I: pbuilder: network access will be disabled during build I: Current time: Sun Mar 22 07:08:54 -12 2026 I: pbuilder-time-stamp: 1774206534 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [kleborate_2.4.1-4.dsc] I: copying [./kleborate_2.4.1.orig.tar.gz] I: copying [./kleborate_2.4.1-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./kleborate_2.4.1-4.dsc: unsupported subcommand 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_2.4.1-4.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/2409666/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d50d4353f25d427a8258251ce1c4e26e' 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='2409666' 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.2iyKOX61/pbuilderrc_GcOy --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2iyKOX61/b1 --logfile b1/build.log kleborate_2.4.1-4.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2409666/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3, 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 ... 19855 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} libcairo2{a} libcapnp-1.1.0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgsl28{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} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmurmurhash2{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} 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-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra 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, 125 newly installed, 0 to remove and 0 not upgraded. Need to get 87.2 MB of archives. After unpacking 341 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 11.0.0 [27.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 37 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.6.0-1 [720 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250108 [113 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 68 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.2+ds-2 [138 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.2+ds-2 [7507 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.1.0-5 [531 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.26.1-2+b1 [130 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.3.0-1 [1157 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-2 [1674 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Get: 120 http://deb.debian.org/debian unstable/main amd64 kaptive all 2.0.8-1 [24.2 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libcapnp-1.1.0 amd64 1.1.0-2 [1479 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libmurmurhash2 amd64 1.6-1+b1 [6180 B] Get: 125 http://deb.debian.org/debian unstable/main amd64 mash amd64 2.3+dfsg-6+b2 [192 kB] Fetched 87.2 MB in 5s (19.2 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19855 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... 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Preparing to unpack .../107-libcapnp-1.1.0_1.1.0-2_amd64.deb ... Unpacking libcapnp-1.1.0:amd64 (1.1.0-2) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../108-libgslcblas0_2.8+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../109-libgsl28_2.8+dfsg-5_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libmurmurhash2:amd64. Preparing to unpack .../110-libmurmurhash2_1.6-1+b1_amd64.deb ... Unpacking libmurmurhash2:amd64 (1.6-1+b1) ... Selecting previously unselected package mash. Preparing to unpack .../111-mash_2.3+dfsg-6+b2_amd64.deb ... Unpacking mash (2.3+dfsg-6+b2) ... Setting up media-types (11.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up ncbi-data (6.1.20170106+dfsg2-5) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... Setting up libmurmurhash2:amd64 (1.6-1+b1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Mar 22 19:09:50 UTC 2026. Universal Time is now: Sun Mar 22 19:09:50 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.46-4) ... Setting up python3-numpy-dev:amd64 (1:2.2.2+ds-2) ... Setting up autopoint (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:amd64 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libopenjp2-7:amd64 (2.5.3-1) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libcapnp-1.1.0:amd64 (1.1.0-2) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libglib2.0-0t64:amd64 (2.83.3-2) ... No schema files found: doing nothing. Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up mash (2.3+dfsg-6+b2) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:2.2.2+ds-2) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up debhelper (13.24.1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:amd64 (11.1.0-5) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-reportlab (4.3.0-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up dh-python (6.20250108) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-2) ... 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_2.4.1-4_source.changes dpkg-buildpackage: info: source package kleborate dpkg-buildpackage: info: source version 2.4.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /build/reproducible-path/kleborate-2.4.1/setup.py:95: SyntaxWarning: invalid escape sequence '\ ' "| | / /| | | ____| _ \ / __ \| __ \ /\|__ __| ____|\n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:96: SyntaxWarning: invalid escape sequence '\ ' "| |/ / | | | |__ | |_) | | | | |__) | / \ | | | |__ \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:97: SyntaxWarning: invalid escape sequence '\ ' "| < | | | __| | _ <| | | | _ / / /\ \ | | | __| \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:98: SyntaxWarning: invalid escape sequence '\ ' "| |\ \ | |___| |____| |_) | |__| | | \ \/ ____ \| | | |____ \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:99: SyntaxWarning: invalid escape sequence '\_' "|_| \_\|_____|______|____/ \____/|_| \_\/ \_\_| |______|\n" running clean removing '/build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /build/reproducible-path/kleborate-2.4.1/setup.py:95: SyntaxWarning: invalid escape sequence '\ ' "| | / /| | | ____| _ \ / __ \| __ \ /\|__ __| ____|\n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:96: SyntaxWarning: invalid escape sequence '\ ' "| |/ / | | | |__ | |_) | | | | |__) | / \ | | | |__ \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:97: SyntaxWarning: invalid escape sequence '\ ' "| < | | | __| | _ <| | | | _ / / /\ \ | | | __| \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:98: SyntaxWarning: invalid escape sequence '\ ' "| |\ \ | |___| |____| |_) | |__| | | \ \/ ____ \| | | |____ \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:99: SyntaxWarning: invalid escape sequence '\_' "|_| \_\|_____|______|____/ \____/|_| \_\/ \_\_| |______|\n" running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build /build/reproducible-path/kleborate-2.4.1/setup.py:95: SyntaxWarning: invalid escape sequence '\ ' "| | / /| | | ____| _ \ / __ \| __ \ /\|__ __| ____|\n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:96: SyntaxWarning: invalid escape sequence '\ ' "| |/ / | | | |__ | |_) | | | | |__) | / \ | | | |__ \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:97: SyntaxWarning: invalid escape sequence '\ ' "| < | | | __| | _ <| | | | _ / / /\ \ | | | __| \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:98: SyntaxWarning: invalid escape sequence '\ ' "| |\ \ | |___| |____| |_) | |__| | | \ \/ ____ \| | | |____ \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:99: SyntaxWarning: invalid escape sequence '\_' "|_| \_\|_____|______|____/ \____/|_| \_\/ \_\_| |______|\n" running build running build_py creating /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/contig_stats.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/blastn.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/rmpA.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/truncation.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/version.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/mlstBLAST.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/kaptive.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/__init__.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/shv_mutations.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/species.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/resBLAST.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/misc.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/__main__.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate copying kleborate/help_formatter.py -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/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:212: _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:212: _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_3.13/build/kleborate/data copying kleborate/data/AbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/CARD_AMR_clustered.csv -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/CARD_v3.1.13.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/CbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/Klebsiella_pneumoniae.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/MgrB_and_PmrB.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/OmpK.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/QRDR_120.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/RmST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/SmST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/YbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/clb_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/iro_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/iuc_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/kpneumoniae.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/rmpA2.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/rmp_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/species_mash_sketches.msh -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/wzi.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/wzi.txt -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data copying kleborate/data/ybt_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data creating /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp1.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp10.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp11.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp12.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp13.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp14.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp15.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp16.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp17.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp18.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp19.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp2.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp20.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp21.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp22.gff -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp3.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp4.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp5.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp6.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp7.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp8.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp9.embl -> /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/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_3.13/build; python3.13 -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) ... 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 71.331s 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 /build/reproducible-path/kleborate-2.4.1/setup.py:95: SyntaxWarning: invalid escape sequence '\ ' "| | / /| | | ____| _ \ / __ \| __ \ /\|__ __| ____|\n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:96: SyntaxWarning: invalid escape sequence '\ ' "| |/ / | | | |__ | |_) | | | | |__) | / \ | | | |__ \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:97: SyntaxWarning: invalid escape sequence '\ ' "| < | | | __| | _ <| | | | _ / / /\ \ | | | __| \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:98: SyntaxWarning: invalid escape sequence '\ ' "| |\ \ | |___| |____| |_) | |__| | | \ \/ ____ \| | | |____ \n" \ /build/reproducible-path/kleborate-2.4.1/setup.py:99: SyntaxWarning: invalid escape sequence '\_' "|_| \_\|_____|______|____/ \____/|_| \_\/ \_\_| |______|\n" 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:212: _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:212: _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/lib/python3.13/dist-packages creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/contig_stats.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/blastn.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/rmpA.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/truncation.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/version.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/mlstBLAST.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/kaptive.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__init__.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/shv_mutations.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/species.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/resBLAST.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/misc.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/rmpA.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/help_formatter.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/truncation.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/version.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/contig_stats.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/resBLAST.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/misc.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/species.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/blastn.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/kaptive.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/mlstBLAST.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/__main__.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__pycache__/shv_mutations.cpython-313.pyc -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__pycache__ copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/__main__.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/kpneumoniae.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/species_mash_sketches.msh -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ybt_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data creating /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp16.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp7.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp21.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp8.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp6.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp20.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp4.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp22.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp13.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp18.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp9.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp5.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp1.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp19.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp3.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp17.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp14.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp10.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp12.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp2.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp11.embl -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/ICEKp_references/ICEKp15.gff -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ICEKp_references copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/MgrB_and_PmrB.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/CARD_v3.1.13.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/AbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/YbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/QRDR_120.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/rmp_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/rmpA2.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/wzi.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/CbST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/SmST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/RmST_profiles.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/iro_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/Klebsiella_pneumoniae.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/wzi.txt -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/OmpK.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/iuc_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/clb_alleles.fasta -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/data/CARD_AMR_clustered.csv -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data copying /build/reproducible-path/kleborate-2.4.1/.pybuild/cpython3_3.13/build/kleborate/help_formatter.py -> /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/contig_stats.py to contig_stats.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/blastn.py to blastn.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/rmpA.py to rmpA.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/truncation.py to truncation.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/version.py to version.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/mlstBLAST.py to mlstBLAST.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/kaptive.py to kaptive.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/shv_mutations.py to shv_mutations.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/species.py to species.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/resBLAST.py to resBLAST.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/misc.py to misc.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/__main__.py to __main__.cpython-313.pyc byte-compiling /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/help_formatter.py to help_formatter.cpython-313.pyc running install_egg_info Copying Kleborate.egg-info to /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/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 /build/reproducible-path/kleborate-2.4.1/setup.py:73: DeprecationWarning: Use shutil.which instead of find_executable if not distutils.spawn.find_executable('makeblastdb'): Building BLAST databases with makeblastdb: makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/CARD_v3.1.13.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/clb_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/rmpA2.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/iro_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/iuc_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/rmp_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/wzi.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/ybt_alleles.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/MgrB_and_PmrB.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/dist-packages/kleborate/data/OmpK.fasta makeblastdb -dbtype nucl -in /build/reproducible-path/kleborate-2.4.1/debian/tmp/usr/lib/python3.13/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 dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/kleborate-2.4.1' # 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 dh_fixperms -O--buildsystem=pybuild debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/reproducible-path/kleborate-2.4.1' 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_2.4.1-4_all.deb'. dpkg-deb: building package 'kleborate' in '../kleborate_2.4.1-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../kleborate_2.4.1-4_amd64.buildinfo dpkg-genchanges --build=binary -O../kleborate_2.4.1-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2409666 and its subdirectories I: Current time: Mon Feb 17 00:49:15 -12 2025 I: pbuilder-time-stamp: 1739796555