https://launchpad.net/ubuntu/+source/kleborate/2.3.1-1/+build/25560810 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-076 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:02 UTC 2023 aarch64 Buildd toolchain package versions: launchpad-buildd_229~619~ubuntu20.04.1 python3-lpbuildd_229~619~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.8 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 6 Feb 17:32:57 ntpdate[1836]: adjust time server 10.211.37.1 offset 0.012623 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25560810 --image-type chroot /home/buildd/filecache-default/f16216f5497f1f0724e8a3a0f3bd4b5063e2189b Creating target for build PACKAGEBUILD-25560810 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25560810 Starting target for build PACKAGEBUILD-25560810 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25560810 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-25560810 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25560810 Updating target for build PACKAGEBUILD-25560810 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main arm64 Packages [1366 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe arm64 Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5913 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 Packages [163 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [63.4 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe arm64 Packages [564 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [240 kB] Fetched 23.7 MB in 8s (2995 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: adduser advancecomp apt bash binutils binutils-aarch64-linux-gnu binutils-common coreutils cpp-12 debconf diffutils dpkg dpkg-dev fakeroot g++-12 gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep libacl1 libapt-pkg6.0 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libfakeroot libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgprofng0 libhwasan0 libitm1 liblsan0 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libreadline8 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libzstd1 linux-libc-dev lsb-base ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata xz-utils zlib1g 92 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 95.5 MB of archives. After this operation, 8348 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar/main arm64 bash arm64 5.2.15-2ubuntu1 [780 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main arm64 coreutils arm64 9.1-1ubuntu2 [1347 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 diffutils arm64 1:3.8-4 [172 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libc-bin arm64 2.37-0ubuntu1 [582 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main arm64 libcrypt-dev arm64 1:4.4.33-2 [118 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libc6-dev arm64 2.37-0ubuntu1 [1544 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libc-dev-bin arm64 2.37-0ubuntu1 [19.4 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main arm64 libcrypt1 arm64 1:4.4.33-2 [83.8 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 linux-libc-dev arm64 6.1.0-14.14 [1412 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main arm64 libcc1-0 arm64 12.2.0-14ubuntu1 [44.2 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main arm64 libgprofng0 arm64 2.40-2ubuntu1 [793 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main arm64 libctf0 arm64 2.40-2ubuntu1 [93.2 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main arm64 libctf-nobfd0 arm64 2.40-2ubuntu1 [97.3 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main arm64 binutils-aarch64-linux-gnu arm64 2.40-2ubuntu1 [3144 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main arm64 libbinutils arm64 2.40-2ubuntu1 [776 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main arm64 binutils-common arm64 2.40-2ubuntu1 [236 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main arm64 binutils arm64 2.40-2ubuntu1 [3176 B] Get:18 http://ftpmaster.internal/ubuntu lunar/main arm64 gcc-12-base arm64 12.2.0-14ubuntu1 [19.3 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main arm64 libgcc-s1 arm64 12.2.0-14ubuntu1 [39.6 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main arm64 libgomp1 arm64 12.2.0-14ubuntu1 [122 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main arm64 libitm1 arm64 12.2.0-14ubuntu1 [27.9 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main arm64 libatomic1 arm64 12.2.0-14ubuntu1 [10.7 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main arm64 libasan8 arm64 12.2.0-14ubuntu1 [2384 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main arm64 liblsan0 arm64 12.2.0-14ubuntu1 [1028 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main arm64 libtsan2 arm64 12.2.0-14ubuntu1 [2514 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main arm64 libubsan1 arm64 12.2.0-14ubuntu1 [957 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main arm64 libhwasan0 arm64 12.2.0-14ubuntu1 [1109 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main arm64 g++-12 arm64 12.2.0-14ubuntu1 [10.9 MB] Get:29 http://ftpmaster.internal/ubuntu lunar/main arm64 libstdc++-12-dev arm64 12.2.0-14ubuntu1 [2155 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main arm64 libgcc-12-dev arm64 12.2.0-14ubuntu1 [1157 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main arm64 gcc-12 arm64 12.2.0-14ubuntu1 [19.1 MB] Get:32 http://ftpmaster.internal/ubuntu lunar/main arm64 cpp-12 arm64 12.2.0-14ubuntu1 [9581 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main arm64 libstdc++6 arm64 12.2.0-14ubuntu1 [647 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main arm64 zlib1g arm64 1:1.2.13.dfsg-1ubuntu4 [59.3 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main arm64 libmpfr6 arm64 4.2.0-1 [256 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main arm64 libzstd1 arm64 1.5.2+dfsg2-3 [255 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libc6 arm64 2.37-0ubuntu1 [2705 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 liblzma5 arm64 5.4.1-0.1 [122 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main arm64 libgcrypt20 arm64 1.10.1-3ubuntu1 [465 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main arm64 libacl1 arm64 2.3.1-3 [16.3 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main arm64 libaudit-common all 1:3.0.7-1.1 [5108 B] Get:42 http://ftpmaster.internal/ubuntu lunar/main arm64 libaudit1 arm64 1:3.0.7-1.1 [45.5 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libcap2 arm64 1:2.66-3ubuntu1 [27.9 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main arm64 libpcre2-8-0 arm64 10.42-1 [210 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libselinux1 arm64 3.4-1build3 [77.3 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main arm64 libperl5.36 arm64 5.36.0-7 [4674 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main arm64 perl arm64 5.36.0-7 [235 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main arm64 perl-base arm64 5.36.0-7 [1726 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main arm64 perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main arm64 libdb5.3 arm64 5.3.28+dfsg2-1 [732 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main arm64 debconf all 1.5.82 [125 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main arm64 libssl3 arm64 3.0.7-1ubuntu1 [1756 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main arm64 systemd-sysv arm64 252.4-1ubuntu1 [11.4 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main arm64 systemd arm64 252.4-1ubuntu1 [2904 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main arm64 libsystemd-shared arm64 252.4-1ubuntu1 [1687 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main arm64 libp11-kit0 arm64 0.24.1-2ubuntu1 [226 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main arm64 libsystemd0 arm64 252.4-1ubuntu1 [321 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main arm64 libudev1 arm64 252.4-1ubuntu1 [87.5 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main arm64 libapt-pkg6.0 arm64 2.5.5 [858 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main arm64 dpkg arm64 1.21.19ubuntu3 [1334 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main arm64 grep arm64 3.8-5 [156 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main arm64 ncurses-bin arm64 6.4-2 [183 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main arm64 sed arm64 4.9-1 [191 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main arm64 ncurses-base all 6.4-2 [21.3 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main arm64 sysvinit-utils arm64 3.05-7ubuntu2 [26.8 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 lsb-base all 11.6 [4606 B] Get:67 http://ftpmaster.internal/ubuntu lunar/main arm64 adduser all 3.129ubuntu1 [59.0 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main arm64 gpgv arm64 2.2.40-1ubuntu2 [133 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main arm64 libgnutls30 arm64 3.7.8-4ubuntu1 [936 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main arm64 apt arm64 2.5.5 [1343 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main arm64 libattr1 arm64 1:2.5.1-4 [12.2 kB] Get:72 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libsemanage-common all 3.4-1build3 [9808 B] Get:73 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libsemanage2 arm64 3.4-1build3 [89.4 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main arm64 libncurses6 arm64 6.4-2 [108 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main arm64 libncursesw6 arm64 6.4-2 [141 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main arm64 libtinfo6 arm64 6.4-2 [98.4 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main arm64 sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main arm64 readline-common all 8.2-1.3 [55.7 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main arm64 libreadline8 arm64 8.2-1.3 [150 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main arm64 libsqlite3-0 arm64 3.40.1-1 [661 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main arm64 openssl arm64 3.0.7-1ubuntu1 [1159 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main arm64 tzdata all 2022g-2ubuntu1 [397 kB] Get:83 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 xz-utils arm64 5.4.1-0.1 [268 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main arm64 advancecomp arm64 2.5-1 [171 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main arm64 dpkg-dev all 1.21.19ubuntu3 [1067 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main arm64 libdpkg-perl all 1.21.19ubuntu3 [247 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main arm64 libfakeroot arm64 1.30.1-1.1ubuntu1 [30.8 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main arm64 fakeroot arm64 1.30.1-1.1ubuntu1 [59.7 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/main arm64 gpg arm64 2.2.40-1ubuntu2 [509 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main arm64 gpgconf arm64 2.2.40-1ubuntu2 [92.5 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main arm64 gpg-agent arm64 2.2.40-1ubuntu2 [211 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main arm64 pkgbinarymangler all 151 [16.0 kB] debconf: delaying package configuration, 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Setting up libstdc++-12-dev:arm64 (12.2.0-14ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.40-2ubuntu1) ... Setting up binutils (2.40-2ubuntu1) ... Setting up dpkg-dev (1.21.19ubuntu3) ... Setting up gcc-12 (12.2.0-14ubuntu1) ... Setting up g++-12 (12.2.0-14ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-25560810 arm64 lunar-proposed -c chroot:build-PACKAGEBUILD-25560810 --arch=arm64 --dist=lunar-proposed --nolog kleborate_2.3.1-1.dsc Initiating build PACKAGEBUILD-25560810 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:02 UTC 2023 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-076.buildd +==============================================================================+ | kleborate 2.3.1-1 (arm64) Mon, 06 Feb 2023 17:34:09 +0000 | +==============================================================================+ Package: kleborate Version: 2.3.1-1 Source Version: 2.3.1-1 Distribution: lunar-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25560810/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/kleborate-iR4l5k/resolver-8fVk3I' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- kleborate_2.3.1-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/kleborate-iR4l5k/kleborate-2.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/kleborate-iR4l5k' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, ncbi-blast+, mash, kaptive, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, ncbi-blast+, mash, kaptive, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [419 B] Get:5 copy:/<>/apt_archive ./ Packages [494 B] Fetched 1870 B in 0s (57.0 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fonts-urw-base35 gettext gettext-base groff-base intltool-debian kaptive libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcapnp-0.9.2 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmpdec3 libmurmurhash2 libopenjp2-7 libpcre3 libpipeline1 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.11-minimal libpython3.11-stdlib libraqm0 libsub-override-perl libtiff6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap man-db mash media-types mime-support ncbi-blast+ ncbi-data po-debconf python3 python3-biopython python3-distutils python3-lib2to3 python3-minimal python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3-setuptools python3.10 python3.10-minimal python3.11 python3.11-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-tomli python3-installer fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev groff kaptive-data kaptive-example low-memory-monitor gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise gfortran python3-dev python3-pytest python-pil-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-setuptools-doc python3.10-venv python3.10-doc binfmt-support python3.11-venv python3.11-doc sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl python-biopython-doc python3-olefile The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fonts-urw-base35 gettext gettext-base groff-base intltool-debian kaptive libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcapnp-0.9.2 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmpdec3 libmurmurhash2 libopenjp2-7 libpcre3 libpipeline1 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.11-minimal libpython3.11-stdlib libraqm0 libsub-override-perl libtiff6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap man-db mash media-types mime-support ncbi-blast+ ncbi-data po-debconf python3 python3-biopython python3-distutils python3-lib2to3 python3-minimal python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3-setuptools python3.10 python3.10-minimal python3.11 python3.11-minimal sbuild-build-depends-main-dummy sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 76.7 MB of archives. After this operation, 298 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [718 B] Get:2 http://ftpmaster.internal/ubuntu lunar/main arm64 libpython3.11-minimal arm64 3.11.1-2 [827 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main arm64 libexpat1 arm64 2.5.0-1 [71.2 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main arm64 python3.11-minimal arm64 3.11.1-2 [2158 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 python3-minimal arm64 3.11.1-3 [24.6 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 media-types all 9.0.0 [26.0 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main arm64 mailcap all 3.70+nmu1ubuntu1 [23.8 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main arm64 mime-support all 3.66 [3696 B] Get:9 http://ftpmaster.internal/ubuntu lunar/main arm64 libmpdec3 arm64 2.5.1-2build2 [89.0 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main arm64 libpython3.11-stdlib arm64 3.11.1-2 [1790 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main arm64 python3.11 arm64 3.11.1-2 [561 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libpython3-stdlib arm64 3.11.1-3 [7208 B] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 python3 arm64 3.11.1-3 [22.9 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main arm64 libpython3.10-minimal arm64 3.10.9-1 [798 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main arm64 python3.10-minimal arm64 3.10.9-1 [1992 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main arm64 sgml-base all 1.31 [11.4 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main arm64 libbsd0 arm64 0.11.7-2 [43.0 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main arm64 libelf1 arm64 0.188-2.1 [53.4 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main arm64 libfribidi0 arm64 1.0.8-2.1ubuntu1 [26.3 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main arm64 libglib2.0-0 arm64 2.74.5-1 [1435 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main arm64 libpython3.10-stdlib arm64 3.10.9-1 [1761 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libicu72 arm64 72.1-3ubuntu1 [10.7 MB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libxml2 arm64 2.9.14+dfsg-1.1build1 [722 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 python3-pkg-resources all 66.1.1-1 [225 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main arm64 python3.10 arm64 3.10.9-1 [503 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main arm64 bsdextrautils arm64 2.38.1-4ubuntu1 [69.1 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main arm64 libmagic-mgc arm64 1:5.44-3 [293 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main arm64 libmagic1 arm64 1:5.44-3 [84.3 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main arm64 file arm64 1:5.44-3 [21.8 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main arm64 gettext-base arm64 0.21-11 [35.4 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main arm64 libuchardet0 arm64 0.0.7-1build2 [77.3 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main arm64 groff-base arm64 1.22.4-9 [899 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main arm64 liblmdb0 arm64 0.9.24-1build2 [49.0 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main arm64 libpipeline1 arm64 1.5.7-1 [23.3 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main arm64 libxau6 arm64 1:1.0.9-1build5 [7624 B] Get:36 http://ftpmaster.internal/ubuntu lunar/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu5 [10.8 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main arm64 libxcb1 arm64 1.15-1 [47.6 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main arm64 man-db arm64 2.11.2-1 [1212 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 m4 arm64 1.4.19-3 [239 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main arm64 autoconf all 2.71-3 [339 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main arm64 autotools-dev all 20220109.1 [44.9 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main arm64 automake all 1:1.16.5-1.3 [558 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main arm64 autopoint all 0.21-11 [420 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main arm64 libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main arm64 libtool all 2.4.7-5 [166 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main arm64 dh-autoreconf all 20 [16.1 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main arm64 libsub-override-perl all 0.09-4 [8706 B] Get:49 http://ftpmaster.internal/ubuntu lunar/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:51 http://ftpmaster.internal/ubuntu lunar/main arm64 libdw1 arm64 0.188-2.1 [247 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main arm64 debugedit arm64 1:5.0-5 [45.9 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main arm64 dwz arm64 0.15-1 [110 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main arm64 gettext arm64 0.21-11 [842 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main arm64 debhelper all 13.11.4ubuntu3 [925 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main arm64 python3-lib2to3 all 3.10.8-1 [77.5 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main arm64 python3-distutils all 3.10.8-1 [139 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/universe arm64 dh-python all 5.20230130 [101 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main arm64 libfontenc1 arm64 1:1.1.4-1build3 [14.1 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main arm64 libbrotli1 arm64 1.0.9-2build7 [311 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main arm64 libfreetype6 arm64 2.12.1+dfsg-4 [382 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main arm64 fonts-urw-base35 all 20200910-7 [11.0 MB] Get:68 http://ftpmaster.internal/ubuntu lunar/main arm64 libblas3 arm64 3.11.0-2 [141 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main arm64 libgfortran5 arm64 12.2.0-14ubuntu1 [417 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main arm64 liblapack3 arm64 3.11.0-2 [2136 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main arm64 python3-numpy arm64 1:1.24.1-2 [6174 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main arm64 python3-renderpm arm64 3.6.12-1 [65.2 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main arm64 python3-reportlab-accel arm64 3.6.12-1 [23.6 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main arm64 libimagequant0 arm64 2.17.0-1 [34.4 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main arm64 libjpeg-turbo8 arm64 2.1.2-0ubuntu1 [129 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main arm64 libjpeg8 arm64 8c-2ubuntu10 [2264 B] Get:77 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 liblcms2-2 arm64 2.14-1build1 [159 kB] Get:78 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libopenjp2-7 arm64 2.5.0-1build1 [170 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main arm64 libgraphite2-3 arm64 1.3.14-1build2 [68.9 kB] Get:80 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3build1 [409 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main arm64 libraqm0 arm64 0.7.0-4.1 [11.1 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main arm64 libdeflate0 arm64 1.14-1 [59.7 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main arm64 libjbig0 arm64 2.1-6ubuntu1 [28.8 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main arm64 liblerc4 arm64 4.0.0+ds-2ubuntu2 [150 kB] Get:85 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libwebp7 arm64 1.2.4-0.1build1 [196 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main arm64 libtiff6 arm64 4.5.0-4ubuntu1 [184 kB] Get:87 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libwebpdemux2 arm64 1.2.4-0.1build1 [9946 B] Get:88 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libwebpmux3 arm64 1.2.4-0.1build1 [21.3 kB] Get:89 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 python3-pil arm64 9.4.0-1.1build1 [420 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main arm64 python3-reportlab all 3.6.12-1 [564 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main arm64 xml-core all 0.18+nmu1 [21.6 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] Get:93 http://ftpmaster.internal/ubuntu lunar/universe arm64 python3-biopython arm64 1.80+dfsg-4 [1636 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/universe arm64 libmbedcrypto7 arm64 2.28.2-1 [203 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/universe arm64 libmbedx509-1 arm64 2.28.2-1 [46.4 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/universe arm64 libmbedtls14 arm64 2.28.2-1 [80.4 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/main arm64 libpcre3 arm64 2:8.39-15 [233 kB] Get:99 http://ftpmaster.internal/ubuntu lunar/universe arm64 ncbi-blast+ arm64 2.12.0+ds-3build1 [11.7 MB] Get:100 http://ftpmaster.internal/ubuntu lunar/universe arm64 kaptive all 2.0.4-1 [24.3 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/universe arm64 libcapnp-0.9.2 arm64 0.9.2-2 [1173 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-3 [72.4 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/universe arm64 libgsl27 arm64 2.7.1+dfsg-3 [919 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/universe arm64 libmurmurhash2 arm64 1.5-3 [6050 B] Get:105 http://ftpmaster.internal/ubuntu lunar/universe arm64 mash arm64 2.3+dfsg-3build1 [147 kB] Get:106 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 python3-setuptools all 66.1.1-1 [453 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 76.7 MB in 20s (3817 kB/s) Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... 15169 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.1-2_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.1-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.1-2_arm64.deb ... Unpacking python3.11-minimal (3.11.1-2) ... Setting up libpython3.11-minimal:arm64 (3.11.1-2) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 15483 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.1-3_arm64.deb ... Unpacking python3-minimal (3.11.1-3) ... Selecting previously unselected package media-types. 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Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:arm64 (0.188-2.1) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-11) ... Setting up mime-support (3.66) ... Setting up libmbedx509-1:arm64 (2.28.2-1) ... Setting up libmbedtls14:arm64 (2.28.2-1) ... Setting up libtool (2.4.7-5) ... Setting up libwebpdemux2:arm64 (1.2.4-0.1build1) ... Setting up libpython3.11-stdlib:arm64 (3.11.1-2) ... Setting up xfonts-utils (1:7.7+6build2) ... Setting up python3.10-minimal (3.10.9-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libpython3.10-stdlib:arm64 (3.10.9-1) ... Setting up dh-autoreconf (20) ... Setting up libraqm0:arm64 (0.7.0-4.1) ... Setting up mash (2.3+dfsg-3build1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-9) ... Setting up libtiff6:arm64 (4.5.0-4ubuntu1) ... Setting up xml-core (0.18+nmu1) ... Setting up debugedit (1:5.0-5) ... Setting up libpython3-stdlib:arm64 (3.11.1-3) ... Setting up python3.11 (3.11.1-2) ... Setting up python3.10 (3.10.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.11.1-3) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up man-db (2.11.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up ncbi-blast+ (2.12.0+ds-3build1) ... Setting up python3-pil:arm64 (9.4.0-1.1build1) ... Setting up python3-reportlab-accel:arm64 (3.6.12-1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-lib2to3 (3.10.8-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.10.8-1) ... Setting up dh-python (5.20230130) ... Setting up python3-renderpm:arm64 (3.6.12-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up python3-numpy (1:1.24.1-2) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... Processing triggers for systemd (252.4-1ubuntu1) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4) ... Setting up kaptive (2.0.4-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:02 UTC 2023 arm64 (aarch64) Toolchain package versions: binutils_2.40-2ubuntu1 dpkg-dev_1.21.19ubuntu3 g++-12_12.2.0-14ubuntu1 gcc-12_12.2.0-14ubuntu1 libc6-dev_2.37-0ubuntu1 libstdc++-12-dev_12.2.0-14ubuntu1 libstdc++6_12.2.0-14ubuntu1 linux-libc-dev_6.1.0-14.14 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.5.5 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-11 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40-2ubuntu1 binutils-aarch64-linux-gnu_2.40-2ubuntu1 binutils-common_2.40-2ubuntu1 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-14ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_5.20230130 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.19ubuntu3 dpkg-dev_1.21.19ubuntu3 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1ubuntu1 fakeroot_1.30.1-1.1ubuntu1 file_1:5.44-3 findutils_4.9.0-3ubuntu1 fonts-urw-base35_20200910-7 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-14ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-14ubuntu1 gcc-12-base_12.2.0-14ubuntu1 gettext_0.21-11 gettext-base_0.21-11 gpg_2.2.40-1ubuntu2 gpg-agent_2.2.40-1ubuntu2 gpgconf_2.2.40-1ubuntu2 gpgv_2.2.40-1ubuntu2 grep_3.8-5 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 hostname_3.23ubuntu2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 kaptive_2.0.4-1 libacl1_2.3.1-3 libapparmor1_3.0.8-1ubuntu1 libapt-pkg6.0_2.5.5 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-14ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-14ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.40-2ubuntu1 libblas3_3.11.0-2 libblkid1_2.38.1-4ubuntu1 libbrotli1_1.0.9-2build7 libbsd0_0.11.7-2 libbz2-1.0_1.0.8-5build1 libc-bin_2.37-0ubuntu1 libc-dev-bin_2.37-0ubuntu1 libc6_2.37-0ubuntu1 libc6-dev_2.37-0ubuntu1 libcap-ng0_0.8.3-1build1 libcap2_1:2.66-3ubuntu1 libcapnp-0.9.2_0.9.2-2 libcc1-0_12.2.0-14ubuntu1 libcom-err2_1.46.6~rc1-1ubuntu1 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libcryptsetup12_2:2.5.0-6ubuntu3 libctf-nobfd0_2.40-2ubuntu1 libctf0_2.40-2ubuntu1 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.264ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate0_1.14-1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.19ubuntu3 libdw1_0.188-2.1 libelf1_0.188-2.1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1ubuntu1 libfakeroot_1.30.1-1.1ubuntu1 libfdisk1_2.38.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libfontenc1_1:1.1.4-1build3 libfreetype6_2.12.1+dfsg-4 libfribidi0_1.0.8-2.1ubuntu1 libgcc-12-dev_12.2.0-14ubuntu1 libgcc-s1_12.2.0-14ubuntu1 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-14ubuntu1 libglib2.0-0_2.74.5-1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.8-4ubuntu1 libgomp1_12.2.0-14ubuntu1 libgpg-error0_1.46-1 libgprofng0_2.40-2ubuntu1 libgraphite2-3_1.3.14-1build2 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.20.1-1build1 libharfbuzz0b_6.0.0+dfsg-3build1 libhogweed6_3.8.1-2 libhwasan0_12.2.0-14ubuntu1 libicu72_72.1-3ubuntu1 libidn2-0_2.3.3-1build1 libimagequant0_2.17.0-1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libitm1_12.2.0-14ubuntu1 libjansson4_2.14-2 libjbig0_2.1-6ubuntu1 libjpeg-turbo8_2.1.2-0ubuntu1 libjpeg8_8c-2ubuntu10 libjson-c5_0.16-2 libk5crypto3_1.20.1-1build1 libkeyutils1_1.6.3-2 libkmod2_30+20220905-1ubuntu1 libkrb5-3_1.20.1-1build1 libkrb5support0_1.20.1-1build1 liblapack3_3.11.0-2 liblcms2-2_2.14-1build1 liblerc4_4.0.0+ds-2ubuntu2 liblmdb0_0.9.24-1build2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_12.2.0-14ubuntu1 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.1 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmbedcrypto7_2.28.2-1 libmbedtls14_2.28.2-1 libmbedx509-1_2.28.2-1 libmd0_1.0.4-2 libmount1_2.38.1-4ubuntu1 libmpc3_1.3.1-1 libmpdec3_2.5.1-2build2 libmpfr6_4.2.0-1 libmurmurhash2_1.5-3 libncurses6_6.4-2 libncursesw6_6.4-2 libnettle8_3.8.1-2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libopenjp2-7_2.5.0-1build1 libp11-kit0_0.24.1-2ubuntu1 libpam-modules_1.5.2-5ubuntu1 libpam-modules-bin_1.5.2-5ubuntu1 libpam-runtime_1.5.2-5ubuntu1 libpam0g_1.5.2-5ubuntu1 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpng16-16_1.6.39-2 libprocps8_2:3.3.17-7ubuntu1 libpython3-stdlib_3.11.1-3 libpython3.10-minimal_3.10.9-1 libpython3.10-stdlib_3.10.9-1 libpython3.11-minimal_3.11.1-2 libpython3.11-stdlib_3.11.1-2 libraqm0_0.7.0-4.1 libreadline8_8.2-1.3 libseccomp2_2.5.4-1ubuntu2 libselinux1_3.4-1build3 libsemanage-common_3.4-1build3 libsemanage2_3.4-1build3 libsepol2_3.4-2 libsmartcols1_2.38.1-4ubuntu1 libsqlite3-0_3.40.1-1 libss2_1.46.6~rc1-1ubuntu1 libssl3_3.0.7-1ubuntu1 libstdc++-12-dev_12.2.0-14ubuntu1 libstdc++6_12.2.0-14ubuntu1 libsub-override-perl_0.09-4 libsystemd-shared_252.4-1ubuntu1 libsystemd0_252.4-1ubuntu1 libtasn1-6_4.19.0-2 libtiff6_4.5.0-4ubuntu1 libtinfo6_6.4-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan2_12.2.0-14ubuntu1 libubsan1_12.2.0-14ubuntu1 libuchardet0_0.0.7-1build2 libudev1_252.4-1ubuntu1 libunistring2_1.0-2 libuuid1_2.38.1-4ubuntu1 libwebp7_1.2.4-0.1build1 libwebpdemux2_1.2.4-0.1build1 libwebpmux3_1.2.4-0.1build1 libxau6_1:1.0.9-1build5 libxcb1_1.15-1 libxdmcp6_1:1.1.3-0ubuntu5 libxml2_2.9.14+dfsg-1.1build1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg2-3 linux-libc-dev_6.1.0-14.14 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.46.6~rc1-1ubuntu1 lsb-base_11.6 lto-disabled-list_37 m4_1.4.19-3 mailcap_3.70+nmu1ubuntu1 make_4.3-4.1build1 man-db_2.11.2-1 mash_2.3+dfsg-3build1 mawk_1.3.4.20200120-3.1 media-types_9.0.0 mime-support_3.66 mount_2.38.1-4ubuntu1 ncbi-blast+_2.12.0+ds-3build1 ncbi-data_6.1.20170106+dfsg1-10 ncurses-base_6.4-2 ncurses-bin_6.4-2 openssl_3.0.7-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-7 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_151 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-7ubuntu1 python3_3.11.1-3 python3-biopython_1.80+dfsg-4 python3-distutils_3.10.8-1 python3-lib2to3_3.10.8-1 python3-minimal_3.11.1-3 python3-numpy_1:1.24.1-2 python3-pil_9.4.0-1.1build1 python3-pkg-resources_66.1.1-1 python3-renderpm_3.6.12-1 python3-reportlab_3.6.12-1 python3-reportlab-accel_3.6.12-1 python3-setuptools_66.1.1-1 python3.10_3.10.9-1 python3.10-minimal_3.10.9-1 python3.11_3.11.1-2 python3.11-minimal_3.11.1-2 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sgml-base_1.31 systemd_252.4-1ubuntu1 systemd-sysv_252.4-1ubuntu1 sysvinit-utils_3.05-7ubuntu2 tar_1.34+dfsg-1.1 tzdata_2022g-2ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_33ubuntu1 util-linux_2.38.1-4ubuntu1 util-linux-extra_2.38.1-4ubuntu1 w3c-sgml-lib_1.3-3 x11-common_1:7.7+23ubuntu2 xfonts-encodings_1:1.0.5-0ubuntu2 xfonts-utils_1:7.7+6build2 xml-core_0.18+nmu1 xz-utils_5.4.1-0.1 zlib1g_1:1.2.13.dfsg-1ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kleborate Binary: kleborate, kleborate-examples Architecture: any all Version: 2.3.1-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/katholt/Kleborate Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/kleborate Vcs-Git: https://salsa.debian.org/med-team/kleborate.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, ncbi-blast+ , mash , kaptive Package-List: kleborate deb science optional arch=any kleborate-examples deb science optional arch=all Checksums-Sha1: c17b29c844df2a03880d376d0ef2aca16715af57 91335255 kleborate_2.3.1.orig.tar.gz 77ee901ea3fa69bd41b0ec0bb0bb707bde524881 5996008 kleborate_2.3.1-1.debian.tar.xz Checksums-Sha256: 81bd01f9c7db7ca1d6763571eddea616e4970d2420dab6dfa8a9b47aebb8a870 91335255 kleborate_2.3.1.orig.tar.gz 3f530ce060ffe9d8f5fa160c10a6bf274b3bc64697a28f6424b5d5548ec51d4f 5996008 kleborate_2.3.1-1.debian.tar.xz Files: 6d39609923dd9932e0221108fb103481 91335255 kleborate_2.3.1.orig.tar.gz 1c1d0d8466ed1b01b66c96ad03e338c2 5996008 kleborate_2.3.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPgpd8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHK/xAAgYmuVcJaRQGR3UeEZPYo8sb2uaJYzvTo jevvMrpvuBWXd13l/9iF3XKtAW+XxvnRl4/+1FKMAxdy1waRVEyKSiTqA23d6rwZ dnTpxtBd2vRkbYqQkrDex63sGQTUJlz4iKXWqrGWUYSASLaHERCBtqdLMQuZnBj6 oO8M5FbszDDFDWPy7AtMaEBHwhlsqhr/PiBBEax3TFsqc4u7lZuMfJ8u7PPelAi2 4cf6foozLZFplsv6ltgXiZdu8tPv60kDAV/h+KO09wZtjrB2uPxpNT3YgLxyHcoz 5gBXrbnReoP8gCiqPuTFEQ1tmU4k72yWB0ZKkkjHdRNvu9zb7KfpUuj1EhOMD8SN ENImpyiXym92xIeAkG93MWmeP9zdZI2kNr4/EC9LFJiGzvhlctpvcfchqlRfg+ZC GP2AZC1hdlZ4H5NTwsGymgYvqBNvJja3HjNGfYbljAYOm29g9JWupbLKfeIuCJoA NcvM7pFR5sdHyTICnZmEIXBMhRIPok3iis1lr1jcUj5/BvZLgNdvZmQsYbJ7jO2p K84ju8YcLeTwpKaYIx/Tjgq9N4JGsbjjlqVwX8PvqIhzrUE/ny+zrcOOYWHo5XUX 0ntZBjCty8gqHz4Cr2xDLtt+pSlbNtUG/B3JnMDtwq8YaVgSQKGRYQdFcMjCajtS Q4+q/9dpbjA= =S2nT -----END PGP SIGNATURE----- gpgv: Signature made Mon Feb 6 07:01:51 2023 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kleborate_2.3.1-1.dsc: no acceptable signature found dpkg-source: info: extracting kleborate in /<> dpkg-source: info: unpacking kleborate_2.3.1.orig.tar.gz dpkg-source: info: unpacking kleborate_2.3.1-1.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 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-25560810 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25560810 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25560810 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package kleborate dpkg-buildpackage: info: source version 2.3.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/contig_stats.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/misc.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__init__.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/shv_mutations.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/version.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/kaptive.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/species.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/blastn.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/mlstBLAST.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/help_formatter.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/resBLAST.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/rmpA.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/truncation.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__main__.py -> /<>/.pybuild/cpython3_3.11/build/kleborate running egg_info creating Kleborate.egg-info writing Kleborate.egg-info/PKG-INFO writing dependency_links to Kleborate.egg-info/dependency_links.txt writing entry points to Kleborate.egg-info/entry_points.txt writing requirements to Kleborate.egg-info/requires.txt writing top-level names to Kleborate.egg-info/top_level.txt writing manifest file 'Kleborate.egg-info/SOURCES.txt' reading manifest file 'Kleborate.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'kleborate/ICEKp_references' warning: no directories found matching 'kaptive/reference_database' warning: no directories found matching 'kaptive/sample_data' adding license file 'LICENSE' writing manifest file 'Kleborate.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'kleborate.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'kleborate.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'kleborate.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'kleborate.data.ICEKp_references' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data.ICEKp_references' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'kleborate.data.ICEKp_references' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'kleborate.data.ICEKp_references' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) creating /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/AbST_profiles.txt -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/CARD_AMR_clustered.csv -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/CARD_v3.1.13.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/CbST_profiles.txt -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/Klebsiella_pneumoniae.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/MgrB_and_PmrB.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/OmpK.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/QRDR_120.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/RmST_profiles.txt -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/SmST_profiles.txt -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/YbST_profiles.txt -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/clb_alleles.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/iro_alleles.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/iuc_alleles.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/kpneumoniae.txt -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/rmpA2.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/rmp_alleles.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/species_mash_sketches.msh -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/wzi.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/wzi.txt -> /<>/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/ybt_alleles.fasta -> /<>/.pybuild/cpython3_3.11/build/kleborate/data creating /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp1.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp10.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp11.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp12.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp13.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp14.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp15.gff -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp16.gff -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp17.gff -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp18.gff -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp19.gff -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp2.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp20.gff -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp21.gff -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp22.gff -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp3.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp4.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp5.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp6.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp7.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp8.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp9.embl -> /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references dh_auto_test -a -O--buildsystem=pybuild I: pybuild base:240: cd /<>/.pybuild/cpython3_3.11/build; python3.11 -m unittest discover -v /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( test_ambiguous_bases_1 (test.test_contig_stats.TestContigStats.test_ambiguous_bases_1) ... ok test_ambiguous_bases_2 (test.test_contig_stats.TestContigStats.test_ambiguous_bases_2) ... ok test_ambiguous_bases_3 (test.test_contig_stats.TestContigStats.test_ambiguous_bases_3) ... ok test_ambiguous_bases_4 (test.test_contig_stats.TestContigStats.test_ambiguous_bases_4) ... ok test_count_1 (test.test_contig_stats.TestContigStats.test_count_1) ... ok test_count_2 (test.test_contig_stats.TestContigStats.test_count_2) ... ok test_longest_1 (test.test_contig_stats.TestContigStats.test_longest_1) ... ok test_longest_2 (test.test_contig_stats.TestContigStats.test_longest_2) ... ok test_n50_1 (test.test_contig_stats.TestContigStats.test_n50_1) ... ok test_n50_2 (test.test_contig_stats.TestContigStats.test_n50_2) ... ok test_qc_warnings_1 (test.test_contig_stats.TestContigStats.test_qc_warnings_1) ... ok test_qc_warnings_2 (test.test_contig_stats.TestContigStats.test_qc_warnings_2) ... ok test_qc_warnings_3 (test.test_contig_stats.TestContigStats.test_qc_warnings_3) ... ok test_qc_warnings_4 (test.test_contig_stats.TestContigStats.test_qc_warnings_4) ... ok test_qc_warnings_5 (test.test_contig_stats.TestContigStats.test_qc_warnings_5) ... ok test_qc_warnings_6 (test.test_contig_stats.TestContigStats.test_qc_warnings_6) ... ok test_qc_warnings_7 (test.test_contig_stats.TestContigStats.test_qc_warnings_7) ... ok test_qc_warnings_8 (test.test_contig_stats.TestContigStats.test_qc_warnings_8) ... ok test_total_size_1 (test.test_contig_stats.TestContigStats.test_total_size_1) ... ok test_total_size_2 (test.test_contig_stats.TestContigStats.test_total_size_2) ... ok test_total_size_3 (test.test_contig_stats.TestContigStats.test_total_size_3) ... ok test_total_size_4 (test.test_contig_stats.TestContigStats.test_total_size_4) ... ok test_iro_exact_1 (test.test_iro.TestIro.test_iro_exact_1) This test is an exact match for SmST1. ... ok test_iro_exact_33 (test.test_iro.TestIro.test_iro_exact_33) This test is an exact match for SmST33. ... ok test_iro_incomplete (test.test_iro.TestIro.test_iro_incomplete) This test is an exact match for only one allele. ... ok test_iro_inexact (test.test_iro.TestIro.test_iro_inexact) This test is an inexact match for SmST33. There are single base changes in iroC and in ... ok test_iro_missing_1 (test.test_iro.TestIro.test_iro_missing_1) This test is a match for SmST1, except that it's missing iroN. ... ok test_iro_novel (test.test_iro.TestIro.test_iro_novel) This test is an exact match for alleles, but an unknown combination. ... ok test_iro_random (test.test_iro.TestIro.test_iro_random) This test has just random sequence and should give no iro call. ... ok test_confidence_meets_threshold_01 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_01) ... ok test_confidence_meets_threshold_02 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_02) ... ok test_confidence_meets_threshold_03 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_03) ... ok test_confidence_meets_threshold_04 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_04) ... ok test_confidence_meets_threshold_05 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_05) ... ok test_confidence_meets_threshold_06 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_06) ... ok test_confidence_meets_threshold_07 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_07) ... ok test_confidence_meets_threshold_08 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_08) ... ok test_confidence_meets_threshold_09 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_09) ... ok test_confidence_meets_threshold_10 (test.test_kaptive.TestKaptive.test_confidence_meets_threshold_10) ... ok test_134 (test.test_mlst.TestMlst.test_134) ... ok test_83 (test.test_mlst.TestMlst.test_83) ... ok test_ba779 (test.test_mlst.TestMlst.test_ba779) ... ok test_chromosome_exact (test.test_mlst.TestMlst.test_chromosome_exact) This test is an exact match for ST23. ... ok test_chromosome_inexact (test.test_mlst.TestMlst.test_chromosome_inexact) This test is is one base off from ST23 (single substitution in mdh_1 of G to A). ... ok test_chromosome_random (test.test_mlst.TestMlst.test_chromosome_random) This test has just random sequence and should give no MLST call. ... ok test_kp_subspecies_1 (test.test_mlst.TestMlst.test_kp_subspecies_1) ... ok test_kp_subspecies_2 (test.test_mlst.TestMlst.test_kp_subspecies_2) ... ok test_kp_subspecies_3 (test.test_mlst.TestMlst.test_kp_subspecies_3) ... ok test_kp_subspecies_4 (test.test_mlst.TestMlst.test_kp_subspecies_4) ... ok test_kp_subspecies_5 (test.test_mlst.TestMlst.test_kp_subspecies_5) ... ok test_kp_subspecies_6 (test.test_mlst.TestMlst.test_kp_subspecies_6) ... ok test_kp_subspecies_7 (test.test_mlst.TestMlst.test_kp_subspecies_7) ... ok test_ozaenae (test.test_mlst.TestMlst.test_ozaenae) ... ok test_rhinoscleromatis (test.test_mlst.TestMlst.test_rhinoscleromatis) ... ok test_unknown_ST (test.test_mlst.TestMlst.test_unknown_ST) This test has exact matches for alleles but in an unknown ST combination ... ok test_res_01 (test.test_res_aac.TestResAac.test_res_01) ... /usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/__init__.py:519: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' mode='r' encoding='utf-8'> matrix = read(path) ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_res_02 (test.test_res_aac.TestResAac.test_res_02) ... ok test_res_03 (test.test_res_aac.TestResAac.test_res_03) ... ok test_res_04 (test.test_res_aac.TestResAac.test_res_04) This is a tricky one (and the one which first highlighted the problem). The best bit-score ... ok test_res_05 (test.test_res_aac.TestResAac.test_res_05) Same as test_res_04, but with the hit on the other strand. ... ok test_exact_aa_match_1 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_1) Simple case: full protein sequence ending in a stop codon. ... ok test_exact_aa_match_2 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_2) These two seqs have a stop codon in the middle but still match exactly. ... ok test_exact_aa_match_3 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_3) These two seqs have a stop codon in the middle and mismatch after the stop. ... ok test_exact_aa_match_4 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_4) These two seqs have a stop codon in the middle and mismatch after the stop. ... ok test_exact_aa_match_5 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_5) These two seqs are non-multiple-of-three in length and match in their remainder. ... ok test_exact_aa_match_6 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_6) These two seqs are non-multiple-of-three in length and match in their remainder. ... ok test_exact_aa_match_7 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_7) These two seqs are non-multiple-of-three in length and don't match in their remainder. ... ok test_exact_aa_match_8 (test.test_res_alleles.TestResAlleles.test_exact_aa_match_8) The first seq's protein sequence contains the second seq's protein sequence. ... ok test_res_01 (test.test_res_alleles.TestResAlleles.test_res_01) ... ok test_res_02 (test.test_res_alleles.TestResAlleles.test_res_02) ... ok test_res_03 (test.test_res_alleles.TestResAlleles.test_res_03) ... ok test_res_04 (test.test_res_alleles.TestResAlleles.test_res_04) ... ok test_res_05 (test.test_res_alleles.TestResAlleles.test_res_05) ... ok test_res_06 (test.test_res_alleles.TestResAlleles.test_res_06) ... ok test_res_07 (test.test_res_alleles.TestResAlleles.test_res_07) ... ok test_res_08 (test.test_res_alleles.TestResAlleles.test_res_08) ... ok test_res_09 (test.test_res_alleles.TestResAlleles.test_res_09) ... ok test_res_10 (test.test_res_alleles.TestResAlleles.test_res_10) ... ok test_res_11 (test.test_res_alleles.TestResAlleles.test_res_11) This test has the ABC-1 gene but with a stop codon in the middle. ... ok test_res_12 (test.test_res_alleles.TestResAlleles.test_res_12) This test has the ABC-1 gene but missing the first (start) codon. ... ok test_res_13 (test.test_res_alleles.TestResAlleles.test_res_13) This test has the ABC-1 gene but at only 50% coverage, so it goes to spurious hits. ... ok test_res_14 (test.test_res_alleles.TestResAlleles.test_res_14) I added this test to catch a weird BLAST-related bug where an exact amino acid match for ... ok test_res_15 (test.test_res_alleles.TestResAlleles.test_res_15) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_res_16 (test.test_res_alleles.TestResAlleles.test_res_16) I added this test to catch a weird BLAST-related bug where an exact amino acid match for ... ok test_res_17 (test.test_res_alleles.TestResAlleles.test_res_17) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_res_18 (test.test_res_alleles.TestResAlleles.test_res_18) This is the uncomplicated case for a OKP-B-6^ result (later tests cover more challenging ... ok test_res_19 (test.test_res_alleles.TestResAlleles.test_res_19) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_res_20 (test.test_res_alleles.TestResAlleles.test_res_20) I added this test to catch a bug where there is an exact amino acid match but inexact ... ok test_res_21 (test.test_res_alleles.TestResAlleles.test_res_21) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_res_22 (test.test_res_alleles.TestResAlleles.test_res_22) I added this test to catch a bug where there is an exact amino acid match but inexact ... ok test_res_23 (test.test_res_alleles.TestResAlleles.test_res_23) Same as the previous test, but with the nucleotide sequence reverse-complemented. ... ok test_both_genes_intact (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_both_genes_intact) ... ok test_mgrb_missing (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_mgrb_missing) ... ok test_mgrb_missing_non_kp_complex (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_mgrb_missing_non_kp_complex) Setting the Kp complex variable to False should turn off the MgrB/PmrB tests. ... ok test_pmrb_early_stop (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_pmrb_early_stop) This tests an early stop mutation (without a frameshift) in pmrB. ... ok test_pmrb_early_stop_SRR2098701 (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_pmrb_early_stop_SRR2098701) ... ok test_pmrb_frameshift (test.test_res_mgrb_pmrb.TestResMgrBPmrB.test_pmrb_frameshift) A frameshift in pmrB should cause an early stop and lead to a colisitin resistance call. ... ok test_both_genes_intact (test.test_res_omp.TestResOmp.test_both_genes_intact) ... ok test_ompk35_early_stop (test.test_res_omp.TestResOmp.test_ompk35_early_stop) This tests an early stop mutation (without a frameshift) in OmpK35. ... ok test_ompk35_frameshift (test.test_res_omp.TestResOmp.test_ompk35_frameshift) A frameshift in OmpK35 should cause an early stop and lead to a carbapenem resistance call. ... ok test_ompk36_missing (test.test_res_omp.TestResOmp.test_ompk36_missing) ... ok test_ompk36gd (test.test_res_omp.TestResOmp.test_ompk36gd) ... ok test_ompk36td (test.test_res_omp.TestResOmp.test_ompk36td) ... ok test_ompk36td_non_kp_complex (test.test_res_omp.TestResOmp.test_ompk36td_non_kp_complex) Setting the Kp complex variable to False should turn off the OmpK tests. ... ok test_gyra (test.test_res_qrdr.TestResGyrAParC.test_gyra) ... ok test_gyra_and_parc (test.test_res_qrdr.TestResGyrAParC.test_gyra_and_parc) ... ok test_gyra_and_parc_non_kp_complex (test.test_res_qrdr.TestResGyrAParC.test_gyra_and_parc_non_kp_complex) Setting the Kp complex variable to False should turn off the QRDR tests. ... ok test_no_mutations (test.test_res_qrdr.TestResGyrAParC.test_no_mutations) ... ok test_parc (test.test_res_qrdr.TestResGyrAParC.test_parc) ... ok test_tem (test.test_res_tem.TestResTem.test_tem) ... ok test_rmp_19 (test.test_rmp.TestRmp.test_rmp_19) This test is an exact match for RmST19, an ST without any truncated alleles. ... ok test_rmp_21 (test.test_rmp.TestRmp.test_rmp_21) This test is an exact match for RmST21, an ST with a truncated allele. ... ok test_rmp_missing_1 (test.test_rmp.TestRmp.test_rmp_missing_1) This test is a match for RmST1, except that it's missing rmpC. ... ok test_rmp_novel (test.test_rmp.TestRmp.test_rmp_novel) This test is an exact match for alleles, but an unknown combination. ... ok test_rmp_random (test.test_rmp.TestRmp.test_rmp_random) This test has just random sequence and should give no rmp call. ... ok test_rmpa2_exact (test.test_rmp.TestRmp.test_rmpa2_exact) This test has an exact match for rmpA2_1. ... ok test_rmpa2_exact_truncated (test.test_rmp.TestRmp.test_rmpa2_exact_truncated) This test has an exact match for rmpA2_7. ... ok test_rmpa2_inexact (test.test_rmp.TestRmp.test_rmpa2_inexact) This test has an inexact match for rmpA2_1. ... ok test_rmpa2_random (test.test_rmp.TestRmp.test_rmpa2_random) This test has just random sequence and should give no rmpA2 call. ... ok test_bla_class_01 (test.test_shv.TestShvMutations.test_bla_class_01) ... ok test_bla_class_02 (test.test_shv.TestShvMutations.test_bla_class_02) ... ok test_bla_class_03 (test.test_shv.TestShvMutations.test_bla_class_03) ... ok test_bla_class_04 (test.test_shv.TestShvMutations.test_bla_class_04) ... ok test_get_class_changing_mutations_01 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_01) ... ok test_get_class_changing_mutations_02 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_02) ... ok test_get_class_changing_mutations_03 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_03) ... ok test_get_class_changing_mutations_04 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_04) ... ok test_get_class_changing_mutations_05 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_05) ... ok test_get_class_changing_mutations_06 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_06) ... ok test_get_class_changing_mutations_07 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_07) ... ok test_get_class_changing_mutations_08 (test.test_shv.TestShvMutations.test_get_class_changing_mutations_08) ... ok test_shv_01 (test.test_shv.TestShvMutations.test_shv_01) This test has an exact match for SHV-1. ... ok test_shv_02 (test.test_shv.TestShvMutations.test_shv_02) This test has a match for SHV-1 with a mutation at site 238 (G -> Y). This changes the ... ok test_shv_03 (test.test_shv.TestShvMutations.test_shv_03) Same as test 2, but the gene is on the reverse strand. ... ok test_shv_04 (test.test_shv.TestShvMutations.test_shv_04) This test has a match for SHV-1 with a mutation at site 50 (G -> Y). This doesn't change ... 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 inhibition mutation. ... ok test_shv_07 (test.test_shv.TestShvMutations.test_shv_07) This test has SHV-1 with position 238 deleted. Since it's not in the omega loop, this isn't ... ok test_shv_08 (test.test_shv.TestShvMutations.test_shv_08) This test has SHV-1 with a synonymous mutation in the omega loop (so not reported). ... ok test_shv_09 (test.test_shv.TestShvMutations.test_shv_09) This test has SHV-1 with a nonsynonymous mutation in the omega loop (so it is reported). ... 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 130.563s 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 -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /<>/debian/tmp running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( 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:202: SetuptoolsDeprecationWarning: Installing 'kleborate.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'kleborate.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'kleborate.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'kleborate.data.ICEKp_references' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data.ICEKp_references' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'kleborate.data.ICEKp_references' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'kleborate.data.ICEKp_references' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running install_lib creating /<>/debian/tmp/usr creating /<>/debian/tmp/usr/lib creating /<>/debian/tmp/usr/lib/python3.11 creating /<>/debian/tmp/usr/lib/python3.11/dist-packages creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/contig_stats.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/misc.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/__init__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/RmST_profiles.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/CARD_AMR_clustered.csv -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/YbST_profiles.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/rmp_alleles.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/iuc_alleles.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ybt_alleles.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/MgrB_and_PmrB.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/QRDR_120.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/species_mash_sketches.msh -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/kpneumoniae.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/wzi.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/iro_alleles.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/rmpA2.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/CbST_profiles.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp4.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp21.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp7.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp14.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp2.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp1.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp12.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp9.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp13.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp6.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp19.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp3.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp11.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp22.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp20.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp16.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp18.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp8.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp15.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp5.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp17.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp10.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/OmpK.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/AbST_profiles.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/wzi.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/CARD_v3.1.13.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/Klebsiella_pneumoniae.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/SmST_profiles.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/clb_alleles.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/__main__.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/shv_mutations.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/misc.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/resBLAST.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/version.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/rmpA.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/contig_stats.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/mlstBLAST.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/__init__.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/truncation.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/help_formatter.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/kaptive.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/blastn.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/species.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/shv_mutations.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/version.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/kaptive.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/species.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/blastn.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/mlstBLAST.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/help_formatter.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/resBLAST.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/rmpA.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/truncation.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/__main__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/contig_stats.py to contig_stats.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/misc.py to misc.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/shv_mutations.py to shv_mutations.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/version.py to version.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/kaptive.py to kaptive.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/species.py to species.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/blastn.py to blastn.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/mlstBLAST.py to mlstBLAST.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/help_formatter.py to help_formatter.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/resBLAST.py to resBLAST.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/rmpA.py to rmpA.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/truncation.py to truncation.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__main__.py to __main__.cpython-311.pyc running install_egg_info Copying Kleborate.egg-info to /<>/debian/tmp/usr/lib/python3.11/dist-packages/Kleborate-2.2.0.egg-info Skipping SOURCES.txt running install_scripts Installing kleborate script to /<>/debian/tmp/usr/bin Building BLAST databases with makeblastdb: makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/CARD_v3.1.13.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/clb_alleles.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/rmpA2.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/iro_alleles.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/iuc_alleles.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/rmp_alleles.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/wzi.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ybt_alleles.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/MgrB_and_PmrB.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/OmpK.fasta makeblastdb -dbtype nucl -in /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/QRDR_120.fasta  _ __ _ ______ ____ ____ _____ _______ ______ | | / /| | | ____| _ \ / __ \| __ \ /\|__ __| ____| | |/ / | | | |__ | |_) | | | | |__) | / \ | | | |__ | < | | | __| | _ <| | | | _ / / /\ \ | | | __| | |\ \ | |___| |____| |_) | |__| | | \ \/ ____ \| | | |____ |_| \_\|_____|______|____/ \____/|_| \_\/ \_\_| |______|  Kleborate is installed and ready to use! Example commands: kleborate --help kleborate -o results.txt -a *.fasta kleborate --resistance -o results.txt -a *.fasta kleborate --all -o results.txt -a *.fasta debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install # fasta.nin files will be (re)build at package installation time to not contain build path find debian -name "*.fasta.nin" -delete make[1]: Leaving directory '/<>' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian -name "*.msh" -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a -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 -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 151 pkgstriptranslations: processing kleborate (in debian/kleborate); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/kleborate/DEBIAN/control, package kleborate, directory debian/kleborate pkgstripfiles: Truncating usr/share/doc/kleborate/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package kleborate ... pkgstripfiles: No PNG files. dpkg-deb: building package 'kleborate' in '../kleborate_2.3.1-1_arm64.deb'. dpkg-genbuildinfo --build=any -O../kleborate_2.3.1-1_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../kleborate_2.3.1-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-02-06T17:40:18Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kleborate_2.3.1-1_arm64.changes: -------------------------------- Format: 1.8 Date: Mon, 06 Feb 2023 07:37:51 +0100 Source: kleborate Binary: kleborate Built-For-Profiles: noudeb Architecture: arm64 Version: 2.3.1-1 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: kleborate - tool to screen Klebsiella genome assemblies Changes: kleborate (2.3.1-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 9e906f7ca1e9bdbd29b7daac44582dfb24fb7b9b 7797 kleborate_2.3.1-1_arm64.buildinfo 9e7996ea741abc669f4ffcc98b55cc39407e56d1 8745618 kleborate_2.3.1-1_arm64.deb Checksums-Sha256: d2a20de1196734486d417062157609defdef5f09d39923f233ce5dfb6fdc24d7 7797 kleborate_2.3.1-1_arm64.buildinfo d1a5bcb05239477c3328819f9af81e5806135d57783fc800737ffebbc1dcde9e 8745618 kleborate_2.3.1-1_arm64.deb Files: 85ae819204520d2616f91cf8b082fee8 7797 science optional kleborate_2.3.1-1_arm64.buildinfo 1a7098ed8addba5f45d01537f52da1b1 8745618 science optional kleborate_2.3.1-1_arm64.deb /<>/kleborate_2.3.1-1_arm64.changes.new could not be renamed to /<>/kleborate_2.3.1-1_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: kleborate Binary: kleborate Architecture: arm64 Version: 2.3.1-1 Checksums-Md5: 1a7098ed8addba5f45d01537f52da1b1 8745618 kleborate_2.3.1-1_arm64.deb Checksums-Sha1: 9e7996ea741abc669f4ffcc98b55cc39407e56d1 8745618 kleborate_2.3.1-1_arm64.deb Checksums-Sha256: d1a5bcb05239477c3328819f9af81e5806135d57783fc800737ffebbc1dcde9e 8745618 kleborate_2.3.1-1_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Mon, 06 Feb 2023 17:40:17 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-11), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.40-2ubuntu1), binutils-aarch64-linux-gnu (= 2.40-2ubuntu1), binutils-common (= 2.40-2ubuntu1), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-14ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-9ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 5.20230130), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.21.19ubuntu3), dpkg-dev (= 1.21.19ubuntu3), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-3ubuntu1), fonts-urw-base35 (= 20200910-7), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-14ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-14ubuntu1), gcc-12-base (= 12.2.0-14ubuntu1), gettext (= 0.21-11), gettext-base (= 0.21-11), grep (= 3.8-5), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), kaptive (= 2.0.4-1), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 12.2.0-14ubuntu1), libatomic1 (= 12.2.0-14ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.7-1.1), libaudit1 (= 1:3.0.7-1.1), libbinutils (= 2.40-2ubuntu1), libblas3 (= 3.11.0-2), libblkid1 (= 2.38.1-4ubuntu1), libbrotli1 (= 1.0.9-2build7), libbsd0 (= 0.11.7-2), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu1), libc-dev-bin (= 2.37-0ubuntu1), libc6 (= 2.37-0ubuntu1), libc6-dev (= 2.37-0ubuntu1), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.66-3ubuntu1), libcapnp-0.9.2 (= 0.9.2-2), libcc1-0 (= 12.2.0-14ubuntu1), libcom-err2 (= 1.46.6~rc1-1ubuntu1), libcrypt-dev (= 1:4.4.33-2), libcrypt1 (= 1:4.4.33-2), libctf-nobfd0 (= 2.40-2ubuntu1), libctf0 (= 2.40-2ubuntu1), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.264ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdeflate0 (= 1.14-1), libdpkg-perl (= 1.21.19ubuntu3), libdw1 (= 0.188-2.1), libelf1 (= 0.188-2.1), libexpat1 (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontenc1 (= 1:1.1.4-1build3), libfreetype6 (= 2.12.1+dfsg-4), libfribidi0 (= 1.0.8-2.1ubuntu1), libgcc-12-dev (= 12.2.0-14ubuntu1), libgcc-s1 (= 12.2.0-14ubuntu1), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 12.2.0-14ubuntu1), libglib2.0-0 (= 2.74.5-1), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgomp1 (= 12.2.0-14ubuntu1), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.40-2ubuntu1), libgraphite2-3 (= 1.3.14-1build2), libgsl27 (= 2.7.1+dfsg-3), libgslcblas0 (= 2.7.1+dfsg-3), libgssapi-krb5-2 (= 1.20.1-1build1), libharfbuzz0b (= 6.0.0+dfsg-3build1), libhwasan0 (= 12.2.0-14ubuntu1), libicu72 (= 72.1-3ubuntu1), libimagequant0 (= 2.17.0-1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-14ubuntu1), libjansson4 (= 2.14-2), libjbig0 (= 2.1-6ubuntu1), libjpeg-turbo8 (= 2.1.2-0ubuntu1), libjpeg8 (= 8c-2ubuntu10), libk5crypto3 (= 1.20.1-1build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1build1), libkrb5support0 (= 1.20.1-1build1), liblapack3 (= 3.11.0-2), liblcms2-2 (= 2.14-1build1), liblerc4 (= 4.0.0+ds-2ubuntu2), liblmdb0 (= 0.9.24-1build2), liblsan0 (= 12.2.0-14ubuntu1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.1-0.1), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmbedcrypto7 (= 2.28.2-1), libmbedtls14 (= 2.28.2-1), libmbedx509-1 (= 2.28.2-1), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4ubuntu1), libmpc3 (= 1.3.1-1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.2.0-1), libmurmurhash2 (= 1.5-3), libncursesw6 (= 6.4-2), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libopenjp2-7 (= 2.5.0-1build1), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpcre2-8-0 (= 10.42-1), libpcre3 (= 2:8.39-15), libperl5.36 (= 5.36.0-7), libpipeline1 (= 1.5.7-1), libpng16-16 (= 1.6.39-2), libpython3-stdlib (= 3.11.1-3), libpython3.10-minimal (= 3.10.9-1), libpython3.10-stdlib (= 3.10.9-1), libpython3.11-minimal (= 3.11.1-2), libpython3.11-stdlib (= 3.11.1-2), libraqm0 (= 0.7.0-4.1), libreadline8 (= 8.2-1.3), libseccomp2 (= 2.5.4-1ubuntu2), libselinux1 (= 3.4-1build3), libsmartcols1 (= 2.38.1-4ubuntu1), libsqlite3-0 (= 3.40.1-1), libssl3 (= 3.0.7-1ubuntu1), libstdc++-12-dev (= 12.2.0-14ubuntu1), libstdc++6 (= 12.2.0-14ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.4-1ubuntu1), libtiff6 (= 4.5.0-4ubuntu1), libtinfo6 (= 6.4-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan2 (= 12.2.0-14ubuntu1), libubsan1 (= 12.2.0-14ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.4-1ubuntu1), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4ubuntu1), libwebp7 (= 1.2.4-0.1build1), libwebpdemux2 (= 1.2.4-0.1build1), libwebpmux3 (= 1.2.4-0.1build1), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxml2 (= 2.9.14+dfsg-1.1build1), libzstd1 (= 1.5.2+dfsg2-3), linux-libc-dev (= 6.1.0-14.14), login (= 1:4.13+dfsg1-1ubuntu1), lsb-base (= 11.6), lto-disabled-list (= 37), m4 (= 1.4.19-3), mailcap (= 3.70+nmu1ubuntu1), make (= 4.3-4.1build1), man-db (= 2.11.2-1), mash (= 2.3+dfsg-3build1), mawk (= 1.3.4.20200120-3.1), media-types (= 9.0.0), mime-support (= 3.66), ncbi-blast+ (= 2.12.0+ds-3build1), ncbi-data (= 6.1.20170106+dfsg1-10), ncurses-base (= 6.4-2), ncurses-bin (= 6.4-2), patch (= 2.7.6-7build2), perl (= 5.36.0-7), perl-base (= 5.36.0-7), perl-modules-5.36 (= 5.36.0-7), po-debconf (= 1.0.21+nmu1), python3 (= 3.11.1-3), python3-biopython (= 1.80+dfsg-4), python3-distutils (= 3.10.8-1), python3-lib2to3 (= 3.10.8-1), python3-minimal (= 3.11.1-3), python3-numpy (= 1:1.24.1-2), python3-pil (= 9.4.0-1.1build1), python3-pkg-resources (= 66.1.1-1), python3-renderpm (= 3.6.12-1), python3-reportlab (= 3.6.12-1), python3-reportlab-accel (= 3.6.12-1), python3-setuptools (= 66.1.1-1), python3.10 (= 3.10.9-1), python3.10-minimal (= 3.10.9-1), python3.11 (= 3.11.1-2), python3.11-minimal (= 3.11.1-2), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.17+nmu1), sgml-base (= 1.31), sysvinit-utils (= 3.05-7ubuntu2), tar (= 1.34+dfsg-1.1), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), w3c-sgml-lib (= 1.3-3), x11-common (= 1:7.7+23ubuntu2), xfonts-encodings (= 1:1.0.5-0ubuntu2), xfonts-utils (= 1:7.7+6build2), xml-core (= 0.18+nmu1), xz-utils (= 5.4.1-0.1), zlib1g (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1675665471" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ kleborate_2.3.1-1_arm64.deb --------------------------- new Debian package, version 2.0. size 8745618 bytes: control archive=4586 bytes. 1035 bytes, 23 lines control 13848 bytes, 141 lines md5sums 717 bytes, 36 lines * postinst #!/bin/sh 638 bytes, 32 lines * prerm #!/bin/sh Package: kleborate Version: 2.3.1-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 62570 Depends: python3-biopython, python3:any, ncbi-blast+, mash, kaptive, kaptive-data, python3-distutils Section: science Priority: optional Homepage: https://github.com/katholt/Kleborate Description: tool to screen Klebsiella genome assemblies Kleborate is a tool to screen Klebsiella genome assemblies for: . * MLST sequence type * species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.) * ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb) * virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2) * antimicrobial resistance genes, including quinolone resistance SNPs and colistin resistance truncations * K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive drwxr-xr-x 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+------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 366452 Build-Time: 195 Distribution: lunar-proposed Host Architecture: arm64 Install-Time: 167 Job: kleborate_2.3.1-1.dsc Machine Architecture: arm64 Package: kleborate Package-Time: 369 Source-Version: 2.3.1-1 Space: 366452 Status: successful Version: 2.3.1-1 -------------------------------------------------------------------------------- Finished at 2023-02-06T17:40:18Z Build needed 00:06:09, 366452k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25560810 Scanning for processes to kill in build PACKAGEBUILD-25560810