Sun Apr 28 12:26:28 UTC 2024 I: starting to build kleborate/trixie/arm64 on jenkins on '2024-04-28 12:26' Sun Apr 28 12:26:28 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/9274/console.log Sun Apr 28 12:26:28 UTC 2024 I: Downloading source for trixie/kleborate=2.4.1-3 --2024-04-28 12:26:28-- http://deb.debian.org/debian/pool/main/k/kleborate/kleborate_2.4.1-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2331 (2.3K) [text/prs.lines.tag] Saving to: ‘kleborate_2.4.1-3.dsc’ 0K .. 100% 210M=0s 2024-04-28 12:26:28 (210 MB/s) - ‘kleborate_2.4.1-3.dsc’ saved [2331/2331] Sun Apr 28 12:26:28 UTC 2024 I: kleborate_2.4.1-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kleborate Binary: kleborate, kleborate-examples Architecture: any all Version: 2.4.1-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/katholt/Kleborate Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/kleborate Vcs-Git: https://salsa.debian.org/med-team/kleborate.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-setuptools, ncbi-blast+ , mash , kaptive Package-List: kleborate deb science optional arch=any kleborate-examples deb science optional arch=all Checksums-Sha1: d2d906edcd39fbe5a259195984c21e6671d7741a 91570170 kleborate_2.4.1.orig.tar.gz 58275df848a2cac6e8a4eaf2574403484bd1d2b8 5997368 kleborate_2.4.1-3.debian.tar.xz Checksums-Sha256: 0fcdac98b1f702c2096de4c791b5880e81e68020e38655f01f292427db0df5a6 91570170 kleborate_2.4.1.orig.tar.gz 7f699d10ab3d24068bf6b740fca1c3003ff35149a7282841c33f8b6664cef1e2 5997368 kleborate_2.4.1-3.debian.tar.xz Files: 0bef62432a97b9c58e25a63f3caa0e56 91570170 kleborate_2.4.1.orig.tar.gz e361726050fa48c27fc64185a994a99a 5997368 kleborate_2.4.1-3.debian.tar.xz Dgit: c4a7173756c4b5e56423e651b1f2aa7e85b85b65 debian archive/debian/2.4.1-3 https://git.dgit.debian.org/kleborate -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmXuBIIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdopEw//aE0e6XwiYgsemOkUg6ZMQp8MZzcT rvJHPnzBkCDtYP/zn0MFCEI0NvnLG9bUZYQQGByqR56FIcZluzK3doqhlxaoVKa4 FhWiZrKIEIixlrEH8I1VZNYnvx9VTZd4nrYoiL05gnr5Vz3aEDCVaGdfQj0Ak/1s 9o0QgQVDngkiviXmaO1XeO9ZR48qH71UxwHlXMc+UokGIXhhgrrSFbW5GCeA+9Ze zZCrLbQlQZySYutaF/cj/3hbT/kwenv99a2afBBxQ2yvSXnyf2z0yk3YXGPHdxE2 VuQzOrhdEa74Oyi2IXhKf4pTjsUvRLUrlY2JRPyVClysF8EK7NZEuIzPsvI4RVTS o+BKcH7bQIAIRKH9UDaTyFZr4j+bk1eL6/dUCfaVsicW86vL/JYeqE8+PlBTO1N5 A4eFu88+tnQYJ3jxpfRE4Lgh6I3T4z4NqUa/6hhLUo/LdHakenxnmvS7G+tdUPNI TYa+u+o0C7shiUiG/rl45ElC0ZW3EYFJX7hFLVluQ/TVlynYJrcVIScGbB6e7lbD q+nOe8mllK6hjCdw4mk15j3G41HBOHFvKqflOE4rP32kL0acViLGattf9KjDexg2 KMcdcQPJwCVnCEyNVfD2XKWnHP6O8JgDfwf78o7evXDqay5k980LZIUzLdSL673G dWpZjN8A1pvz8OI= =INZ7 -----END PGP SIGNATURE----- Sun Apr 28 12:26:28 UTC 2024 I: Checking whether the package is not for us Sun Apr 28 12:26:28 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Sun Apr 28 12:26:28 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Sun Apr 28 12:30:10 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 28 00:26:33 -12 2024 I: pbuilder-time-stamp: 1714307193 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 [kleborate_2.4.1-3.dsc] I: copying [./kleborate_2.4.1.orig.tar.gz] I: copying [./kleborate_2.4.1-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Mar 10 19:05:38 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kleborate_2.4.1-3.dsc: no acceptable signature found dpkg-source: info: extracting kleborate in kleborate-2.4.1 dpkg-source: info: unpacking kleborate_2.4.1.orig.tar.gz dpkg-source: info: unpacking kleborate_2.4.1-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3.patch dpkg-source: info: applying use_debian_installed_kaptive.patch dpkg-source: info: applying bigendian.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2833261/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='0605ceb6816e447a803f3ee2aee0ca7f' 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='2833261' 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.Al7l5qSs/pbuilderrc_pciX --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.Al7l5qSs/b1 --logfile b1/build.log kleborate_2.4.1-3.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 codethink02-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:15 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2833261/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, python3-setuptools, ncbi-blast+, mash, kaptive dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19940 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; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on mash; however: Package mash is not installed. pbuilder-satisfydepends-dummy depends on kaptive; however: Package kaptive is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} kaptive{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcapnp-1.0.1{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgsl27{a} libgslcblas0{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblcms2-2{a} liblerc4{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmurmurhash2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} mash{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} po-debconf{a} python3{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-distutils{a} python3-freetype{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx python-biopython-doc python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 119 newly installed, 0 to remove and 0 not upgraded. Need to get 81.8 MB of archives. After unpacking 331 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.8-1 [811 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.8-1 [1848 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1781 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.8-1 [597 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.6-1 [9224 B] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.6-1 [26.2 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.2-1 [800 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.2-1 [1983 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 62 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.2-1 [1872 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.2-1 [653 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.24.2-2 [4122 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-2+b2 [172 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.78.4-7 [1364 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.3.2-0.4+b1 [107 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.3.2-0.4+b1 [263 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.3.2-0.4+b1 [107 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.3.2-0.4+b1 [119 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.3.0-2 [552 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.0-1+b1 [478 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.0-1 [139 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 104 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.1.0-4 [1113 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.81+dfsg-3 [1611 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 liblmdb0 arm64 0.9.31-1+b1 [43.0 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libmbedcrypto7t64 arm64 2.28.8-1 [269 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libmbedx509-1t64 arm64 2.28.8-1 [131 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libmbedtls14t64 arm64 2.28.8-1 [160 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 ncbi-blast+ arm64 2.12.0+ds-4+b1 [11.6 MB] Get: 114 http://deb.debian.org/debian trixie/main arm64 kaptive all 2.0.8-1 [24.2 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libcapnp-1.0.1 arm64 1.0.1-3+b1 [1269 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libgslcblas0 arm64 2.7.1+dfsg-6+b1 [72.7 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libgsl27 arm64 2.7.1+dfsg-6+b1 [822 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libmurmurhash2 arm64 1.6-1 [6232 B] Get: 119 http://deb.debian.org/debian trixie/main arm64 mash arm64 2.3+dfsg-6 [171 kB] Fetched 81.8 MB in 1s (63.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19940 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_arm64.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20256 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_arm64.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_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 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_arm64.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... 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 ... 21250 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_arm64.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../001-libpython3.12-minimal_3.12.2-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.2-1_arm64.deb ... Unpacking python3.12-minimal (3.12.2-1) ... 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_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../006-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-3+b1_arm64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... 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Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../022-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../023-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../024-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../025-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../026-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../027-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../028-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../029-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../031-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../032-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../033-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../034-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../035-python3-lib2to3_3.12.3-1_all.deb ... Unpacking python3-lib2to3 (3.12.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../036-python3-distutils_3.12.3-1_all.deb ... Unpacking python3-distutils (3.12.3-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../037-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../038-dh-python_6.20240422_all.deb ... Unpacking dh-python (6.20240422) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../039-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../040-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:arm64. Preparing to unpack .../041-libfontenc1_1%3a1.1.8-1_arm64.deb ... Unpacking libfontenc1:arm64 (1:1.1.8-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../042-libbrotli1_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../043-libpng16-16t64_1.6.43-5_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.43-5) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../044-libfreetype6_2.13.2+dfsg-1+b4_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package x11-common. Preparing to unpack .../045-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../046-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../047-xfonts-utils_1%3a7.7+6_arm64.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../048-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../049-fontconfig-config_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../050-libpython3.12-stdlib_3.12.2-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.2-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../051-python3.12_3.12.2-1_arm64.deb ... Unpacking python3.12 (3.12.2-1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../052-libblas3_3.12.0-3_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../053-libgfortran5_14-20240330-1_arm64.deb ... Unpacking libgfortran5:arm64 (14-20240330-1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../054-liblapack3_3.12.0-3_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-3) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../055-python3-numpy_1%3a1.24.2-2_arm64.deb ... Unpacking python3-numpy (1:1.24.2-2) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../056-python3-chardet_5.2.0+dfsg-1_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-1) ... Selecting previously unselected package libimagequant0:arm64. Preparing to unpack .../057-libimagequant0_2.18.0-1+b1_arm64.deb ... Unpacking libimagequant0:arm64 (2.18.0-1+b1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../058-libjpeg62-turbo_1%3a2.1.5-2+b2_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-2+b2) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../059-liblcms2-2_2.14-2+b1_arm64.deb ... Unpacking liblcms2-2:arm64 (2.14-2+b1) ... Selecting previously unselected package libopenjp2-7:arm64. 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Selecting previously unselected package kaptive. Preparing to unpack .../101-kaptive_2.0.8-1_all.deb ... Unpacking kaptive (2.0.8-1) ... Selecting previously unselected package libcapnp-1.0.1:arm64. Preparing to unpack .../102-libcapnp-1.0.1_1.0.1-3+b1_arm64.deb ... Unpacking libcapnp-1.0.1:arm64 (1.0.1-3+b1) ... Selecting previously unselected package libgslcblas0:arm64. Preparing to unpack .../103-libgslcblas0_2.7.1+dfsg-6+b1_arm64.deb ... Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6+b1) ... Selecting previously unselected package libgsl27:arm64. Preparing to unpack .../104-libgsl27_2.7.1+dfsg-6+b1_arm64.deb ... Unpacking libgsl27:arm64 (2.7.1+dfsg-6+b1) ... Selecting previously unselected package libmurmurhash2:arm64. Preparing to unpack .../105-libmurmurhash2_1.6-1_arm64.deb ... Unpacking libmurmurhash2:arm64 (1.6-1) ... Selecting previously unselected package mash. Preparing to unpack .../106-mash_2.3+dfsg-6_arm64.deb ... Unpacking mash (2.3+dfsg-6) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up liblmdb0:arm64 (0.9.31-1+b1) ... Setting up libgraphite2-3:arm64 (1.3.14-2) ... Setting up liblcms2-2:arm64 (2.14-2+b1) ... Setting up ncbi-data (6.1.20170106+dfsg1-10) ... Setting up libpixman-1-0:arm64 (0.42.2-1+b1) ... Setting up libsharpyuv0:arm64 (1.3.2-0.4+b1) ... Setting up libxau6:arm64 (1:1.0.9-1+b1) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmbedcrypto7t64:arm64 (2.28.8-1) ... Setting up libgslcblas0:arm64 (2.7.1+dfsg-6+b1) ... Setting up libmurmurhash2:arm64 (1.6-1) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libcapnp-1.0.1:arm64 (1.0.1-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libpython3.12-minimal:arm64 (3.12.2-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:arm64 (1:5.45-2+b1) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up libgsl27:arm64 (2.7.1+dfsg-6+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libjbig0:arm64 (2.1-6.1+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Apr 28 12:27:19 UTC 2024. Universal Time is now: Sun Apr 28 12:27:19 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.78.4-7) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-3) ... 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 libjpeg62-turbo:arm64 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.13-3+b1) ... Setting up libimagequant0:arm64 (2.18.0-1+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.43-5) ... Setting up mash (2.3+dfsg-6) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:arm64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.3.2-0.4+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:arm64 (4.5.1+git230720-4) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b3) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libwebpmux3:arm64 (1.3.2-0.4+b1) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... 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 (1.13.1-1) ... Setting up python3.12-minimal (3.12.2-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up liblapack3:arm64 (3.12.0-3) ... 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 libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:arm64 (2.28.8-1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:arm64 (1.3.2-0.4+b1) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libmbedtls14t64:arm64 (2.28.8-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up xml-core (0.19) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up libpython3.12-stdlib:arm64 (3.12.2-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... Setting up python3.12 (3.12.2-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.0-1+b1) ... Setting up libraqm0:arm64 (0.10.1-1+b1) ... Setting up libpython3-stdlib:arm64 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up ncbi-blast+ (2.12.0+ds-4+b1) ... Setting up python3-pil:arm64 (10.3.0-2) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-cairo (1.26.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-reportlab (4.1.0-4) ... Setting up dh-python (6.20240422) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.81+dfsg-3) ... Setting up kaptive (2.0.8-1) ... 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/kleborate-2.4.1/ && 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 > ../kleborate_2.4.1-3_source.changes dpkg-buildpackage: info: source package kleborate dpkg-buildpackage: info: source version 2.4.1-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.11 setup.py clean running clean removing '/build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it 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: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__main__.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/blastn.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/kaptive.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/version.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/truncation.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/species.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/shv_mutations.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/rmpA.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/resBLAST.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/mlstBLAST.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/misc.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/help_formatter.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/contig_stats.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__init__.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate running egg_info creating Kleborate.egg-info writing Kleborate.egg-info/PKG-INFO writing dependency_links to Kleborate.egg-info/dependency_links.txt writing entry points to Kleborate.egg-info/entry_points.txt writing requirements to Kleborate.egg-info/requires.txt writing top-level names to Kleborate.egg-info/top_level.txt writing manifest file 'Kleborate.egg-info/SOURCES.txt' reading manifest file 'Kleborate.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'kleborate/ICEKp_references' warning: no directories found matching 'kaptive/reference_database' warning: no directories found matching 'kaptive/sample_data' adding license file 'LICENSE' writing manifest file 'Kleborate.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'kleborate.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'kleborate.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'kleborate.data' to be distributed and are already explicitly excluding 'kleborate.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'kleborate.data.ICEKp_references' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data.ICEKp_references' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'kleborate.data.ICEKp_references' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'kleborate.data.ICEKp_references' to be distributed and are already explicitly excluding 'kleborate.data.ICEKp_references' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/AbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/CARD_AMR_clustered.csv -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/CARD_v3.1.13.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/CbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/Klebsiella_pneumoniae.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/MgrB_and_PmrB.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/OmpK.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/QRDR_120.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/RmST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/SmST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/YbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/clb_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/iro_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/iuc_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/kpneumoniae.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/rmpA2.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/rmp_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/species_mash_sketches.msh -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/wzi.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/wzi.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/ybt_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data creating /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp1.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp10.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp11.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp12.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp13.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp14.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp15.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp16.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp17.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp18.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp19.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp2.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp20.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp21.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp22.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp3.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp4.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp5.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp6.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp7.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp8.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp9.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build; python3.11 -m unittest discover -v /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( test_ambiguous_bases_1 (test.test_contig_stats.TestContigStats.test_ambiguous_bases_1) ... ok test_ambiguous_bases_2 (test.test_contig_stats.TestContigStats.test_ambiguous_bases_2) ... ok test_ambiguous_bases_3 (test.test_contig_stats.TestContigStats.test_ambiguous_bases_3) ... ok test_ambiguous_bases_4 (test.test_contig_stats.TestContigStats.test_ambiguous_bases_4) ... ok test_count_1 (test.test_contig_stats.TestContigStats.test_count_1) ... ok test_count_2 (test.test_contig_stats.TestContigStats.test_count_2) ... ok test_longest_1 (test.test_contig_stats.TestContigStats.test_longest_1) ... ok test_longest_2 (test.test_contig_stats.TestContigStats.test_longest_2) ... ok test_n50_1 (test.test_contig_stats.TestContigStats.test_n50_1) ... ok test_n50_2 (test.test_contig_stats.TestContigStats.test_n50_2) ... ok test_qc_warnings_1 (test.test_contig_stats.TestContigStats.test_qc_warnings_1) ... ok test_qc_warnings_2 (test.test_contig_stats.TestContigStats.test_qc_warnings_2) ... ok test_qc_warnings_3 (test.test_contig_stats.TestContigStats.test_qc_warnings_3) ... ok test_qc_warnings_4 (test.test_contig_stats.TestContigStats.test_qc_warnings_4) ... ok test_qc_warnings_5 (test.test_contig_stats.TestContigStats.test_qc_warnings_5) ... ok test_qc_warnings_6 (test.test_contig_stats.TestContigStats.test_qc_warnings_6) ... ok test_qc_warnings_7 (test.test_contig_stats.TestContigStats.test_qc_warnings_7) ... ok test_qc_warnings_8 (test.test_contig_stats.TestContigStats.test_qc_warnings_8) ... ok test_total_size_1 (test.test_contig_stats.TestContigStats.test_total_size_1) ... ok test_total_size_2 (test.test_contig_stats.TestContigStats.test_total_size_2) ... ok test_total_size_3 (test.test_contig_stats.TestContigStats.test_total_size_3) ... ok test_total_size_4 (test.test_contig_stats.TestContigStats.test_total_size_4) ... ok test_iro_exact_1 (test.test_iro.TestIro.test_iro_exact_1) This test is an exact match for SmST1. ... ok test_iro_exact_33 (test.test_iro.TestIro.test_iro_exact_33) This test is an exact match for SmST33. ... ok test_iro_incomplete (test.test_iro.TestIro.test_iro_incomplete) This test is an exact match for only one allele. ... ok test_iro_inexact (test.test_iro.TestIro.test_iro_inexact) This test is an inexact match for SmST33. There are single base changes in iroC and in ... ok test_iro_missing_1 (test.test_iro.TestIro.test_iro_missing_1) This test is a match for SmST1, except that it's missing iroN. ... ok test_iro_novel (test.test_iro.TestIro.test_iro_novel) This test is an exact match for alleles, but an unknown combination. ... ok test_iro_random (test.test_iro.TestIro.test_iro_random) This test has just random sequence and should give no iro call. ... ok test_confidence_meets_threshold_01 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_01) ... ok test_confidence_meets_threshold_02 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_02) ... ok test_confidence_meets_threshold_03 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_03) ... ok test_confidence_meets_threshold_04 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_04) ... ok test_confidence_meets_threshold_05 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_05) ... ok test_confidence_meets_threshold_06 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_06) ... ok test_confidence_meets_threshold_07 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_07) ... ok test_confidence_meets_threshold_08 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_08) ... ok test_confidence_meets_threshold_09 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_09) ... ok test_confidence_meets_threshold_10 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_10) ... ok test_134 (test.test_mlst.TestMlst.test_134) ... ok test_83 (test.test_mlst.TestMlst.test_83) ... ok test_ba779 (test.test_mlst.TestMlst.test_ba779) ... ok test_chromosome_exact (test.test_mlst.TestMlst.test_chromosome_exact) This test is an exact match for ST23. ... ok test_chromosome_inexact (test.test_mlst.TestMlst.test_chromosome_inexact) This test is is one base off from ST23 (single substitution in mdh_1 of G to A). ... ok test_chromosome_random (test.test_mlst.TestMlst.test_chromosome_random) This test has just random sequence and should give no MLST call. ... ok test_kp_subspecies_1 (test.test_mlst.TestMlst.test_kp_subspecies_1) ... ok test_kp_subspecies_2 (test.test_mlst.TestMlst.test_kp_subspecies_2) ... ok test_kp_subspecies_3 (test.test_mlst.TestMlst.test_kp_subspecies_3) ... ok test_kp_subspecies_4 (test.test_mlst.TestMlst.test_kp_subspecies_4) ... ok test_kp_subspecies_5 (test.test_mlst.TestMlst.test_kp_subspecies_5) ... ok test_kp_subspecies_6 (test.test_mlst.TestMlst.test_kp_subspecies_6) ... ok test_kp_subspecies_7 (test.test_mlst.TestMlst.test_kp_subspecies_7) ... ok test_ozaenae (test.test_mlst.TestMlst.test_ozaenae) ... ok test_rhinoscleromatis (test.test_mlst.TestMlst.test_rhinoscleromatis) ... ok test_unknown_ST (test.test_mlst.TestMlst.test_unknown_ST) This test has exact matches for alleles but in an unknown ST combination ... ok test_res_01 (test.test_res_aac.TestResAac.test_res_01) ... /usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/__init__.py:519: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' mode='r' encoding='utf-8'> matrix = read(path) ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_res_02 (test.test_res_aac.TestResAac.test_res_02) ... ok test_res_03 (test.test_res_aac.TestResAac.test_res_03) ... ok test_res_04 (test.test_res_aac.TestResAac.test_res_04) This is a tricky one (and the one which first highlighted the problem). The best bit-score ... ok test_res_05 (test.test_res_aac.TestResAac.test_res_05) Same as test_res_04, but with the hit on the other strand. ... ok test_exact_aa_match_1 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_1) Simple case: full protein sequence ending in a stop codon. ... ok test_exact_aa_match_2 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_2) These two seqs have a stop codon in the middle but still match exactly. ... ok test_exact_aa_match_3 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_3) These two seqs have a stop codon in the middle and mismatch after the stop. ... ok test_exact_aa_match_4 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_4) These two seqs have a stop codon in the middle and mismatch after the stop. ... ok test_exact_aa_match_5 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_5) These two seqs are non-multiple-of-three in length and match in their remainder. ... ok test_exact_aa_match_6 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_6) These two seqs are non-multiple-of-three in length and match in their remainder. ... ok test_exact_aa_match_7 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_7) These two seqs are non-multiple-of-three in length and don't match in their remainder. ... ok test_exact_aa_match_8 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_8) The first seq's protein sequence contains the second seq's protein sequence. ... ok test_res_01 (test.test_res_alleles.TestResAlleles.test_res_01) ... ok test_res_02 (test.test_res_alleles.TestResAlleles.test_res_02) ... ok test_res_03 (test.test_res_alleles.TestResAlleles.test_res_03) ... ok test_res_04 (test.test_res_alleles.TestResAlleles.test_res_04) ... ok test_res_05 (test.test_res_alleles.TestResAlleles.test_res_05) ... ok test_res_06 (test.test_res_alleles.TestResAlleles.test_res_06) ... ok test_res_07 (test.test_res_alleles.TestResAlleles.test_res_07) ... ok test_res_08 (test.test_res_alleles.TestResAlleles.test_res_08) ... ok test_res_09 (test.test_res_alleles.TestResAlleles.test_res_09) ... ok test_res_10 (test.test_res_alleles.TestResAlleles.test_res_10) ... ok test_res_11 (test.test_res_alleles.TestResAlleles.test_res_11) This test has the ABC-1 gene but with a stop codon in the middle. ... ok test_res_12 (test.test_res_alleles.TestResAlleles.test_res_12) This test has the ABC-1 gene but missing the first (start) codon. ... ok test_res_13 (test.test_res_alleles.TestResAlleles.test_res_13) This test has the ABC-1 gene but at only 50% coverage, so it goes to spurious hits. ... ok test_res_14 (test.test_res_alleles.TestResAlleles.test_res_14) I added this test to catch a weird BLAST-related bug where an exact amino acid match for ... ok test_res_15 (test.test_res_alleles.TestResAlleles.test_res_15) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_res_16 (test.test_res_alleles.TestResAlleles.test_res_16) I added this test to catch a weird BLAST-related bug where an exact amino acid match for ... ok test_res_17 (test.test_res_alleles.TestResAlleles.test_res_17) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_res_18 (test.test_res_alleles.TestResAlleles.test_res_18) This is the uncomplicated case for a OKP-B-6^ result (later tests cover more challenging ... ok test_res_19 (test.test_res_alleles.TestResAlleles.test_res_19) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_res_20 (test.test_res_alleles.TestResAlleles.test_res_20) I added this test to catch a bug where there is an exact amino acid match but inexact ... ok test_res_21 (test.test_res_alleles.TestResAlleles.test_res_21) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_res_22 (test.test_res_alleles.TestResAlleles.test_res_22) I added this test to catch a bug where there is an exact amino acid match but inexact ... ok test_res_23 (test.test_res_alleles.TestResAlleles.test_res_23) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_both_genes_intact (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_both_genes_intact) ... ok test_mgrb_missing (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_mgrb_missing) ... ok test_mgrb_missing_non_kp_complex (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_mgrb_missing_non_kp_complex) Setting the Kp complex variable to False should turn off the MgrB/PmrB tests. ... ok test_pmrb_early_stop (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_pmrb_early_stop) This tests an early stop mutation (without a frameshift) in pmrB. ... ok test_pmrb_early_stop_SRR2098701 (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_pmrb_early_stop_SRR2098701) ... ok test_pmrb_frameshift (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_pmrb_frameshift) A frameshift in pmrB should cause an early stop and lead to a colisitin resistance call. ... ok test_both_genes_intact (test.test_res_omp.TestResOmp.test_both_genes_intact) ... ok test_ompk35_early_stop (test.test_res_omp.TestResOmp.test_ompk35_early_stop) This tests an early stop mutation (without a frameshift) in OmpK35. ... ok test_ompk35_frameshift (test.test_res_omp.TestResOmp.test_ompk35_frameshift) A frameshift in OmpK35 should cause an early stop and lead to a carbapenem resistance call. ... ok test_ompk36_missing (test.test_res_omp.TestResOmp.test_ompk36_missing) ... ok test_ompk36gd (test.test_res_omp.TestResOmp.test_ompk36gd) ... ok test_ompk36td (test.test_res_omp.TestResOmp.test_ompk36td) ... ok test_ompk36td_non_kp_complex (test.test_res_omp.TestResOmp.test_ompk36td_non_kp_complex) Setting the Kp complex variable to False should turn off the OmpK tests. ... ok test_gyra (test.test_res_qrdr.TestResGyrAParC.test_gyra) ... ok test_gyra_and_parc (test.test_res_qrdr.TestResGyrAParC.test_gyra_and_parc) ... ok test_gyra_and_parc_non_kp_complex (test.test_res_qrdr.TestResGyrAParC.test_gyra_and_parc_non_kp_complex) Setting the Kp complex variable to False should turn off the QRDR tests. ... ok test_no_mutations (test.test_res_qrdr.TestResGyrAParC.test_no_mutations) ... ok test_parc (test.test_res_qrdr.TestResGyrAParC.test_parc) ... ok test_tem (test.test_res_tem.TestResTem.test_tem) ... ok test_rmp_19 (test.test_rmp.TestRmp.test_rmp_19) This test is an exact match for RmST19, an ST without any truncated alleles. ... ok test_rmp_21 (test.test_rmp.TestRmp.test_rmp_21) This test is an exact match for RmST21, an ST with a truncated allele. ... ok test_rmp_missing_1 (test.test_rmp.TestRmp.test_rmp_missing_1) This test is a match for RmST1, except that it's missing rmpC. ... ok test_rmp_novel (test.test_rmp.TestRmp.test_rmp_novel) This test is an exact match for alleles, but an unknown combination. ... ok test_rmp_random (test.test_rmp.TestRmp.test_rmp_random) This test has just random sequence and should give no rmp call. ... ok test_rmpa2_exact (test.test_rmp.TestRmp.test_rmpa2_exact) This test has an exact match for rmpA2_1. ... ok test_rmpa2_exact_truncated (test.test_rmp.TestRmp.test_rmpa2_exact_truncated) This test has an exact match for rmpA2_7. ... ok test_rmpa2_inexact (test.test_rmp.TestRmp.test_rmpa2_inexact) This test has an inexact match for rmpA2_1. ... ok test_rmpa2_random (test.test_rmp.TestRmp.test_rmpa2_random) This test has just random sequence and should give no rmpA2 call. ... ok test_bla_class_01 (test.test_shv.TestShvMutations.test_bla_class_01) ... ok test_bla_class_02 (test.test_shv.TestShvMutations.test_bla_class_02) ... ok test_bla_class_03 (test.test_shv.TestShvMutations.test_bla_class_03) ... ok test_bla_class_04 (test.test_shv.TestShvMutations.test_bla_class_04) ... ok test_get_class_changing_mutations_01 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_01) ... ok test_get_class_changing_mutations_02 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_02) ... ok test_get_class_changing_mutations_03 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_03) ... ok test_get_class_changing_mutations_04 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_04) ... ok test_get_class_changing_mutations_05 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_05) ... ok test_get_class_changing_mutations_06 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_06) ... ok test_get_class_changing_mutations_07 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_07) ... ok test_get_class_changing_mutations_08 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_08) ... ok test_shv_01 (test.test_shv.TestShvMutations.test_shv_01) This test has an exact match for SHV-1. ... ok test_shv_02 (test.test_shv.TestShvMutations.test_shv_02) This test has a match for SHV-1 with a mutation at site 238 (G -> Y). This changes the ... ok test_shv_03 (test.test_shv.TestShvMutations.test_shv_03) Same as test 2, but the gene is on the reverse strand. ... ok test_shv_04 (test.test_shv.TestShvMutations.test_shv_04) This test has a match for SHV-1 with a mutation at site 50 (G -> Y). This is not class-modifying ... ok test_shv_05 (test.test_shv.TestShvMutations.test_shv_05) This test has an exact match for SHV-29. ... ok test_shv_06 (test.test_shv.TestShvMutations.test_shv_06) This test has SHV-29 plus an beta-lactamase inhibitor resistant mutation. ... ok test_shv_07 (test.test_shv.TestShvMutations.test_shv_07) This test has SHV-1 with position 238 deleted. Is not ... ok test_shv_08 (test.test_shv.TestShvMutations.test_shv_08) This test has SHV-1 with a synonymous mutation in the omega loop (not ESBL-conferring mutation). ... ok test_shv_09 (test.test_shv.TestShvMutations.test_shv_09) This test has SHV-1 with a nonsynonymous mutation in the omega loop (reported but not ESBL-conferring mutation). ... ok test_citrobacter (test.test_species.TestKpComplex.test_citrobacter) ... ok test_klebsiella_aerogenes (test.test_species.TestKpComplex.test_klebsiella_aerogenes) ... ok test_klebsiella_africanensis (test.test_species.TestKpComplex.test_klebsiella_africanensis) ... ok test_klebsiella_grimontii (test.test_species.TestKpComplex.test_klebsiella_grimontii) ... ok test_klebsiella_michiganensis (test.test_species.TestKpComplex.test_klebsiella_michiganensis) ... ok test_klebsiella_oxytoca (test.test_species.TestKpComplex.test_klebsiella_oxytoca) ... ok test_klebsiella_pneumoniae (test.test_species.TestKpComplex.test_klebsiella_pneumoniae) ... ok test_klebsiella_quasipneumoniae_subsp_quasipneumoniae (test.test_species.TestKpComplex.test_klebsiella_quasipneumoniae_subsp_quasipneumoniae) ... ok test_klebsiella_quasipneumoniae_subsp_similipneumoniae (test.test_species.TestKpComplex.test_klebsiella_quasipneumoniae_subsp_similipneumoniae) ... ok test_klebsiella_quasivariicola (test.test_species.TestKpComplex.test_klebsiella_quasivariicola) ... ok test_klebsiella_variicola_subsp_tropicalensis (test.test_species.TestKpComplex.test_klebsiella_variicola_subsp_tropicalensis) ... ok test_klebsiella_variicola_subsp_variicola (test.test_species.TestKpComplex.test_klebsiella_variicola_subsp_variicola) ... ok test_raoultella_ornithinolytica (test.test_species.TestKpComplex.test_raoultella_ornithinolytica) ... ok test_raoultella_planticola (test.test_species.TestKpComplex.test_raoultella_planticola) ... ok test_raoultella_terrigena (test.test_species.TestKpComplex.test_raoultella_terrigena) ... ok test_salmonella (test.test_species.TestKpComplex.test_salmonella) ... ok test_citrobacter (test.test_species.TestSpecies.test_citrobacter) ... ok test_klebsiella_aerogenes (test.test_species.TestSpecies.test_klebsiella_aerogenes) ... ok test_klebsiella_africana (test.test_species.TestSpecies.test_klebsiella_africana) ... ok test_klebsiella_grimontii (test.test_species.TestSpecies.test_klebsiella_grimontii) ... ok test_klebsiella_indica (test.test_species.TestSpecies.test_klebsiella_indica) ... ok test_klebsiella_michiganensis (test.test_species.TestSpecies.test_klebsiella_michiganensis) ... ok test_klebsiella_oxytoca (test.test_species.TestSpecies.test_klebsiella_oxytoca) ... ok test_klebsiella_pasteurii (test.test_species.TestSpecies.test_klebsiella_pasteurii) ... ok test_klebsiella_pneumoniae (test.test_species.TestSpecies.test_klebsiella_pneumoniae) ... ok test_klebsiella_quasipneumoniae_subsp_quasipneumoniae (test.test_species.TestSpecies.test_klebsiella_quasipneumoniae_subsp_quasipneumoniae) ... ok test_klebsiella_quasipneumoniae_subsp_similipneumoniae (test.test_species.TestSpecies.test_klebsiella_quasipneumoniae_subsp_similipneumoniae) ... ok test_klebsiella_quasivariicola (test.test_species.TestSpecies.test_klebsiella_quasivariicola) ... ok test_klebsiella_spallanzanii (test.test_species.TestSpecies.test_klebsiella_spallanzanii) ... ok test_klebsiella_variicola_subsp_tropicalensis (test.test_species.TestSpecies.test_klebsiella_variicola_subsp_tropicalensis) ... ok test_klebsiella_variicola_subsp_variicola (test.test_species.TestSpecies.test_klebsiella_variicola_subsp_variicola) ... ok test_raoultella_ornithinolytica (test.test_species.TestSpecies.test_raoultella_ornithinolytica) ... ok test_raoultella_planticola (test.test_species.TestSpecies.test_raoultella_planticola) ... ok test_raoultella_terrigena (test.test_species.TestSpecies.test_raoultella_terrigena) ... ok test_salmonella (test.test_species.TestSpecies.test_salmonella) ... ok test_yersinia_unknown (test.test_species.TestSpecies.test_yersinia_unknown) ... ok test_nothing (test.test_summary.TestResScore.test_nothing) ... ok test_res_counts_1 (test.test_summary.TestResScore.test_res_counts_1) ... ok test_res_counts_10 (test.test_summary.TestResScore.test_res_counts_10) Resistance-by-truncation should add to the class count but not to the gene count (because ... ok test_res_counts_11 (test.test_summary.TestResScore.test_res_counts_11) Spurious hits should not add to either the gene or class counts. ... ok test_res_counts_2 (test.test_summary.TestResScore.test_res_counts_2) ... ok test_res_counts_3 (test.test_summary.TestResScore.test_res_counts_3) Intrinsic Bla genes should not add to the counts. ... ok test_res_counts_4 (test.test_summary.TestResScore.test_res_counts_4) Bla genes in columns other than 'Bla_chr' (e.g. 'Bla_ESBL_acquired') should add to the ... ok test_res_counts_5 (test.test_summary.TestResScore.test_res_counts_5) Bla genes in columns other than 'Bla_chr' (e.g. 'Bla_acquired') should add to the counts. ... ok test_res_counts_6 (test.test_summary.TestResScore.test_res_counts_6) Omp gene truncations should not add to the gene or class counts. ... ok test_res_counts_7 (test.test_summary.TestResScore.test_res_counts_7) Mutations should add to the class count but not to the gene count (because that is for ... ok test_res_counts_8 (test.test_summary.TestResScore.test_res_counts_8) Mutations should add to the class count but not to the gene count (because that is for ... ok test_res_counts_9 (test.test_summary.TestResScore.test_res_counts_9) Mutations should add to the class count but not to the gene count (because that is for ... ok test_res_score_1 (test.test_summary.TestResScore.test_res_score_1) ... ok test_res_score_2 (test.test_summary.TestResScore.test_res_score_2) ... ok test_res_score_3 (test.test_summary.TestResScore.test_res_score_3) ... ok test_res_score_4 (test.test_summary.TestResScore.test_res_score_4) ... ok test_res_score_5 (test.test_summary.TestResScore.test_res_score_5) ... ok test_res_score_6 (test.test_summary.TestResScore.test_res_score_6) ... ok test_res_score_7 (test.test_summary.TestResScore.test_res_score_7) ... ok test_res_score_8 (test.test_summary.TestResScore.test_res_score_8) ... ok test_vir_score_1 (test.test_summary.TestResScore.test_vir_score_1) ... ok test_vir_score_2 (test.test_summary.TestResScore.test_vir_score_2) ... ok test_vir_score_3 (test.test_summary.TestResScore.test_vir_score_3) ... ok test_vir_score_4 (test.test_summary.TestResScore.test_vir_score_4) ... ok test_vir_score_5 (test.test_summary.TestResScore.test_vir_score_5) ... ok test_vir_score_6 (test.test_summary.TestResScore.test_vir_score_6) ... ok test_vir_score_7 (test.test_summary.TestResScore.test_vir_score_7) ... ok ---------------------------------------------------------------------- Ran 203 tests in 73.309s OK {'Sul_acquired': 'sul2^', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': '-', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/kleborate-2.4.1/debian/tmp 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 Kleborate.egg-info/PKG-INFO writing dependency_links to Kleborate.egg-info/dependency_links.txt writing entry points to Kleborate.egg-info/entry_points.txt writing requirements to Kleborate.egg-info/requires.txt writing top-level names to Kleborate.egg-info/top_level.txt reading manifest file 'Kleborate.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'kleborate/ICEKp_references' warning: no directories found matching 'kaptive/reference_database' warning: no directories found matching 'kaptive/sample_data' adding license file 'LICENSE' writing manifest file 'Kleborate.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'kleborate.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'kleborate.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'kleborate.data' to be distributed and are already explicitly excluding 'kleborate.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'kleborate.data.ICEKp_references' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data.ICEKp_references' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'kleborate.data.ICEKp_references' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'kleborate.data.ICEKp_references' to be distributed and are already explicitly excluding 'kleborate.data.ICEKp_references' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running install_lib creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11 creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/version.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/rmpA.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/shv_mutations.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/resBLAST.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/truncation.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/blastn.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/mlstBLAST.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/species.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/kaptive.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/help_formatter.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/__main__.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/misc.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/contig_stats.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp9.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp8.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp7.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp6.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp5.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp4.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp3.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp22.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp21.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp20.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp2.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp19.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp18.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp17.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp16.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp15.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp14.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp13.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp12.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp11.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp10.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp1.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/ybt_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/wzi.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/wzi.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/species_mash_sketches.msh -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/rmp_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/rmpA2.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/kpneumoniae.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/iuc_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/iro_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/clb_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/YbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/SmST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/RmST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/QRDR_120.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/OmpK.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/MgrB_and_PmrB.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/Klebsiella_pneumoniae.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/CbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/CARD_v3.1.13.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/CARD_AMR_clustered.csv -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/data/AbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__init__.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/contig_stats.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/help_formatter.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/misc.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/mlstBLAST.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/resBLAST.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/rmpA.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/shv_mutations.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/species.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/truncation.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/version.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/kaptive.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/blastn.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.11/build/kleborate/__main__.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/contig_stats.py to contig_stats.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/help_formatter.py to help_formatter.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/misc.py to misc.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/mlstBLAST.py to mlstBLAST.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/resBLAST.py to resBLAST.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/rmpA.py to rmpA.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/shv_mutations.py to shv_mutations.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/species.py to species.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/truncation.py to truncation.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/version.py to version.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/kaptive.py to kaptive.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/blastn.py to blastn.cpython-311.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__main__.py to __main__.cpython-311.pyc running install_egg_info Copying Kleborate.egg-info to /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/Kleborate-2.4.0.egg-info Skipping SOURCES.txt running install_scripts Installing kleborate script to /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/bin Building BLAST databases with makeblastdb: makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/CARD_v3.1.13.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/clb_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/rmpA2.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/iro_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/iuc_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/rmp_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/wzi.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ybt_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/MgrB_and_PmrB.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/OmpK.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/QRDR_120.fasta  _ __ _ ______ ____ ____ _____ _______ ______ | | / /| | | ____| _ \ / __ \| __ \ /\|__ __| ____| | |/ / | | | |__ | |_) | | | | |__) | / \ | | | |__ | < | | | __| | _ <| | | | _ / / /\ \ | | | __| | |\ \ | |___| |____| |_) | |__| | | \ \/ ____ \| | | |____ |_| \_\|_____|______|____/ \____/|_| \_\/ \_\_| |______|  Kleborate is installed and ready to use! Example commands: kleborate --help kleborate -o results.txt -a *.fasta kleborate --resistance -o results.txt -a *.fasta kleborate --all -o results.txt -a *.fasta debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/kleborate-2.4.1' dh_install # fasta.nin files will be (re)build at package installation time to not # contain build path. Other fasta.* are rebuilt by makeblastdb and may # cause inconsistencies in the package itself when makeblastdb is # upgraded and changes format, e.g. during a major operating system # upgrade. See Bug#1036743. find debian -name "*.fasta.nin" -delete find debian -name "*.fasta.ndb" -delete find debian -name "*.fasta.ntf" -delete make[1]: Leaving directory '/build/reproducible-path/kleborate-2.4.1' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild 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 debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/kleborate-2.4.1' dh_fixperms find debian -name "*.msh" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/kleborate-2.4.1' 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 'kleborate-examples' in '../kleborate-examples_2.4.1-3_all.deb'. dpkg-deb: building package 'kleborate' in '../kleborate_2.4.1-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../kleborate_2.4.1-3_arm64.buildinfo dpkg-genchanges --build=binary -O../kleborate_2.4.1-3_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/2833261 and its subdirectories I: Current time: Sun Apr 28 00:30:08 -12 2024 I: pbuilder-time-stamp: 1714307408 Sun Apr 28 12:30:11 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Sun Apr 28 12:30:11 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Sun Apr 28 12:33:25 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Sun Apr 28 12:33:26 UTC 2024 I: kleborate_2.4.1-3_arm64.changes: Format: 1.8 Date: Sun, 10 Mar 2024 19:39:36 +0100 Source: kleborate Binary: kleborate kleborate-examples Architecture: all arm64 Version: 2.4.1-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: kleborate - tool to screen Klebsiella genome assemblies kleborate-examples - tool to screen Klebsiella genome assemblies (example data) Closes: 1065889 Changes: kleborate (2.4.1-3) unstable; urgency=medium . * d/control: delete remaining dependency on distutils. (Closes: #1065889) * bigendian.patch: unfuzz. Checksums-Sha1: 73018e7f3843479d7c26c7dfb463c1ae02795b32 5993376 kleborate-examples_2.4.1-3_all.deb cad0596269c1899c1cbcec9a6d64382579f103dc 8133 kleborate_2.4.1-3_arm64.buildinfo 5e54b35b86c1109478b743aa7f6275f99359bba1 7740192 kleborate_2.4.1-3_arm64.deb Checksums-Sha256: fba75bfdf579c7228e6fb73c47ddbd0732dace098d35ac1ceef5c96a427a84b4 5993376 kleborate-examples_2.4.1-3_all.deb 4eb8b15448311eea81da340da9b7be1fe92fae5f0dbc64c3242499a9804ea333 8133 kleborate_2.4.1-3_arm64.buildinfo f2f89a12ddb4723cc2738c19089284fcb1c5ff04de7dc2dbeec7e31baec1828c 7740192 kleborate_2.4.1-3_arm64.deb Files: cd7cffb5cce83a57d209efa482b86b33 5993376 science optional kleborate-examples_2.4.1-3_all.deb 8d5bcb0ec63edeb2ef75d5f8976ec914 8133 science optional kleborate_2.4.1-3_arm64.buildinfo 319e6adcc6e609f81ef1dc488f825a59 7740192 science optional kleborate_2.4.1-3_arm64.deb Sun Apr 28 12:33:27 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_8-9274.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Al7l5qSs/kleborate_2.4.1-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Al7l5qSs/kleborate_2.4.1-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Al7l5qSs/kleborate_2.4.1-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Al7l5qSs/b1/kleborate_2.4.1-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Al7l5qSs/b2/kleborate_2.4.1-3_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: 0.476s) 0.476s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.161s) 0.161s 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: 805ms CPU time consumed: 797ms Sun Apr 28 12:33:28 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 28 12:33:28 UTC 2024 I: kleborate from trixie built successfully and reproducibly on arm64. Sun Apr 28 12:33:30 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Apr 28 12:33:30 UTC 2024 I: Submitting 12K b1/kleborate_2.4.1-3_arm64.buildinfo.asc Sun Apr 28 12:33:31 UTC 2024 I: Submitting 12K b2/kleborate_2.4.1-3_arm64.buildinfo.asc Sun Apr 28 12:33:33 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 28 12:33:33 UTC 2024 I: Done submitting .buildinfo files. Sun Apr 28 12:33:33 UTC 2024 I: Removing signed kleborate_2.4.1-3_arm64.buildinfo.asc files: removed './b1/kleborate_2.4.1-3_arm64.buildinfo.asc' removed './b2/kleborate_2.4.1-3_arm64.buildinfo.asc'