manifest file 'pyani.egg-info/SOURCES.txt' reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts creating build/scripts-3.13 copying and adjusting bin/average_nucleotide_identity.py -> build/scripts-3.13 copying and adjusting bin/genbank_get_genomes_by_taxon.py -> build/scripts-3.13 copying and adjusting bin/delta_filter_wrapper.py -> build/scripts-3.13 changing mode of build/scripts-3.13/average_nucleotide_identity.py from 644 to 755 changing mode of build/scripts-3.13/genbank_get_genomes_by_taxon.py from 644 to 755 changing mode of build/scripts-3.13/delta_filter_wrapper.py from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts creating build/scripts-3.12 copying and adjusting bin/average_nucleotide_identity.py -> build/scripts-3.12 copying and adjusting bin/genbank_get_genomes_by_taxon.py -> build/scripts-3.12 copying and adjusting bin/delta_filter_wrapper.py -> build/scripts-3.12 changing mode of build/scripts-3.12/average_nucleotide_identity.py from 644 to 755 changing mode of build/scripts-3.12/genbank_get_genomes_by_taxon.py from 644 to 755 changing mode of build/scripts-3.12/delta_filter_wrapper.py from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build; python3.13 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pyani-0.2.12 plugins: typeguard-4.4.1 collected 56 items tests/test_anib.py sss.....sss...ss [ 28%] tests/test_anim.py ...... [ 39%] tests/test_concordance.py .s.. [ 46%] tests/test_dependencies.py ......s. [ 60%] tests/test_graphics.py ...... [ 71%] tests/test_jobs.py ......... [ 87%] tests/test_multiprocessing.py ... [ 92%] tests/test_parsing.py . [ 94%] tests/test_tetra.py ... [100%] =============================== warnings summary =============================== pyani/pyani_graphics.py:70 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:70: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD) pyani/pyani_graphics.py:71 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:71: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD) pyani/pyani_graphics.py:72 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:72: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_BURD) .pybuild/cpython3_3.13_pyani/build/tests/test_anib.py::TestParsing::test_blastdir_processing .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.13_pyani/build/tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 1.0 .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = float(val) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 100.0 .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 46 passed, 10 skipped, 31 warnings in 127.96s (0:02:07) ============ I: pybuild base:311: cd /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pyani-0.2.12 plugins: typeguard-4.4.1 collected 56 items tests/test_anib.py sss.....sss...ss [ 28%] tests/test_anim.py ...... [ 39%] tests/test_concordance.py .s.. [ 46%] tests/test_dependencies.py ......s. [ 60%] tests/test_graphics.py ...... [ 71%] tests/test_jobs.py ......... [ 87%] tests/test_multiprocessing.py ... [ 92%] tests/test_parsing.py . [ 94%] tests/test_tetra.py ... [100%] =============================== warnings summary =============================== pyani/pyani_graphics.py:70 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:70: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD) pyani/pyani_graphics.py:71 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:71: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD) pyani/pyani_graphics.py:72 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:72: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_BURD) .pybuild/cpython3_3.12_pyani/build/tests/test_anib.py::TestParsing::test_blastdir_processing .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.12_pyani/build/tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 1.0 .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = float(val) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 100.0 .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 46 passed, 10 skipped, 31 warnings in 129.49s (0:02:09) ============ create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-pyani/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_graphics.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/tetra.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/run_multiprocessing.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/anim.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_tools.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_jobs.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_files.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_config.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/anib.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/anib.py to anib.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/anim.py to anim.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_config.py to pyani_config.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_files.py to pyani_files.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_graphics.py to pyani_graphics.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_jobs.py to pyani_jobs.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_tools.py to pyani_tools.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/run_multiprocessing.py to run_multiprocessing.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/run_sge.py to run_sge.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/tetra.py to tetra.cpython-313.pyc running install_egg_info Copying pyani.egg-info to /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani-0.2.12.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/delta_filter_wrapper.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/genbank_get_genomes_by_taxon.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/average_nucleotide_identity.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/delta_filter_wrapper.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/genbank_get_genomes_by_taxon.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/average_nucleotide_identity.py to 755 I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_graphics.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/tetra.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/run_multiprocessing.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/anim.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_tools.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_jobs.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_files.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_config.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/anib.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/anib.py to anib.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/anim.py to anim.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_config.py to pyani_config.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_files.py to pyani_files.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_graphics.py to pyani_graphics.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_jobs.py to pyani_jobs.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_tools.py to pyani_tools.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/run_multiprocessing.py to run_multiprocessing.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/run_sge.py to run_sge.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/tetra.py to tetra.cpython-312.pyc running install_egg_info Copying pyani.egg-info to /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani-0.2.12.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.12/delta_filter_wrapper.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.12/genbank_get_genomes_by_taxon.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.12/average_nucleotide_identity.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/delta_filter_wrapper.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/genbank_get_genomes_by_taxon.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/average_nucleotide_identity.py to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/python-pyani-0.2.12' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/python-pyani-0.2.12' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pyani' in '../python3-pyani_0.2.12-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../python-pyani_0.2.12-3_arm64.buildinfo dpkg-genchanges --build=binary -O../python-pyani_0.2.12-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2419425 and its subdirectories I: Current time: Mon Feb 23 07:23:51 -12 2026 I: pbuilder-time-stamp: 1771874631 Mon Feb 23 19:23:51 UTC 2026 I: Signing ./b1/python-pyani_0.2.12-3_arm64.buildinfo as python-pyani_0.2.12-3_arm64.buildinfo.asc Mon Feb 23 19:23:51 UTC 2026 I: Signed ./b1/python-pyani_0.2.12-3_arm64.buildinfo as ./b1/python-pyani_0.2.12-3_arm64.buildinfo.asc Mon Feb 23 19:23:51 UTC 2026 - build #1 for python-pyani/trixie/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Mon Feb 23 19:23:51 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-mwsgmnxD, removing. /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 13:00 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 12:53 b2 -rw-r--r-- 1 jenkins jenkins 2404 Nov 24 2023 python-pyani_0.2.12-3.dsc -rw------- 1 jenkins jenkins 3550 Jan 21 12:53 rbuildlog.uZuTbPM /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/b1: total 228 -rw-r--r-- 1 jenkins jenkins 134075 Jan 21 13:00 build.log -rw-r--r-- 1 jenkins jenkins 11404 Jan 21 13:00 python-pyani_0.2.12-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2404 Jan 21 13:00 python-pyani_0.2.12-3.dsc -rw-r--r-- 1 jenkins jenkins 9842 Jan 21 13:00 python-pyani_0.2.12-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 10724 Jan 21 13:00 python-pyani_0.2.12-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1317 Jan 21 13:00 python-pyani_0.2.12-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 1472 Jan 21 13:00 python-pyani_0.2.12-3_source.changes -rw-r--r-- 1 jenkins jenkins 48288 Jan 21 13:00 python3-pyani_0.2.12-3_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/b2: total 0 Tue Jan 21 13:00:53 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 23 07:16:32 -12 2026 I: pbuilder-time-stamp: 1771874192 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 [python-pyani_0.2.12-3.dsc] I: copying [./python-pyani_0.2.12.orig.tar.gz] I: copying [./python-pyani_0.2.12-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-pyani_0.2.12-3.dsc: unsupported subcommand dpkg-source: info: extracting python-pyani in python-pyani-0.2.12 dpkg-source: info: unpacking python-pyani_0.2.12.orig.tar.gz dpkg-source: info: unpacking python-pyani_0.2.12-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying pytest.patch dpkg-source: info: applying dataframe_sort.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2419425/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='fd9d109c59e84ca992f9622bbc954a65' 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='2419425' 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.cDh5QhHd/pbuilderrc_xOOA --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.cDh5QhHd/b1 --logfile b1/build.log python-pyani_0.2.12-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2419425/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-setuptools, python3-biopython, python3-matplotlib, python3-pandas, python3-scipy, python3-seaborn, mummer, ncbi-blast+, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19970 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest 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} blt{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-lyx{a} fonts-urw-base35{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libnghttp2-14{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsigsegv2{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{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} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} m4{a} man-db{a} media-types{a} mummer{a} ncbi-blast+{a} ncbi-data{a} netbase{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-biopython{a} python3-brotli{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pyparsing{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-sympy{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libltdl-dev libmail-sendmail-perl lynx python-biopython-doc python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-pygments python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 195 newly installed, 0 to remove and 0 not upgraded. Need to get 158 MB of archives. After unpacking 742 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libsigsegv2 arm64 2.14-1+b2 [34.3 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 gawk arm64 1:5.2.1-2+b2 [644 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-5 [810 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.8-5 [1934 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.8-1 [26.9 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 17 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-5 [1904 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.8-5 [677 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.8-1 [9788 B] Get: 25 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.8-1 [27.9 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.2 [216 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 55 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b3 [27.2 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b3 [51.6 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7+b1 [538 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 blt arm64 2.5.3+dfsg-7+b1 [6344 B] Get: 69 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 75 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 90 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20250108 [113 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 liblmdb0 arm64 0.9.31-1+b2 [43.5 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libmbedcrypto16 arm64 3.6.2-3 [341 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libmbedx509-7 arm64 3.6.2-3 [146 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libmbedtls21 arm64 3.6.2-3 [222 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.8-5 [1985 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.8-5 [4822 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.12.8-1 [10.1 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libpython3.13 arm64 3.13.1-3 [1971 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libpython3.13-dev arm64 3.13.1-3 [4710 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.12.8-1 [1068 B] Get: 136 http://deb.debian.org/debian trixie/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 mummer arm64 3.23+dfsg-8+b1 [643 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 ncbi-blast+ arm64 2.16.0+ds-6+b1 [13.8 MB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.1-3 [740 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.8-1 [1048 B] Get: 151 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.8-5 [506 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.12.8-1 [26.1 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 python3.13-dev arm64 3.13.1-3 [504 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.12.8-1 [1068 B] Get: 155 http://deb.debian.org/debian trixie/main arm64 python3-attr all 24.3.0-1 [68.8 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 python3.12-tk arm64 3.12.8-5 [111 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 python3.13-tk arm64 3.13.1-3 [101 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 python3-tk arm64 3.13.1-1 [9464 B] Get: 161 http://deb.debian.org/debian trixie/main arm64 python3-pil.imagetk arm64 10.4.0-1.1 [79.7 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.4.0-1.1 [498 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.1-2+b1 [130 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.84+dfsg-4+b1 [1644 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 python3-brotli arm64 1.1.0-2+b6 [306 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-contourpy arm64 1.3.1-1 [237 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.2-1 [31.0 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-fs all 2.4.16-6 [95.1 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-lxml arm64 5.3.0-1+b1 [1433 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-lz4 arm64 4.4.0+dfsg-1 [25.6 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.14.1-3 [18.5 MB] Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-sympy all 1.13.3-1 [4147 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 python3-fonttools arm64 4.55.3-1 [1501 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 187 http://deb.debian.org/debian trixie/main arm64 python3-kiwisolver arm64 1.4.7-2+b1 [71.6 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib arm64 3.8.3-3+b1 [5586 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-seaborn all 0.13.2-4 [215 kB] Fetched 158 MB in 1s (246 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19970 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../libsigsegv2_2.14-1+b2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.14-1+b2) ... Setting up readline-common (8.2-6) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up libsigsegv2:arm64 (2.14-1+b2) ... Selecting previously unselected package gawk. (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 ... 20012 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.2.1-2+b2_arm64.deb ... Unpacking gawk (1:5.2.1-2+b2) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.8-5_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-5) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-5_arm64.deb ... Unpacking python3.12-minimal (3.12.8-5) ... Setting up libpython3.12-minimal:arm64 (3.12.8-5) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-5) ... 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 ... 20521 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.8-1_arm64.deb ... Unpacking python3-minimal (3.12.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-6_all.deb ... Unpacking tzdata (2024b-6) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../04-libffi8_3.4.6-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.6-1) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../05-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../06-libcom-err2_1.47.2-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../07-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../08-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../09-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../10-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../11-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../12-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... 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(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 ... 21557 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.8-1_arm64.deb ... Unpacking python3 (3.12.8-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../001-libpython3.13-minimal_3.13.1-3_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3) ... Selecting previously unselected package python3.13-minimal. 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Setting up libpython3.13-minimal:arm64 (3.13.1-3) ... Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.6.4-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-3) ... Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... Setting up autopoint (0.22.5-4) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libgfortran5:arm64 (14.2.0-12) ... 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Setting up libpython3.13:arm64 (3.13.1-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-4) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b3) ... Setting up libtool (2.5.4-2) ... Setting up python3.13 (3.13.1-3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... Setting up libxext6:arm64 (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:arm64 (2.82.4-2) ... No schema files found: doing nothing. Setting up libmbedx509-7:arm64 (3.6.2-3) ... 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Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up python3.13-tk (3.13.1-3) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7+b1) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-5) ... Setting up blt (2.5.3+dfsg-7+b1) ... Setting up python3.12 (3.12.8-5) ... Setting up debhelper (13.23) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3.12t64:arm64 (3.12.8-5) ... Setting up libpython3-stdlib:arm64 (3.12.8-1) ... Setting up python3 (3.12.8-1) ... Setting up libpython3.12-dev:arm64 (3.12.8-5) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-tz (2024.2-1) ... Setting up python3-fs (2.4.16-6) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up python3-pil:arm64 (10.4.0-1.1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-2+b1) ... Setting up python3.12-dev (3.12.8-5) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lxml:arm64 (5.3.0-1+b1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (24.3.0-1) ... Setting up libpython3-dev:arm64 (3.12.8-1) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-lz4 (4.4.0+dfsg-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.8-1) ... Setting up python3-tk:arm64 (3.13.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:arm64 (10.4.0-1.1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up libpython3-all-dev:arm64 (3.12.8-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.8-1) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-all-dev (3.12.8-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-contourpy (1.3.1-1) ... Setting up dh-python (6.20250108) ... Setting up python3-scipy (1.14.1-3) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-fonttools (4.55.3-1) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Setting up python3-seaborn (0.13.2-4) ... Processing triggers for libc-bin (2.40-5) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... 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/python-pyani-0.2.12/ && 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 > ../python-pyani_0.2.12-3_source.changes dpkg-buildpackage: info: source package python-pyani dpkg-buildpackage: info: source version 0.2.12-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pyani-0.2.12' dh_auto_clean I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -f pyani.egg-info/PKG-INFO pyani.egg-info/SOURCES.txt pyani.egg-info/dependency_links.txt pyani.egg-info/requires.txt pyani.egg-info/top_level.txt make[1]: Leaving directory '/build/reproducible-path/python-pyani-0.2.12' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani running egg_info creating pyani.egg-info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt writing manifest file 'pyani.egg-info/SOURCES.txt' reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts creating build/scripts-3.13 copying and adjusting bin/average_nucleotide_identity.py -> build/scripts-3.13 copying and adjusting bin/genbank_get_genomes_by_taxon.py -> build/scripts-3.13 copying and adjusting bin/delta_filter_wrapper.py -> build/scripts-3.13 changing mode of build/scripts-3.13/average_nucleotide_identity.py from 644 to 755 changing mode of build/scripts-3.13/genbank_get_genomes_by_taxon.py from 644 to 755 changing mode of build/scripts-3.13/delta_filter_wrapper.py from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts creating build/scripts-3.12 copying and adjusting bin/average_nucleotide_identity.py -> build/scripts-3.12 copying and adjusting bin/genbank_get_genomes_by_taxon.py -> build/scripts-3.12 copying and adjusting bin/delta_filter_wrapper.py -> build/scripts-3.12 changing mode of build/scripts-3.12/average_nucleotide_identity.py from 644 to 755 changing mode of build/scripts-3.12/genbank_get_genomes_by_taxon.py from 644 to 755 changing mode of build/scripts-3.12/delta_filter_wrapper.py from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build; python3.13 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pyani-0.2.12 plugins: typeguard-4.4.1 collected 56 items tests/test_anib.py sss.....sss...ss [ 28%] tests/test_anim.py ...... [ 39%] tests/test_concordance.py .s.. [ 46%] tests/test_dependencies.py ......s. [ 60%] tests/test_graphics.py ...... [ 71%] tests/test_jobs.py ......... [ 87%] tests/test_multiprocessing.py ... [ 92%] tests/test_parsing.py . [ 94%] tests/test_tetra.py ... [100%] =============================== warnings summary =============================== pyani/pyani_graphics.py:70 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:70: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD) pyani/pyani_graphics.py:71 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:71: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD) pyani/pyani_graphics.py:72 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:72: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_BURD) .pybuild/cpython3_3.13_pyani/build/tests/test_anib.py::TestParsing::test_blastdir_processing .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.13_pyani/build/tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 1.0 .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = float(val) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 100.0 .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 46 passed, 10 skipped, 31 warnings in 127.96s (0:02:07) ============ I: pybuild base:311: cd /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pyani-0.2.12 plugins: typeguard-4.4.1 collected 56 items tests/test_anib.py sss.....sss...ss [ 28%] tests/test_anim.py ...... [ 39%] tests/test_concordance.py .s.. [ 46%] tests/test_dependencies.py ......s. [ 60%] tests/test_graphics.py ...... [ 71%] tests/test_jobs.py ......... [ 87%] tests/test_multiprocessing.py ... [ 92%] tests/test_parsing.py . [ 94%] tests/test_tetra.py ... [100%] =============================== warnings summary =============================== pyani/pyani_graphics.py:70 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:70: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD) pyani/pyani_graphics.py:71 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:71: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD) pyani/pyani_graphics.py:72 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:72: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_BURD) .pybuild/cpython3_3.12_pyani/build/tests/test_anib.py::TestParsing::test_blastdir_processing .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.12_pyani/build/tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 1.0 .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = float(val) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 100.0 .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 46 passed, 10 skipped, 31 warnings in 129.49s (0:02:09) ============ create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-pyani/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_graphics.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/tetra.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/run_multiprocessing.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/anim.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_tools.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_jobs.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_files.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_config.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/anib.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/anib.py to anib.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/anim.py to anim.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_config.py to pyani_config.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_files.py to pyani_files.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_graphics.py to pyani_graphics.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_jobs.py to pyani_jobs.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_tools.py to pyani_tools.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/run_multiprocessing.py to run_multiprocessing.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/run_sge.py to run_sge.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/tetra.py to tetra.cpython-313.pyc running install_egg_info Copying pyani.egg-info to /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani-0.2.12.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/delta_filter_wrapper.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/genbank_get_genomes_by_taxon.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/average_nucleotide_identity.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/delta_filter_wrapper.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/genbank_get_genomes_by_taxon.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/average_nucleotide_identity.py to 755 I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_graphics.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/tetra.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/run_multiprocessing.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/anim.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_tools.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_jobs.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_files.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_config.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/anib.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/anib.py to anib.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/anim.py to anim.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_config.py to pyani_config.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_files.py to pyani_files.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_graphics.py to pyani_graphics.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_jobs.py to pyani_jobs.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_tools.py to pyani_tools.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/run_multiprocessing.py to run_multiprocessing.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/run_sge.py to run_sge.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/tetra.py to tetra.cpython-312.pyc running install_egg_info Copying pyani.egg-info to /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani-0.2.12.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.12/delta_filter_wrapper.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.12/genbank_get_genomes_by_taxon.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.12/average_nucleotide_identity.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/delta_filter_wrapper.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/genbank_get_genomes_by_taxon.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/average_nucleotide_identity.py to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/python-pyani-0.2.12' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/python-pyani-0.2.12' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pyani' in '../python3-pyani_0.2.12-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../python-pyani_0.2.12-3_arm64.buildinfo dpkg-genchanges --build=binary -O../python-pyani_0.2.12-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2419425 and its subdirectories I: Current time: Mon Feb 23 07:23:51 -12 2026 I: pbuilder-time-stamp: 1771874631 Tue Jan 21 13:00:53 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Tue Jan 21 13:00:53 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Tue Jan 21 13:00:53 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Tue Jan 21 13:00:53 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-nWVNeJ' ==================================================================================== Tue Jan 21 13:00:55 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 python-pyani trixie /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd 0.2.12-3" as arguments. Tue Jan 21 13:00:55 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-jEJwgkq4" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 21 13:00:55 UTC 2025 I: Downloading source for trixie/python-pyani=0.2.12-3 Reading package lists... NOTICE: 'python-pyani' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-pyani.git Please use: git clone https://salsa.debian.org/med-team/python-pyani.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 49.1 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (dsc) [2404 B] Get:2 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (tar) [49.0 MB] Get:3 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (diff) [11.4 kB] Fetched 49.1 MB in 1s (62.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'python-pyani' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-pyani.git Please use: git clone https://salsa.debian.org/med-team/python-pyani.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 49.1 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (dsc) [2404 B] Get:2 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (tar) [49.0 MB] Get:3 http://deb.debian.org/debian trixie/main python-pyani 0.2.12-3 (diff) [11.4 kB] Fetched 49.1 MB in 1s (62.1 MB/s) Download complete and in download only mode ============================================================================= Re-Building python-pyani in trixie on arm64 on codethink04-arm64 now. Date: Tue Jan 21 13:00:56 GMT 2025 Date UTC: Tue Jan 21 13:00:56 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/pbuilderrc_iSdi + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' python-pyani = debian-installer -o python-pyani = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' python-pyani = u-boot ']' + case "${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.cDh5QhHd/pbuilderrc_iSdi --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.cDh5QhHd/b2 --logfile b2/build.log python-pyani_0.2.12-3.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 Jan 22 03:00:56 +14 2025 I: pbuilder-time-stamp: 1737464456 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 [python-pyani_0.2.12-3.dsc] I: copying [./python-pyani_0.2.12.orig.tar.gz] I: copying [./python-pyani_0.2.12-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-pyani_0.2.12-3.dsc: unsupported subcommand dpkg-source: info: extracting python-pyani in python-pyani-0.2.12 dpkg-source: info: unpacking python-pyani_0.2.12.orig.tar.gz dpkg-source: info: unpacking python-pyani_0.2.12-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying pytest.patch dpkg-source: info: applying dataframe_sort.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 21 13:01 /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/1940951/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=4fa7923cfd414c03970602795ff90be0 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1940951 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.cDh5QhHd/pbuilderrc_iSdi --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.cDh5QhHd/b2 --logfile b2/build.log python-pyani_0.2.12-3.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-setuptools, python3-biopython, python3-matplotlib, python3-pandas, python3-scipy, python3-seaborn, mummer, ncbi-blast+, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19970 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest 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} blt{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-lyx{a} fonts-urw-base35{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libnghttp2-14{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsigsegv2{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{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} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} m4{a} man-db{a} media-types{a} mummer{a} ncbi-blast+{a} ncbi-data{a} netbase{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-biopython{a} python3-brotli{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pyparsing{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-sympy{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libltdl-dev libmail-sendmail-perl lynx python-biopython-doc python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-pygments python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 195 newly installed, 0 to remove and 0 not upgraded. Need to get 158 MB of archives. After unpacking 742 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libsigsegv2 arm64 2.14-1+b2 [34.3 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 gawk arm64 1:5.2.1-2+b2 [644 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-5 [810 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.8-5 [1934 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.8-1 [26.9 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 17 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-5 [1904 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.8-5 [677 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.8-1 [9788 B] Get: 25 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.8-1 [27.9 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.2 [216 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 55 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b3 [27.2 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b3 [51.6 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7+b1 [538 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 blt arm64 2.5.3+dfsg-7+b1 [6344 B] Get: 69 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 75 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 90 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20250108 [113 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 liblmdb0 arm64 0.9.31-1+b2 [43.5 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libmbedcrypto16 arm64 3.6.2-3 [341 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libmbedx509-7 arm64 3.6.2-3 [146 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libmbedtls21 arm64 3.6.2-3 [222 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.8-5 [1985 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.8-5 [4822 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.12.8-1 [10.1 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libpython3.13 arm64 3.13.1-3 [1971 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libpython3.13-dev arm64 3.13.1-3 [4710 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.12.8-1 [1068 B] Get: 136 http://deb.debian.org/debian trixie/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 mummer arm64 3.23+dfsg-8+b1 [643 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 ncbi-blast+ arm64 2.16.0+ds-6+b1 [13.8 MB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.1-3 [740 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.8-1 [1048 B] Get: 151 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.8-5 [506 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.12.8-1 [26.1 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 python3.13-dev arm64 3.13.1-3 [504 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.12.8-1 [1068 B] Get: 155 http://deb.debian.org/debian trixie/main arm64 python3-attr all 24.3.0-1 [68.8 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 python3.12-tk arm64 3.12.8-5 [111 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 python3.13-tk arm64 3.13.1-3 [101 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 python3-tk arm64 3.13.1-1 [9464 B] Get: 161 http://deb.debian.org/debian trixie/main arm64 python3-pil.imagetk arm64 10.4.0-1.1 [79.7 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.4.0-1.1 [498 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.1-2+b1 [130 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.84+dfsg-4+b1 [1644 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 python3-brotli arm64 1.1.0-2+b6 [306 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-contourpy arm64 1.3.1-1 [237 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.2-1 [31.0 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-fs all 2.4.16-6 [95.1 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-lxml arm64 5.3.0-1+b1 [1433 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-lz4 arm64 4.4.0+dfsg-1 [25.6 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.14.1-3 [18.5 MB] Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-sympy all 1.13.3-1 [4147 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 python3-fonttools arm64 4.55.3-1 [1501 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 187 http://deb.debian.org/debian trixie/main arm64 python3-kiwisolver arm64 1.4.7-2+b1 [71.6 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib arm64 3.8.3-3+b1 [5586 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-seaborn all 0.13.2-4 [215 kB] Fetched 158 MB in 2s (104 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19970 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../libsigsegv2_2.14-1+b2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.14-1+b2) ... Setting up readline-common (8.2-6) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up libsigsegv2:arm64 (2.14-1+b2) ... Selecting previously unselected package gawk. (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 ... 20012 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.2.1-2+b2_arm64.deb ... Unpacking gawk (1:5.2.1-2+b2) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.8-5_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-5) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-5_arm64.deb ... Unpacking python3.12-minimal (3.12.8-5) ... Setting up libpython3.12-minimal:arm64 (3.12.8-5) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-5) ... 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 ... 20521 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.8-1_arm64.deb ... Unpacking python3-minimal (3.12.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../09-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../10-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../11-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../12-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../13-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../14-libpython3.12-stdlib_3.12.8-5_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-5) ... Selecting previously unselected package python3.12. Preparing to unpack .../15-python3.12_3.12.8-5_arm64.deb ... Unpacking python3.12 (3.12.8-5) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../16-libpython3-stdlib_3.12.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.8-1) ... Setting up python3-minimal (3.12.8-1) ... 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 ... 21557 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.8-1_arm64.deb ... Unpacking python3 (3.12.8-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../001-libpython3.13-minimal_3.13.1-3_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.1-3_arm64.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-4_arm64.deb ... Unpacking gettext-base (0.22.5-4) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.4-1_arm64.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-5_arm64.deb ... 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Setting up libpython3.13:arm64 (3.13.1-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-4) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b3) ... Setting up libtool (2.5.4-2) ... Setting up python3.13 (3.13.1-3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... Setting up libxext6:arm64 (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:arm64 (2.82.4-2) ... No schema files found: doing nothing. Setting up libmbedx509-7:arm64 (3.6.2-3) ... 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Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up python3.13-tk (3.13.1-3) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7+b1) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-5) ... Setting up blt (2.5.3+dfsg-7+b1) ... Setting up python3.12 (3.12.8-5) ... Setting up debhelper (13.23) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3.12t64:arm64 (3.12.8-5) ... Setting up libpython3-stdlib:arm64 (3.12.8-1) ... Setting up python3 (3.12.8-1) ... Setting up libpython3.12-dev:arm64 (3.12.8-5) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-tz (2024.2-1) ... Setting up python3-fs (2.4.16-6) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up python3-pil:arm64 (10.4.0-1.1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-2+b1) ... Setting up python3.12-dev (3.12.8-5) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lxml:arm64 (5.3.0-1+b1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (24.3.0-1) ... Setting up libpython3-dev:arm64 (3.12.8-1) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-lz4 (4.4.0+dfsg-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.8-1) ... Setting up python3-tk:arm64 (3.13.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:arm64 (10.4.0-1.1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up libpython3-all-dev:arm64 (3.12.8-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.8-1) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-all-dev (3.12.8-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-contourpy (1.3.1-1) ... Setting up dh-python (6.20250108) ... Setting up python3-scipy (1.14.1-3) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-fonttools (4.55.3-1) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Setting up python3-seaborn (0.13.2-4) ... Processing triggers for libc-bin (2.40-5) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... 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/1940951/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/python-pyani-0.2.12/ && 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 > ../python-pyani_0.2.12-3_source.changes dpkg-buildpackage: info: source package python-pyani dpkg-buildpackage: info: source version 0.2.12-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pyani-0.2.12' dh_auto_clean I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -f pyani.egg-info/PKG-INFO pyani.egg-info/SOURCES.txt pyani.egg-info/dependency_links.txt pyani.egg-info/requires.txt pyani.egg-info/top_level.txt make[1]: Leaving directory '/build/reproducible-path/python-pyani-0.2.12' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani running egg_info creating pyani.egg-info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt writing manifest file 'pyani.egg-info/SOURCES.txt' reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts creating build/scripts-3.13 copying and adjusting bin/average_nucleotide_identity.py -> build/scripts-3.13 copying and adjusting bin/genbank_get_genomes_by_taxon.py -> build/scripts-3.13 copying and adjusting bin/delta_filter_wrapper.py -> build/scripts-3.13 changing mode of build/scripts-3.13/average_nucleotide_identity.py from 644 to 755 changing mode of build/scripts-3.13/genbank_get_genomes_by_taxon.py from 644 to 755 changing mode of build/scripts-3.13/delta_filter_wrapper.py from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts creating build/scripts-3.12 copying and adjusting bin/average_nucleotide_identity.py -> build/scripts-3.12 copying and adjusting bin/genbank_get_genomes_by_taxon.py -> build/scripts-3.12 copying and adjusting bin/delta_filter_wrapper.py -> build/scripts-3.12 changing mode of build/scripts-3.12/average_nucleotide_identity.py from 644 to 755 changing mode of build/scripts-3.12/genbank_get_genomes_by_taxon.py from 644 to 755 changing mode of build/scripts-3.12/delta_filter_wrapper.py from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build; python3.13 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pyani-0.2.12 plugins: typeguard-4.4.1 collected 56 items tests/test_anib.py sss.....sss...ss [ 28%] tests/test_anim.py ...... [ 39%] tests/test_concordance.py .s.. [ 46%] tests/test_dependencies.py ......s. [ 60%] tests/test_graphics.py ...... [ 71%] tests/test_jobs.py ......... [ 87%] tests/test_multiprocessing.py ... [ 92%] tests/test_parsing.py . [ 94%] tests/test_tetra.py ... [100%] =============================== warnings summary =============================== pyani/pyani_graphics.py:70 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:70: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD) pyani/pyani_graphics.py:71 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:71: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD) pyani/pyani_graphics.py:72 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:72: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_BURD) .pybuild/cpython3_3.13_pyani/build/tests/test_anib.py::TestParsing::test_blastdir_processing .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.13_pyani/build/tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 1.0 .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = float(val) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 100.0 .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 46 passed, 10 skipped, 31 warnings in 516.49s (0:08:36) ============ I: pybuild base:311: cd /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pyani-0.2.12 plugins: typeguard-4.4.1 collected 56 items tests/test_anib.py sss.....sss...ss [ 28%] tests/test_anim.py ...... [ 39%] tests/test_concordance.py .s.. [ 46%] tests/test_dependencies.py ......s. [ 60%] tests/test_graphics.py ...... [ 71%] tests/test_jobs.py ......... [ 87%] tests/test_multiprocessing.py ... [ 92%] tests/test_parsing.py . [ 94%] tests/test_tetra.py ... [100%] =============================== warnings summary =============================== pyani/pyani_graphics.py:70 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:70: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD) pyani/pyani_graphics.py:71 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:71: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD) pyani/pyani_graphics.py:72 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:72: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_BURD) .pybuild/cpython3_3.12_pyani/build/tests/test_anib.py::TestParsing::test_blastdir_processing .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.12_pyani/build/tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 1.0 .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = float(val) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 100.0 .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 46 passed, 10 skipped, 31 warnings in 553.96s (0:09:13) ============ create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-pyani/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_graphics.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/tetra.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/run_multiprocessing.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/anim.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_tools.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_jobs.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_files.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_config.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/anib.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/anib.py to anib.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/anim.py to anim.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_config.py to pyani_config.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_files.py to pyani_files.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_graphics.py to pyani_graphics.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_jobs.py to pyani_jobs.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_tools.py to pyani_tools.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/run_multiprocessing.py to run_multiprocessing.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/run_sge.py to run_sge.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/tetra.py to tetra.cpython-313.pyc running install_egg_info Copying pyani.egg-info to /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani-0.2.12.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/delta_filter_wrapper.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/genbank_get_genomes_by_taxon.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/average_nucleotide_identity.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/delta_filter_wrapper.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/genbank_get_genomes_by_taxon.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/average_nucleotide_identity.py to 755 I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani /usr/lib/python3/dist-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_graphics.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/tetra.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/run_multiprocessing.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/anim.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_tools.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_jobs.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_files.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_config.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/anib.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/anib.py to anib.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/anim.py to anim.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_config.py to pyani_config.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_files.py to pyani_files.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_graphics.py to pyani_graphics.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_jobs.py to pyani_jobs.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_tools.py to pyani_tools.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/run_multiprocessing.py to run_multiprocessing.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/run_sge.py to run_sge.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/tetra.py to tetra.cpython-312.pyc running install_egg_info Copying pyani.egg-info to /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani-0.2.12.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.12/delta_filter_wrapper.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.12/genbank_get_genomes_by_taxon.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.12/average_nucleotide_identity.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/delta_filter_wrapper.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/genbank_get_genomes_by_taxon.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/average_nucleotide_identity.py to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/python-pyani-0.2.12' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/python-pyani-0.2.12' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pyani' in '../python3-pyani_0.2.12-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../python-pyani_0.2.12-3_arm64.buildinfo dpkg-genchanges --build=binary -O../python-pyani_0.2.12-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1940951/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/1940951 and its subdirectories I: Current time: Wed Jan 22 03:26:21 +14 2025 I: pbuilder-time-stamp: 1737465981 + false + set +x Tue Jan 21 13:26:21 UTC 2025 I: Signing ./b2/python-pyani_0.2.12-3_arm64.buildinfo as python-pyani_0.2.12-3_arm64.buildinfo.asc Tue Jan 21 13:26:21 UTC 2025 I: Signed ./b2/python-pyani_0.2.12-3_arm64.buildinfo as ./b2/python-pyani_0.2.12-3_arm64.buildinfo.asc Tue Jan 21 13:26:21 UTC 2025 - build #2 for python-pyani/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Tue Jan 21 13:26:21 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-jEJwgkq4, removing. /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd: total 152 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 13:00 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 13:26 b2 -rw-r--r-- 1 jenkins jenkins 2404 Nov 24 2023 python-pyani_0.2.12-3.dsc -rw------- 1 jenkins jenkins 137926 Jan 21 13:00 rbuildlog.uZuTbPM /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/b1: total 232 -rw-r--r-- 1 jenkins jenkins 134075 Jan 21 13:00 build.log -rw-r--r-- 1 jenkins jenkins 11404 Jan 21 13:00 python-pyani_0.2.12-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2404 Jan 21 13:00 python-pyani_0.2.12-3.dsc -rw-r--r-- 1 jenkins jenkins 9842 Jan 21 13:00 python-pyani_0.2.12-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 10724 Jan 21 13:00 python-pyani_0.2.12-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1317 Jan 21 13:00 python-pyani_0.2.12-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 1472 Jan 21 13:00 python-pyani_0.2.12-3_source.changes -rw-r--r-- 1 jenkins jenkins 48288 Jan 21 13:00 python3-pyani_0.2.12-3_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/b2: total 232 -rw-r--r-- 1 jenkins jenkins 136010 Jan 21 13:26 build.log -rw-r--r-- 1 jenkins jenkins 11404 Jan 21 13:26 python-pyani_0.2.12-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2404 Jan 21 13:26 python-pyani_0.2.12-3.dsc -rw-r--r-- 1 jenkins jenkins 9842 Jan 21 13:26 python-pyani_0.2.12-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 10724 Jan 21 13:26 python-pyani_0.2.12-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1317 Jan 21 13:26 python-pyani_0.2.12-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 1472 Jan 21 13:26 python-pyani_0.2.12-3_source.changes -rw-r--r-- 1 jenkins jenkins 48288 Jan 21 13:26 python3-pyani_0.2.12-3_arm64.deb Tue Jan 21 13:26:22 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Tue Jan 21 13:26:23 UTC 2025 I: python-pyani_0.2.12-3_arm64.changes: Format: 1.8 Date: Fri, 24 Nov 2023 22:32:48 +0530 Source: python-pyani Binary: python3-pyani Architecture: arm64 Version: 0.2.12-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Ananthu C V Description: python3-pyani - Python3 module for average nucleotide identity analyses Closes: 1044066 Changes: python-pyani (0.2.12-3) unstable; urgency=medium . [ Ananthu C V ] * Team upload * add patch to fix dataframe sorting syntax (Closes: #1044066) . [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) Checksums-Sha1: 917aeae99ab1095cc9ee5a06c0d8c0972679fa30 9842 python-pyani_0.2.12-3_arm64.buildinfo 776a1a066f05ab9716c887e335d259e9b5c8493b 48288 python3-pyani_0.2.12-3_arm64.deb Checksums-Sha256: 7c84ae509694a473e48f1dc1443a59e4eeb207ef634cb5c6c99b9e86a0af5524 9842 python-pyani_0.2.12-3_arm64.buildinfo b1a538bb58f1adfc3ad20f866a761fb4711e72a2a9bd838783096191ba21bdbb 48288 python3-pyani_0.2.12-3_arm64.deb Files: c5f87fd79deed2cf0ec1d3c190ab302d 9842 science optional python-pyani_0.2.12-3_arm64.buildinfo bd6c2ae2404fc0f37e82d133b5b5041d 48288 python optional python3-pyani_0.2.12-3_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/python-pyani_0.2.12-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/python-pyani_0.2.12-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/python-pyani_0.2.12-3.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/python-pyani_0.2.12-3.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/python-pyani_0.2.12-3_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/python-pyani_0.2.12-3.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-01-21 13:00:52.896235974 +0000 +++ b2/build.log 2025-01-21 13:26:22.731534934 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 23 07:16:32 -12 2026 -I: pbuilder-time-stamp: 1771874192 +I: Current time: Wed Jan 22 03:00:56 +14 2025 +I: pbuilder-time-stamp: 1737464456 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying dataframe_sort.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2419425/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 21 13:01 /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/1940951/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='fd9d109c59e84ca992f9622bbc954a65' - 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='2419425' - PS1='# ' - PS2='> ' + INVOCATION_ID=4fa7923cfd414c03970602795ff90be0 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1940951 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.cDh5QhHd/pbuilderrc_xOOA --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.cDh5QhHd/b1 --logfile b1/build.log python-pyani_0.2.12-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/pbuilderrc_iSdi --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.cDh5QhHd/b2 --logfile b2/build.log python-pyani_0.2.12-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2419425/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -323,7 +355,7 @@ Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-seaborn all 0.13.2-4 [215 kB] -Fetched 158 MB in 1s (246 MB/s) +Fetched 158 MB in 2s (104 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19970 files and directories currently installed.) @@ -971,8 +1003,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Feb 23 19:17:06 UTC 2026. -Universal Time is now: Mon Feb 23 19:17:06 UTC 2026. +Local time is now: Tue Jan 21 13:02:32 UTC 2025. +Universal Time is now: Tue Jan 21 13:02:32 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -1139,7 +1171,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/python-pyani-0.2.12/ && 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 > ../python-pyani_0.2.12-3_source.changes +I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1940951/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-pyani-0.2.12/ && 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 > ../python-pyani_0.2.12-3_source.changes dpkg-buildpackage: info: source package python-pyani dpkg-buildpackage: info: source version 0.2.12-3 dpkg-buildpackage: info: source distribution unstable @@ -1159,8 +1195,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - This deprecation is overdue, please update your project and remove deprecated - calls to avoid build errors in the future. + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1179,8 +1215,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - This deprecation is overdue, please update your project and remove deprecated - calls to avoid build errors in the future. + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1208,8 +1244,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - This deprecation is overdue, please update your project and remove deprecated - calls to avoid build errors in the future. + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1225,8 +1261,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - This deprecation is overdue, please update your project and remove deprecated - calls to avoid build errors in the future. + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1243,8 +1279,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - This deprecation is overdue, please update your project and remove deprecated - calls to avoid build errors in the future. + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1292,8 +1328,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - This deprecation is overdue, please update your project and remove deprecated - calls to avoid build errors in the future. + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1481,7 +1517,7 @@ correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -=========== 46 passed, 10 skipped, 31 warnings in 127.96s (0:02:07) ============ +=========== 46 passed, 10 skipped, 31 warnings in 516.49s (0:08:36) ============ I: pybuild base:311: cd /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 @@ -1631,7 +1667,7 @@ correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -=========== 46 passed, 10 skipped, 31 warnings in 129.49s (0:02:09) ============ +=========== 46 passed, 10 skipped, 31 warnings in 553.96s (0:09:13) ============ create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -1644,8 +1680,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - This deprecation is overdue, please update your project and remove deprecated - calls to avoid build errors in the future. + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1733,8 +1769,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - This deprecation is overdue, please update your project and remove deprecated - calls to avoid build errors in the future. + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1844,12 +1880,14 @@ 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/1940951/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1940951/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/2419425 and its subdirectories -I: Current time: Mon Feb 23 07:23:51 -12 2026 -I: pbuilder-time-stamp: 1771874631 +I: removing directory /srv/workspace/pbuilder/1940951 and its subdirectories +I: Current time: Wed Jan 22 03:26:21 +14 2025 +I: pbuilder-time-stamp: 1737465981 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/python-pyani_0.2.12-3.diff: 75.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/python-pyani_0.2.12-3.diff.gz b2/build.log: 86.7% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.1% -- replaced with stdout Tue Jan 21 13:26:24 UTC 2025 I: diffoscope 285 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_python-pyani_trixie_arm64_1737465984 + touch /var/log/reproducible-builds/diffoscope_stamp_python-pyani_trixie_arm64_1737465984 + RESULT=0 + systemd-run '--description=diffoscope on python-pyani/0.2.12-3 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_23-76846 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd --run-session -c jenkins-reproducible-trixie-diffoscope-91637deb-686f-43b1-ace0-b6a72565ae6e -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/dbd-tmp-aEUvNFh ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/python-pyani_0.2.12-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/python-pyani_0.2.12-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/python-pyani_0.2.12-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/b1/python-pyani_0.2.12-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/b2/python-pyani_0.2.12-3_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_23-76846.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/python-pyani_0.2.12-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/python-pyani_0.2.12-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/python-pyani_0.2.12-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/b1/python-pyani_0.2.12-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.cDh5QhHd/b2/python-pyani_0.2.12-3_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.526s) 0.526s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.020s) 0.020s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.000s CPU time consumed: 986ms _ _ _ _ __ _ _| |_| |__ ___ _ __ _ __ _ _ __ _ _ __ (_) | '_ \| | | | __| '_ \ / _ \| '_ \ _____| '_ \| | | |/ _` | '_ \| | | |_) | |_| | |_| | | | (_) | | | |_____| |_) | |_| | (_| | | | | | | .__/ \__, |\__|_| |_|\___/|_| |_| | .__/ \__, |\__,_|_| |_|_| |_| |___/ |_| |___/ Tue Jan 21 13:26:26 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists. Tue Jan 21 13:26:26 UTC 2025 I: python-pyani from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-01-21 13:26:26] INFO: Starting at 2025-01-21 13:26:26.719899 [2025-01-21 13:26:26] INFO: Generating the pages of 1 package(s) [2025-01-21 13:26:26] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/python-pyani didn't produce a buildlog, even though it has been built. [2025-01-21 13:26:27] INFO: Finished at 2025-01-21 13:26:27.067021, took: 0:00:00.347129 Tue Jan 21 13:26:27 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/python-pyani.html Tue Jan 21 13:26:27 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Jan 21 13:26:27 UTC 2025 I: Submitting 12K b1/python-pyani_0.2.12-3_arm64.buildinfo.asc https://buildinfo.debian.net/917aeae99ab1095cc9ee5a06c0d8c0972679fa30/python-pyani_0.2.12-3_arm64 Tue Jan 21 13:26:27 UTC 2025 I: Submitting 12K b2/python-pyani_0.2.12-3_arm64.buildinfo.asc https://buildinfo.debian.net/d25cb13d5f2dc4daa5fc103671c934f826c23a52/python-pyani_0.2.12-3_arm64 Tue Jan 21 13:26:29 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jan 21 13:26:29 UTC 2025 I: Done submitting .buildinfo files. Tue Jan 21 13:26:29 UTC 2025 I: Removing signed python-pyani_0.2.12-3_arm64.buildinfo.asc files: removed './b1/python-pyani_0.2.12-3_arm64.buildinfo.asc' removed './b2/python-pyani_0.2.12-3_arm64.buildinfo.asc' 1737465989 arm64 trixie python-pyani Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/python-pyani_0.2.12-3.rbuild.log: 85.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/python-pyani_0.2.12-3.rbuild.log.gz [2025-01-21 13:26:29] INFO: Starting at 2025-01-21 13:26:29.922722 [2025-01-21 13:26:30] INFO: Generating the pages of 1 package(s) [2025-01-21 13:26:30] INFO: Finished at 2025-01-21 13:26:30.309964, took: 0:00:00.387249 All cleanup done. Tue Jan 21 13:26:30 UTC 2025 - total duration: 0h 33m 5s. Tue Jan 21 13:26:30 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-8JcZCrB6, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 33min 8.901s CPU time consumed: 7.668s