https://launchpad.net/ubuntu/+source/kleborate/2.3.1-1/+build/25560809 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-034 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:22 UTC 2023 x86_64 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 17:31:27 ntpdate[1818]: adjust time server 10.131.248.1 offset 0.000364 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25560809 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3 Creating target for build PACKAGEBUILD-25560809 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25560809 Starting target for build PACKAGEBUILD-25560809 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25560809 '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-25560809 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25560809 Updating target for build PACKAGEBUILD-25560809 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 amd64 Packages [1385 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe amd64 Packages [14.5 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5913 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 Packages [164 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [63.4 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 Packages [581 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [240 kB] Fetched 24.0 MB in 4s (5878 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-common binutils-x86-64-linux-gnu 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 libitm1 liblsan0 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libquadmath0 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 102 MB of archives. After this operation, 2400 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 diffutils amd64 1:3.8-4 [176 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libc-bin amd64 2.37-0ubuntu1 [670 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 libcrypt-dev amd64 1:4.4.33-2 [113 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libc6-dev amd64 2.37-0ubuntu1 [2091 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libc-dev-bin amd64 2.37-0ubuntu1 [20.0 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main amd64 libcrypt1 amd64 1:4.4.33-2 [80.7 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 linux-libc-dev amd64 6.1.0-14.14 [1495 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main amd64 libcc1-0 amd64 12.2.0-14ubuntu1 [46.5 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main amd64 libgprofng0 amd64 2.40-2ubuntu1 [897 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main amd64 libctf0 amd64 2.40-2ubuntu1 [97.4 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main amd64 libctf-nobfd0 amd64 2.40-2ubuntu1 [100 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2ubuntu1 [2484 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main amd64 libbinutils amd64 2.40-2ubuntu1 [633 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main amd64 binutils-common amd64 2.40-2ubuntu1 [236 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main amd64 binutils amd64 2.40-2ubuntu1 [3196 B] Get:18 http://ftpmaster.internal/ubuntu lunar/main amd64 gcc-12-base amd64 12.2.0-14ubuntu1 [19.2 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcc-s1 amd64 12.2.0-14ubuntu1 [53.9 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main amd64 libgomp1 amd64 12.2.0-14ubuntu1 [125 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main amd64 libitm1 amd64 12.2.0-14ubuntu1 [29.5 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main amd64 libatomic1 amd64 12.2.0-14ubuntu1 [10.4 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main amd64 libasan8 amd64 12.2.0-14ubuntu1 [2429 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main amd64 liblsan0 amd64 12.2.0-14ubuntu1 [1061 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main amd64 libtsan2 amd64 12.2.0-14ubuntu1 [2456 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main amd64 libubsan1 amd64 12.2.0-14ubuntu1 [969 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main amd64 libquadmath0 amd64 12.2.0-14ubuntu1 [152 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main amd64 g++-12 amd64 12.2.0-14ubuntu1 [12.0 MB] Get:29 http://ftpmaster.internal/ubuntu lunar/main amd64 libstdc++-12-dev amd64 12.2.0-14ubuntu1 [2157 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcc-12-dev amd64 12.2.0-14ubuntu1 [2577 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main amd64 gcc-12 amd64 12.2.0-14ubuntu1 [21.4 MB] Get:32 http://ftpmaster.internal/ubuntu lunar/main amd64 cpp-12 amd64 12.2.0-14ubuntu1 [10.6 MB] Get:33 http://ftpmaster.internal/ubuntu lunar/main amd64 libstdc++6 amd64 12.2.0-14ubuntu1 [678 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu4 [61.2 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main amd64 libmpfr6 amd64 4.2.0-1 [352 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main amd64 libzstd1 amd64 1.5.2+dfsg2-3 [282 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libc6 amd64 2.37-0ubuntu1 [3164 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblzma5 amd64 5.4.1-0.1 [125 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcrypt20 amd64 1.10.1-3ubuntu1 [529 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main amd64 libaudit-common all 1:3.0.7-1.1 [5108 B] Get:42 http://ftpmaster.internal/ubuntu lunar/main amd64 libaudit1 amd64 1:3.0.7-1.1 [45.3 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcap2 amd64 1:2.66-3ubuntu1 [28.0 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main amd64 libpcre2-8-0 amd64 10.42-1 [228 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libselinux1 amd64 3.4-1build3 [77.9 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main amd64 libperl5.36 amd64 5.36.0-7 [4834 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main amd64 perl amd64 5.36.0-7 [235 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main amd64 perl-base amd64 5.36.0-7 [1779 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main amd64 perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [742 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main amd64 debconf all 1.5.82 [125 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main amd64 libssl3 amd64 3.0.7-1ubuntu1 [1896 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main amd64 systemd-sysv amd64 252.4-1ubuntu1 [11.4 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main amd64 systemd amd64 252.4-1ubuntu1 [3001 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main amd64 libsystemd-shared amd64 252.4-1ubuntu1 [1771 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main amd64 libp11-kit0 amd64 0.24.1-2ubuntu1 [248 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main amd64 libsystemd0 amd64 252.4-1ubuntu1 [328 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main amd64 libudev1 amd64 252.4-1ubuntu1 [89.6 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main amd64 libapt-pkg6.0 amd64 2.5.5 [903 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main amd64 dpkg amd64 1.21.19ubuntu3 [1336 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main amd64 grep amd64 3.8-5 [160 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main amd64 ncurses-bin amd64 6.4-2 [185 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main amd64 sed amd64 4.9-1 [193 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main amd64 ncurses-base all 6.4-2 [21.3 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main amd64 sysvinit-utils amd64 3.05-7ubuntu2 [27.4 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 lsb-base all 11.6 [4606 B] Get:67 http://ftpmaster.internal/ubuntu lunar/main amd64 adduser all 3.129ubuntu1 [59.0 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main amd64 gpgv amd64 2.2.40-1ubuntu2 [137 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main amd64 libgnutls30 amd64 3.7.8-4ubuntu1 [986 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main amd64 apt amd64 2.5.5 [1378 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB] Get:72 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsemanage-common all 3.4-1build3 [9808 B] Get:73 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsemanage2 amd64 3.4-1build3 [92.7 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main amd64 libncurses6 amd64 6.4-2 [112 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main amd64 libncursesw6 amd64 6.4-2 [147 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main amd64 libtinfo6 amd64 6.4-2 [101 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main amd64 sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main amd64 readline-common all 8.2-1.3 [55.7 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main amd64 libreadline8 amd64 8.2-1.3 [151 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main amd64 libsqlite3-0 amd64 3.40.1-1 [654 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main amd64 openssl amd64 3.0.7-1ubuntu1 [1179 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main amd64 tzdata all 2022g-2ubuntu1 [397 kB] Get:83 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 xz-utils amd64 5.4.1-0.1 [268 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main amd64 advancecomp amd64 2.5-1 [180 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main amd64 dpkg-dev all 1.21.19ubuntu3 [1067 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main amd64 libdpkg-perl all 1.21.19ubuntu3 [247 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main amd64 libfakeroot amd64 1.30.1-1.1ubuntu1 [30.9 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main amd64 fakeroot amd64 1.30.1-1.1ubuntu1 [60.2 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/main amd64 gpg amd64 2.2.40-1ubuntu2 [523 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main amd64 gpgconf amd64 2.2.40-1ubuntu2 [93.7 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main amd64 gpg-agent amd64 2.2.40-1ubuntu2 [217 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main amd64 pkgbinarymangler all 151 [16.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 102 MB in 11s (9573 kB/s) (Reading database ... 13093 files and directories currently installed.) 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Setting up systemd-sysv (252.4-1ubuntu1) ... Setting up gpg-agent (2.2.40-1ubuntu2) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14ubuntu1) ... 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-25560809 amd64 lunar-proposed -c chroot:build-PACKAGEBUILD-25560809 --arch=amd64 --dist=lunar-proposed --nolog -A kleborate_2.3.1-1.dsc Initiating build PACKAGEBUILD-25560809 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:22 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-034.buildd +==============================================================================+ | kleborate 2.3.1-1 (amd64) Mon, 06 Feb 2023 17:32:03 +0000 | +==============================================================================+ Package: kleborate Version: 2.3.1-1 Source Version: 2.3.1-1 Distribution: lunar-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25560809/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/kleborate-46IIFm/resolver-QdtPrp' 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-46IIFm/kleborate-2.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/kleborate-46IIFm' 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 [491 B] Fetched 1867 B in 0s (0 B/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 79.6 MB of archives. After this operation, 304 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 amd64 libpython3.11-minimal amd64 3.11.1-2 [830 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main amd64 libexpat1 amd64 2.5.0-1 [84.2 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main amd64 python3.11-minimal amd64 3.11.1-2 [2253 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 python3-minimal amd64 3.11.1-3 [24.6 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 media-types all 9.0.0 [26.0 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main amd64 mailcap all 3.70+nmu1ubuntu1 [23.8 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main amd64 mime-support all 3.66 [3696 B] Get:9 http://ftpmaster.internal/ubuntu lunar/main amd64 libmpdec3 amd64 2.5.1-2build2 [86.8 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main amd64 libpython3.11-stdlib amd64 3.11.1-2 [1816 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main amd64 python3.11 amd64 3.11.1-2 [561 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpython3-stdlib amd64 3.11.1-3 [7208 B] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 python3 amd64 3.11.1-3 [22.9 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main amd64 libpython3.10-minimal amd64 3.10.9-1 [803 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main amd64 python3.10-minimal amd64 3.10.9-1 [2118 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main amd64 sgml-base all 1.31 [11.4 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main amd64 libbsd0 amd64 0.11.7-2 [44.1 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main amd64 libelf1 amd64 0.188-2.1 [53.4 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main amd64 libfribidi0 amd64 1.0.8-2.1ubuntu1 [25.9 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main amd64 libglib2.0-0 amd64 2.74.5-1 [1458 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main amd64 libpython3.10-stdlib amd64 3.10.9-1 [1782 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libicu72 amd64 72.1-3ubuntu1 [10.8 MB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libxml2 amd64 2.9.14+dfsg-1.1build1 [762 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 python3-pkg-resources all 66.1.1-1 [225 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main amd64 python3.10 amd64 3.10.9-1 [503 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main amd64 bsdextrautils amd64 2.38.1-4ubuntu1 [71.0 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main amd64 libmagic-mgc amd64 1:5.44-3 [293 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main amd64 libmagic1 amd64 1:5.44-3 [85.6 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main amd64 file amd64 1:5.44-3 [21.8 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main amd64 gettext-base amd64 0.21-11 [36.5 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main amd64 groff-base amd64 1.22.4-9 [937 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main amd64 liblmdb0 amd64 0.9.24-1build2 [47.6 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:36 http://ftpmaster.internal/ubuntu lunar/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb1 amd64 1.15-1 [48.0 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main amd64 man-db amd64 2.11.2-1 [1218 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 m4 amd64 1.4.19-3 [243 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main amd64 autoconf all 2.71-3 [339 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:42 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[64.8 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main amd64 libjbig0 amd64 2.1-6ubuntu1 [29.1 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main amd64 liblerc4 amd64 4.0.0+ds-2ubuntu2 [185 kB] Get:85 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libwebp7 amd64 1.2.4-0.1build1 [212 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main amd64 libtiff6 amd64 4.5.0-4ubuntu1 [195 kB] Get:87 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libwebpdemux2 amd64 1.2.4-0.1build1 [9886 B] Get:88 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libwebpmux3 amd64 1.2.4-0.1build1 [20.8 kB] Get:89 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 python3-pil amd64 9.4.0-1.1build1 [431 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main amd64 xml-core all 0.18+nmu1 [21.6 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] Get:93 http://ftpmaster.internal/ubuntu lunar/universe amd64 python3-biopython amd64 1.80+dfsg-4 [1644 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/universe amd64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/universe amd64 libmbedcrypto7 amd64 2.28.2-1 [206 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/universe amd64 libmbedx509-1 amd64 2.28.2-1 [45.7 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/universe amd64 libmbedtls14 amd64 2.28.2-1 [82.6 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/main amd64 libpcre3 amd64 2:8.39-15 [250 kB] Get:99 http://ftpmaster.internal/ubuntu lunar/universe amd64 ncbi-blast+ amd64 2.12.0+ds-3build1 [12.3 MB] Get:100 http://ftpmaster.internal/ubuntu lunar/universe amd64 kaptive all 2.0.4-1 [24.3 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/universe amd64 libcapnp-0.9.2 amd64 0.9.2-2 [1288 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/universe amd64 libgslcblas0 amd64 2.7.1+dfsg-3 [94.4 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/universe amd64 libgsl27 amd64 2.7.1+dfsg-3 [1000 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/universe amd64 libmurmurhash2 amd64 1.5-3 [5776 B] Get:105 http://ftpmaster.internal/ubuntu lunar/universe amd64 mash amd64 2.3+dfsg-3build1 [158 kB] Get:106 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 python3-setuptools all 66.1.1-1 [453 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 79.6 MB in 10s (8281 kB/s) Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... 15221 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.1-2_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.1-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.1-2_amd64.deb ... Unpacking python3.11-minimal (3.11.1-2) ... Setting up libpython3.11-minimal:amd64 (3.11.1-2) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 15535 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.1-3_amd64.deb ... Unpacking python3-minimal (3.11.1-3) ... Selecting previously unselected package media-types. 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Setting up libpython3.10-stdlib:amd64 (3.10.9-1) ... Setting up dh-autoreconf (20) ... Setting up libraqm0:amd64 (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:amd64 (4.5.0-4ubuntu1) ... Setting up xml-core (0.18+nmu1) ... Setting up debugedit (1:5.0-5) ... Setting up libpython3-stdlib:amd64 (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:amd64 (9.4.0-1.1build1) ... Setting up python3-reportlab-accel:amd64 (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:amd64 (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 (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:22 UTC 2023 amd64 (x86_64) 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-common_2.40-2ubuntu1 binutils-x86-64-linux-gnu_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 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 libquadmath0_12.2.0-14ubuntu1 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 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---------------- 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-25560809 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25560809 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25560809 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 amd64 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-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -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/mlstBLAST.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/shv_mutations.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/rmpA.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__main__.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/truncation.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__init__.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/resBLAST.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/blastn.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/help_formatter.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/species.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/misc.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/contig_stats.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 -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 35.905s OK {'Sul_acquired': 'sul2^', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': '-', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base: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/mlstBLAST.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/shv_mutations.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/__main__.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/__init__.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/blastn.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/AbST_profiles.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data 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/species_mash_sketches.msh -> /<>/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 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/ybt_alleles.fasta -> /<>/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 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/YbST_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/ICEKp11.embl -> /<>/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/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/ICEKp10.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/ICEKp16.gff -> /<>/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/ICEKp5.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/ICEKp1.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/ICEKp7.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/ICEKp8.embl -> /<>/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/ICEKp19.gff -> /<>/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/ICEKp15.gff -> /<>/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/ICEKp20.gff -> /<>/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/Klebsiella_pneumoniae.fasta -> /<>/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/rmpA2.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/MgrB_and_PmrB.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/SmST_profiles.txt -> /<>/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.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/wzi.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/help_formatter.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 creating /<>/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__/species.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__/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__/__main__.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__/mlstBLAST.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__/version.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__/__init__.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__/blastn.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ 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/contig_stats.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate 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/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/shv_mutations.py to shv_mutations.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/__main__.py to __main__.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/__init__.py to __init__.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/blastn.py to blastn.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/species.py to species.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/contig_stats.py to contig_stats.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 -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian -name "*.msh" -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 pkgstriptranslations: processing kleborate-examples (in debian/kleborate-examples); do_strip: , oemstrip: pkgstriptranslations: processing kleborate (in debian/kleborate); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/kleborate/DEBIAN/control, package kleborate, directory debian/kleborate pkgstripfiles: processing control file: debian/kleborate-examples/DEBIAN/control, package kleborate-examples, directory debian/kleborate-examples pkgstripfiles: Truncating usr/share/doc/kleborate/changelog.Debian.gz to topmost ten records INFO: pkgstripfiles: waiting for lock (kleborate-examples) ... 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_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/kleborate-examples/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package kleborate-examples ... pkgstripfiles: No PNG files. dpkg-deb: building package 'kleborate-examples' in '../kleborate-examples_2.3.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../kleborate_2.3.1-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../kleborate_2.3.1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-02-06T17:33:52Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kleborate_2.3.1-1_amd64.changes: -------------------------------- Format: 1.8 Date: Mon, 06 Feb 2023 07:37:51 +0100 Source: kleborate Binary: kleborate kleborate-examples Built-For-Profiles: noudeb Architecture: all amd64 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 kleborate-examples - tool to screen Klebsiella genome assemblies (example data) Changes: kleborate (2.3.1-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: ca86157bf6b3face1d0b0f897bae69b6b7ffff80 5989024 kleborate-examples_2.3.1-1_all.deb 83e5a75f77e52bd6a9ed754299d295429454050c 8092 kleborate_2.3.1-1_amd64.buildinfo e029e57442d3c3570f5eba637bb820f5b6b6de94 8745620 kleborate_2.3.1-1_amd64.deb Checksums-Sha256: fca0d384c1230b116aed9d6624c410748b430024bd3e268d23d5c09e88289bc2 5989024 kleborate-examples_2.3.1-1_all.deb 6b8f8155e67579666cb3a812b03966f377a58c072eb239743b4dd136f74db16e 8092 kleborate_2.3.1-1_amd64.buildinfo cbf0658a22feed89f3c09e448069a77c81c54fb4584299f4e61cab062e7b3858 8745620 kleborate_2.3.1-1_amd64.deb Files: 9328c464e5d375548b78dcac9022cfcf 5989024 science optional kleborate-examples_2.3.1-1_all.deb 19da22e931d662ab4b3c9d2df8869e4e 8092 science optional kleborate_2.3.1-1_amd64.buildinfo a2c214de4b26984b94d65c7a879121c1 8745620 science optional kleborate_2.3.1-1_amd64.deb /<>/kleborate_2.3.1-1_amd64.changes.new could not be renamed to /<>/kleborate_2.3.1-1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: kleborate Binary: kleborate kleborate-examples Architecture: all amd64 Version: 2.3.1-1 Checksums-Md5: 9328c464e5d375548b78dcac9022cfcf 5989024 kleborate-examples_2.3.1-1_all.deb a2c214de4b26984b94d65c7a879121c1 8745620 kleborate_2.3.1-1_amd64.deb Checksums-Sha1: ca86157bf6b3face1d0b0f897bae69b6b7ffff80 5989024 kleborate-examples_2.3.1-1_all.deb e029e57442d3c3570f5eba637bb820f5b6b6de94 8745620 kleborate_2.3.1-1_amd64.deb Checksums-Sha256: fca0d384c1230b116aed9d6624c410748b430024bd3e268d23d5c09e88289bc2 5989024 kleborate-examples_2.3.1-1_all.deb cbf0658a22feed89f3c09e448069a77c81c54fb4584299f4e61cab062e7b3858 8745620 kleborate_2.3.1-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Mon, 06 Feb 2023 17:33:51 +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-common (= 2.40-2ubuntu1), binutils-x86-64-linux-gnu (= 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), 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), libquadmath0 (= 12.2.0-14ubuntu1), 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-examples_2.3.1-1_all.deb ---------------------------------- new Debian package, version 2.0. size 5989024 bytes: control archive=1063 bytes. 1094 bytes, 27 lines control 680 bytes, 8 lines md5sums Package: kleborate-examples Source: kleborate Version: 2.3.1-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 5862 Recommends: kleborate Section: science Priority: optional Multi-Arch: foreign Homepage: https://github.com/katholt/Kleborate Description: tool to screen Klebsiella genome assemblies (example data) 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 . This package provides example data end tests that are used in autopkgtest. drwxr-xr-x root/root 0 2023-02-06 06:37 ./ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/share/ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/share/doc/kleborate-examples/ -rw-r--r-- root/root 941 2023-02-06 06:37 ./usr/share/doc/kleborate-examples/changelog.Debian.gz -rw-r--r-- root/root 1146 2023-02-06 06:37 ./usr/share/doc/kleborate-examples/copyright drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/share/doc/kleborate/ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/share/doc/kleborate/examples/ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/share/doc/kleborate/examples/data/ -rw-r--r-- root/root 1529920 2023-02-06 06:37 ./usr/share/doc/kleborate/examples/data/Klebs_HS11286.fna.xz -rw-r--r-- root/root 1455464 2023-02-06 06:37 ./usr/share/doc/kleborate/examples/data/Klebs_Kp1084.fna.xz -rw-r--r-- root/root 1521788 2023-02-06 06:37 ./usr/share/doc/kleborate/examples/data/MGH78578.fna.xz -rw-r--r-- root/root 1477412 2023-02-06 06:37 ./usr/share/doc/kleborate/examples/data/NTUH-K2044.fna.xz -rwxr-xr-x root/root 1144 2023-02-06 06:37 ./usr/share/doc/kleborate/examples/data/get-data -rw-r--r-- root/root 454 2023-02-06 06:37 ./usr/share/doc/kleborate/run-unit-test kleborate_2.3.1-1_amd64.deb --------------------------- new Debian package, version 2.0. size 8745620 bytes: control archive=4588 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: amd64 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 root/root 0 2023-02-06 06:37 ./ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/bin/ -rwxr-xr-x root/root 968 2023-02-06 06:37 ./usr/bin/kleborate drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/lib/ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/lib/python3/ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2023-02-06 06:37 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2023-02-06 06:37 ./usr/share/doc/kleborate/changelog.Debian.gz -rw-r--r-- root/root 1146 2023-02-06 06:37 ./usr/share/doc/kleborate/copyright drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/share/man/ drwxr-xr-x root/root 0 2023-02-06 06:37 ./usr/share/man/man1/ -rw-r--r-- root/root 808 2023-02-06 06:37 ./usr/share/man/man1/kleborate.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 378228 Build-Time: 56 Distribution: lunar-proposed Host Architecture: amd64 Install-Time: 50 Job: kleborate_2.3.1-1.dsc Machine Architecture: amd64 Package: kleborate Package-Time: 109 Source-Version: 2.3.1-1 Space: 378228 Status: successful Version: 2.3.1-1 -------------------------------------------------------------------------------- Finished at 2023-02-06T17:33:52Z Build needed 00:01:49, 378228k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25560809 Scanning for processes to kill in build PACKAGEBUILD-25560809