https://launchpad.net/ubuntu/+source/kleborate/2.3.1-2/+build/26218145 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-098 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:51:45 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_232~632~ubuntu20.04.1 python3-lpbuildd_232~632~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 25 May 17:14:01 ntpdate[1832]: adjust time server 10.131.248.1 offset 0.000661 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26218145 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3 Creating target for build PACKAGEBUILD-26218145 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26218145 Starting target for build PACKAGEBUILD-26218145 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26218145 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26218145 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26218145 Updating target for build PACKAGEBUILD-26218145 Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 Packages [1398 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [514 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe amd64 Packages [14.6 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5928 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 Packages [68.0 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [23.2 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 Packages [109 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [47.8 kB] Fetched 23.2 MB in 2s (10.7 MB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-13-base libproc2-0 The following packages will be upgraded: adduser advancecomp apt base-files bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils ca-certificates coreutils cpp cpp-12 dash debconf diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libext2fs2 libfakeroot libfdisk1 libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgprofng0 libgssapi-krb5-2 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmount1 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev logsave lsb-base lto-disabled-list mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g 133 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 110 MB of archives. After this operation, 503 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt-dev amd64 1:4.4.33-2 [113 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6-dev amd64 2.37-0ubuntu2 [2092 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-dev-bin amd64 2.37-0ubuntu2 [20.0 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt1 amd64 1:4.4.33-2 [80.7 kB] Get:5 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 linux-libc-dev amd64 6.3.0-4.4 [1507 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6 amd64 2.37-0ubuntu2 [3179 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-bin amd64 2.37-0ubuntu2 [669 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-13-base amd64 13.1.0-2ubuntu2 [41.2 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-s1 amd64 13.1.0-2ubuntu2 [62.4 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 base-files amd64 12.3ubuntu3 [76.1 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 bsdutils amd64 1:2.38.1-5ubuntu1 [91.4 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 liblzma5 amd64 5.4.1-0.2 [125 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcrypt20 amd64 1.10.1-3ubuntu1 [529 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++6 amd64 13.1.0-2ubuntu2 [772 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 libapparmor1 amd64 3.0.8-1ubuntu2 [46.0 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit-common all 1:3.0.9-1 [5142 B] Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap-ng0 amd64 0.8.3-1build2 [15.3 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit1 amd64 1:3.0.9-1 [46.0 kB] Get:22 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libblkid1 amd64 2.38.1-5ubuntu1 [111 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap2 amd64 1:2.66-3ubuntu2 [28.2 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libperl5.36 amd64 5.36.0-7 [4834 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 perl amd64 5.36.0-7 [235 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-base amd64 5.36.0-7 [1779 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [742 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu4 [61.2 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 debconf all 1.5.82 [125 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 libssl3 amd64 3.0.8-1ubuntu2 [1903 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [292 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 libkmod2 amd64 30+20221128-1ubuntu1 [49.5 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libpcre2-8-0 amd64 10.42-1 [228 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 libselinux1 amd64 3.4-1build4 [78.1 kB] Get:36 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libmount1 amd64 2.38.1-5ubuntu1 [121 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam0g amd64 1.5.2-6ubuntu1 [65.9 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 libseccomp2 amd64 2.5.4-1ubuntu3 [49.1 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd-sysv amd64 252.5-2ubuntu3 [11.5 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd amd64 252.5-2ubuntu3 [3002 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd-shared amd64 252.5-2ubuntu3 [1832 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 libargon2-1 amd64 0~20190702+dfsg-3 [20.3 kB] Get:43 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libuuid1 amd64 2.38.1-5ubuntu1 [32.6 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main amd64 libcryptsetup12 amd64 2:2.6.1-4ubuntu1 [243 kB] Get:45 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libfdisk1 amd64 2.38.1-5ubuntu1 [144 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 libp11-kit0 amd64 0.24.1-2ubuntu1 [248 kB] Get:47 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 mount amd64 2.38.1-5ubuntu1 [114 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd0 amd64 252.5-2ubuntu3 [389 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 libudev1 amd64 252.5-2ubuntu3 [150 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 libapt-pkg6.0 amd64 2.7.0 [929 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 tar amd64 1.34+dfsg-1.2 [293 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg amd64 1.21.22ubuntu1 [1393 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main amd64 dash amd64 0.5.12-2ubuntu1 [88.2 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main amd64 diffutils amd64 1:3.8-4 [176 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 findutils amd64 4.9.0-4ubuntu1 [299 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 grep amd64 3.8-5 [160 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 hostname amd64 3.23+nmu1ubuntu1 [11.0 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-bin amd64 6.4-4 [185 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 sed amd64 4.9-1 [193 kB] Get:60 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libsmartcols1 amd64 2.38.1-5ubuntu1 [59.4 kB] Get:61 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 util-linux-extra amd64 2.38.1-5ubuntu1 [83.8 kB] Get:62 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 util-linux amd64 2.38.1-5ubuntu1 [1076 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-base all 6.4-4 [23.3 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main amd64 sysvinit-utils amd64 3.06-4ubuntu1 [33.0 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main amd64 lsb-base all 11.6 [4606 B] Get:66 http://ftpmaster.internal/ubuntu mantic/main amd64 adduser all 3.129ubuntu1 [59.0 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgv amd64 2.2.40-1.1ubuntu1 [140 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main amd64 libgnutls30 amd64 3.7.9-2ubuntu1 [999 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main amd64 apt amd64 2.7.0 [1359 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules-bin amd64 1.5.2-6ubuntu1 [47.3 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules amd64 1.5.2-6ubuntu1 [284 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 logsave amd64 1.47.0-1ubuntu1 [14.2 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 libext2fs2 amd64 1.47.0-1ubuntu1 [212 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main amd64 e2fsprogs amd64 1.47.0-1ubuntu1 [598 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebconfclient0 amd64 0.267ubuntu1 [7892 B] Get:77 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage-common all 3.4-1build4 [9852 B] Get:79 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage2 amd64 3.4-1build4 [92.7 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main amd64 libncurses6 amd64 6.4-4 [112 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 libncursesw6 amd64 6.4-4 [147 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 libtinfo6 amd64 6.4-4 [103 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 usrmerge all 35ubuntu1 [58.2 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main amd64 libcom-err2 amd64 1.47.0-1ubuntu1 [14.5 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main amd64 libproc2-0 amd64 2:4.0.3-1ubuntu1 [55.9 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main amd64 libss2 amd64 1.47.0-1ubuntu1 [16.8 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main amd64 procps amd64 2:4.0.3-1ubuntu1 [609 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main amd64 sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main amd64 openssl amd64 3.0.8-1ubuntu2 [1182 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main amd64 ca-certificates all 20230311ubuntu1 [152 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main amd64 libgssapi-krb5-2 amd64 1.20.1-2 [142 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5-3 amd64 1.20.1-2 [346 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5support0 amd64 1.20.1-2 [32.7 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main amd64 libk5crypto3 amd64 1.20.1-2 [81.1 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main amd64 readline-common all 8.2-1.3 [55.7 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/main amd64 libreadline8 amd64 8.2-1.3 [151 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main amd64 libsqlite3-0 amd64 3.40.1-2 [660 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main amd64 tzdata all 2023c-4exp1ubuntu1 [271 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main amd64 xz-utils amd64 5.4.1-0.2 [270 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main amd64 advancecomp amd64 2.5-1 [180 kB] Get:101 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgprofng0 amd64 2.40-2ubuntu6 [897 kB] Get:102 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libctf0 amd64 2.40-2ubuntu6 [97.4 kB] Get:103 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libctf-nobfd0 amd64 2.40-2ubuntu6 [101 kB] Get:104 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2ubuntu6 [2502 kB] Get:105 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libbinutils amd64 2.40-2ubuntu6 [633 kB] Get:106 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 binutils amd64 2.40-2ubuntu6 [18.5 kB] Get:107 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 binutils-common amd64 2.40-2ubuntu6 [239 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/main amd64 libmpfr6 amd64 4.2.0-1 [352 kB] Get:109 http://ftpmaster.internal/ubuntu mantic/main amd64 g++-12 amd64 12.3.0-1ubuntu1 [12.1 MB] Get:110 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12 amd64 12.3.0-1ubuntu1 [21.6 MB] Get:111 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp-12 amd64 12.3.0-1ubuntu1 [10.7 MB] Get:112 http://ftpmaster.internal/ubuntu mantic/main amd64 libubsan1 amd64 13.1.0-2ubuntu2 [1105 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++-12-dev amd64 12.3.0-1ubuntu1 [2178 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/main amd64 libgomp1 amd64 13.1.0-2ubuntu2 [142 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/main amd64 libitm1 amd64 13.1.0-2ubuntu2 [29.3 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/main amd64 libatomic1 amd64 13.1.0-2ubuntu2 [10.4 kB] Get:117 http://ftpmaster.internal/ubuntu mantic/main amd64 libasan8 amd64 13.1.0-2ubuntu2 [2826 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main amd64 liblsan0 amd64 13.1.0-2ubuntu2 [1203 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main amd64 libquadmath0 amd64 13.1.0-2ubuntu2 [153 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-12-dev amd64 12.3.0-1ubuntu1 [2577 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main amd64 libtsan2 amd64 13.1.0-2ubuntu2 [2600 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main amd64 libcc1-0 amd64 13.1.0-2ubuntu2 [48.1 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12-base amd64 12.3.0-1ubuntu1 [42.3 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main amd64 g++ amd64 4:12.2.0-3ubuntu1 [1120 B] Get:125 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc amd64 4:12.2.0-3ubuntu1 [5160 B] Get:126 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp amd64 4:12.2.0-3ubuntu1 [27.8 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg-dev all 1.21.22ubuntu1 [1118 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main amd64 libdpkg-perl all 1.21.22ubuntu1 [247 kB] Get:129 http://ftpmaster.internal/ubuntu mantic/main amd64 lto-disabled-list all 41 [12.4 kB] Get:130 http://ftpmaster.internal/ubuntu mantic/main amd64 libfakeroot amd64 1.31-1.2 [32.0 kB] Get:131 http://ftpmaster.internal/ubuntu mantic/main amd64 fakeroot amd64 1.31-1.2 [60.1 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg amd64 2.2.40-1.1ubuntu1 [523 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgconf amd64 2.2.40-1.1ubuntu1 [96.3 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg-agent amd64 2.2.40-1.1ubuntu1 [216 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main amd64 pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 110 MB in 2s (53.4 MB/s) (Reading database ... 13093 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.33-2) over (1:4.4.33-1) ... Preparing to unpack .../libc6-dev_2.37-0ubuntu2_amd64.deb ... Unpacking libc6-dev:amd64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.37-0ubuntu2_amd64.deb ... Unpacking libc-dev-bin (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libcrypt1_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.33-2) over (1:4.4.33-1) ... Setting up libcrypt1:amd64 (1:4.4.33-2) ... (Reading database ... 13093 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.3.0-4.4_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.3.0-4.4) over (5.19.0-21.21) ... Preparing to unpack .../libc6_2.37-0ubuntu2_amd64.deb ... Unpacking libc6:amd64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Setting up libc6:amd64 (2.37-0ubuntu2) ... (Reading database ... 13094 files and directories currently installed.) 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Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 19 added, 6 removed; done. Setting up perl (5.36.0-7) ... Setting up libgprofng0:amd64 (2.40-2ubuntu6) ... Setting up libgcc-12-dev:amd64 (12.3.0-1ubuntu1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2) ... Setting up libsystemd-shared:amd64 (252.5-2ubuntu3) ... Setting up libdpkg-perl (1.21.22ubuntu1) ... Setting up cpp (4:12.2.0-3ubuntu1) ... Setting up gpgconf (2.2.40-1.1ubuntu1) ... Setting up libc6-dev:amd64 (2.37-0ubuntu2) ... Setting up gpg (2.2.40-1.1ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.40-2ubuntu6) ... Setting up gpg-agent (2.2.40-1.1ubuntu1) ... Setting up libstdc++-12-dev:amd64 (12.3.0-1ubuntu1) ... Setting up systemd (252.5-2ubuntu3) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up binutils (2.40-2ubuntu6) ... Setting up dpkg-dev (1.21.22ubuntu1) ... Setting up gcc-12 (12.3.0-1ubuntu1) ... Setting up g++-12 (12.3.0-1ubuntu1) ... Setting up systemd-sysv (252.5-2ubuntu3) ... Setting up gcc (4:12.2.0-3ubuntu1) ... Setting up g++ (4:12.2.0-3ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for ca-certificates (20230311ubuntu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26218145 amd64 mantic-proposed -c chroot:build-PACKAGEBUILD-26218145 --arch=amd64 --dist=mantic-proposed --nolog -A kleborate_2.3.1-2.dsc Initiating build PACKAGEBUILD-26218145 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:51:45 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-098.buildd +==============================================================================+ | kleborate 2.3.1-2 (amd64) Thu, 25 May 2023 17:14:26 +0000 | +==============================================================================+ Package: kleborate Version: 2.3.1-2 Source Version: 2.3.1-2 Distribution: mantic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26218145/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/kleborate-POStZI/resolver-AhWOZ2' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- kleborate_2.3.1-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/kleborate-POStZI/kleborate-2.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/kleborate-POStZI' 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 [489 B] Fetched 1865 B in 0s (185 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fonts-urw-base35 gettext gettext-base groff-base intltool-debian kaptive libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcapnp-0.9.2 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmurmurhash2 libopenjp2-7 libpcre3 libpipeline1 libpython3-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 python3.11 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-installer python3-wheel 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 python3.11-venv python3.11-doc binfmt-support 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 libmurmurhash2 libopenjp2-7 libpcre3 libpipeline1 libpython3-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 python3.11 python3.11-minimal sbuild-build-depends-main-dummy sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. 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Setting up libmurmurhash2:amd64 (1.5-3) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.76.2-1ubuntu1) ... No schema files found: doing nothing. Setting up libpython3.11-stdlib:amd64 (3.11.3-1) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:amd64 (1.0.9-2build8) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.15-1) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:amd64 (2.7.1+dfsg-4) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ... Setting up libpcre3:amd64 (2:8.39-15) ... Setting up libfontenc1:amd64 (1:1.1.4-1build3) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up libfribidi0:amd64 (1.0.8-2.1ubuntu1) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up autopoint (0.21-12) ... Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... Setting up libgfortran5:amd64 (13.1.0-2ubuntu2) ... Setting up libcapnp-0.9.2:amd64 (0.9.2-2) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.2) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libopenjp2-7:amd64 (2.5.0-1build1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3build1) ... Setting up sgml-base (1.31) ... Setting up libwebpmux3:amd64 (1.2.4-0.2) ... Setting up libbsd0:amd64 (0.11.7-4) ... Setting up mailcap (3.70+nmu1ubuntu1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.3-1) ... Setting up libdw1:amd64 (0.188-2.1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up mime-support (3.66) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2) ... Setting up python3 (3.11.2-1) ... Setting up xfonts-utils (1:7.7+6build2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up ncbi-blast+ (2.12.0+ds-3build1) ... Setting up dh-autoreconf (20) ... Setting up libraqm0:amd64 (0.10.1-1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1build1) ... 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 (1.22.4-10) ... Setting up libtiff6:amd64 (4.5.0-6ubuntu1) ... Setting up xml-core (0.18+nmu1) ... Setting up debugedit (1:5.0-5) ... Setting up python3-lib2to3 (3.11.3-2) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.3-2) ... Setting up dh-python (5.20230510) ... Setting up python3-setuptools (66.1.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up man-db (2.11.2-2) ... 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 python3-pil:amd64 (9.4.0-1.1build1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-reportlab (3.6.12-1build1) ... Setting up python3-renderpm:amd64 (3.6.12-1build1) ... Setting up debhelper (13.11.4ubuntu3) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for systemd (252.5-2ubuntu3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4build1) ... 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 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:51:45 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.40-2ubuntu6 dpkg-dev_1.21.22ubuntu1 g++-12_12.3.0-1ubuntu1 gcc-12_12.3.0-1ubuntu1 libc6-dev_2.37-0ubuntu2 libstdc++-12-dev_12.3.0-1ubuntu1 libstdc++6_13.1.0-2ubuntu2 linux-libc-dev_6.3.0-4.4 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.7.0 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_12.3ubuntu3 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40-2ubuntu6 binutils-common_2.40-2ubuntu6 binutils-x86-64-linux-gnu_2.40-2ubuntu6 bsdextrautils_2.38.1-5ubuntu1 bsdutils_1:2.38.1-5ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-3ubuntu1 cpp-12_12.3.0-1ubuntu1 dash_0.5.12-2ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_5.20230510 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.22ubuntu1 dpkg-dev_1.21.22ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-1ubuntu1 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4ubuntu1 fonts-urw-base35_20200910-7 g++_4:12.2.0-3ubuntu1 g++-12_12.3.0-1ubuntu1 gcc_4:12.2.0-3ubuntu1 gcc-12_12.3.0-1ubuntu1 gcc-12-base_12.3.0-1ubuntu1 gcc-13-base_13.1.0-2ubuntu2 gettext_0.21-12 gettext-base_0.21-12 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 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_3.0.8-1ubuntu2 libapt-pkg6.0_2.7.0 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libasan8_13.1.0-2ubuntu2 libassuan0_2.5.5-5 libatomic1_13.1.0-2ubuntu2 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2ubuntu6 libblas3_3.11.0-2 libblkid1_2.38.1-5ubuntu1 libbrotli1_1.0.9-2build8 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5build1 libc-bin_2.37-0ubuntu2 libc-dev-bin_2.37-0ubuntu2 libc6_2.37-0ubuntu2 libc6-dev_2.37-0ubuntu2 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-3ubuntu2 libcapnp-0.9.2_0.9.2-2 libcc1-0_13.1.0-2ubuntu2 libcom-err2_1.47.0-1ubuntu1 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libcryptsetup12_2:2.6.1-4ubuntu1 libctf-nobfd0_2.40-2ubuntu6 libctf0_2.40-2ubuntu6 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.267ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate0_1.15-1 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libxdmcp6_1:1.1.3-0ubuntu5 libxml2_2.9.14+dfsg-1.2 libxxhash0_0.8.1-1 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.3.0-4.4 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-1ubuntu1 lsb-base_11.6 lto-disabled-list_41 m4_1.4.19-3 mailcap_3.70+nmu1ubuntu1 make_4.3-4.1build1 man-db_2.11.2-2 mash_2.3+dfsg-3build1 mawk_1.3.4.20200120-3.1 media-types_10.0.0 mime-support_3.66 mount_2.38.1-5ubuntu1 ncbi-blast+_2.12.0+ds-3build1 ncbi-data_6.1.20170106+dfsg1-10 ncurses-base_6.4-4 ncurses-bin_6.4-4 openssl_3.0.8-1ubuntu2 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_153 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.3-1ubuntu1 python3_3.11.2-1 python3-biopython_1.80+dfsg-4build1 python3-distutils_3.11.3-2 python3-lib2to3_3.11.3-2 python3-minimal_3.11.2-1 python3-numpy_1:1.24.2-1 python3-pil_9.4.0-1.1build1 python3-pkg-resources_66.1.1-1 python3-renderpm_3.6.12-1build1 python3-reportlab_3.6.12-1build1 python3-reportlab-accel_3.6.12-1build1 python3-setuptools_66.1.1-1 python3.11_3.11.3-1 python3.11-minimal_3.11.3-1 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_252.5-2ubuntu3 systemd-sysv_252.5-2ubuntu3 sysvinit-utils_3.06-4ubuntu1 tar_1.34+dfsg-1.2 tzdata_2023c-4exp1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.38.1-5ubuntu1 util-linux-extra_2.38.1-5ubuntu1 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_5.4.1-0.2 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: 2.3.1-2 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 fc580d9e2c38f21151677b3fc747a6c6e2facca0 5996392 kleborate_2.3.1-2.debian.tar.xz Checksums-Sha256: 81bd01f9c7db7ca1d6763571eddea616e4970d2420dab6dfa8a9b47aebb8a870 91335255 kleborate_2.3.1.orig.tar.gz 0dfe70cdc650e530d3fdad90d1196a23d13cf04a6990c8a656781a87e2bbf255 5996392 kleborate_2.3.1-2.debian.tar.xz Files: 6d39609923dd9932e0221108fb103481 91335255 kleborate_2.3.1.orig.tar.gz 45970d991da5a484fd90f8e378254345 5996392 kleborate_2.3.1-2.debian.tar.xz Dgit: 663fa9e0971c8922a23ef821ea68147ec7336073 debian archive/debian/2.3.1-2 https://git.dgit.debian.org/kleborate -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmRvZEAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrkBg/+MxXWaKOnkoAT/vH7U0HPJzipeqcg deU/F0d0COj5ghuXmTxNED8ytqvf7+jX4PnZ1/IjLtaQfFmT/LuQxrxlndE4kpl6 ALYaBLh/1vvm2csDcftjS2b4/jz3vMf2xUC5Qk0XFDNlVtj8yFcxR1YjjAQzvXoa phIKT2cIjH2ysMdRz9f7blMs96rgXt5zie5ol2Sxjlz56IgtedaJ3PeBTvaKf4eU 0IZOUXzb4pfl3QrMCU3tt6G6MMgWP807b6bZPNmEgCO/SPodXQYZ2Tg7R8ugkuhz +VcnqAMj9qFvrzGFipYMhSOd/ecCEhxsPKn12+WjuXGGNrAMlhu2QS/0QzL9XCC2 Kf648zNfW2a5HTcd+gZ0BVE51lA1/jAfj5PQ1nOfdxJbmkl/rKbmB+DeBQ9sqFuJ PhDf1UXFniEzKTZ3pslH1iyhe2qHhgBWOO+juJ2l7D//sYLMJpE/3n9RV3KC2Ybb 4FAFyufv5GIlG7UrFNSahoGPXaAq+ljTOAQs3VnWBZwizWFosrRLSd4h4A6DJaKw 0JqhAb7DvySMWRz8Wf0ZNErPHg1m9srM+yfQWhWbOTOMEwLwIDLat4j++7T7g8nj ByTQ9wAae639oElKLgzuymsEd9yLyujTmjfqkIsX113FrY4/HcDre78OV1I/EQj2 0VnTvku75v7ZNoI= =2UkI -----END PGP SIGNATURE----- gpgv: Signature made Thu May 25 13:36:00 2023 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kleborate_2.3.1-2.dsc: no acceptable signature found dpkg-source: info: extracting kleborate in /<> dpkg-source: info: unpacking kleborate_2.3.1.orig.tar.gz dpkg-source: info: unpacking kleborate_2.3.1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3.patch dpkg-source: info: applying use_debian_installed_kaptive.patch dpkg-source: info: applying bigendian.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26218145 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26218145 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26218145 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 2.3.1-2 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:275: 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:275: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:275: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/misc.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/species.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/blastn.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/rmpA.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/version.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__init__.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/help_formatter.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/kaptive.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/resBLAST.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/mlstBLAST.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/truncation.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__main__.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/shv_mutations.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:275: 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 34.457s 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:275: /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/misc.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/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/iuc_alleles.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/ybt_alleles.fasta -> /<>/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/iro_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/Klebsiella_pneumoniae.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/rmp_alleles.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/SmST_profiles.txt -> /<>/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/QRDR_120.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/YbST_profiles.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/rmpA2.fasta -> /<>/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/CARD_AMR_clustered.csv -> /<>/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/ICEKp21.gff -> /<>/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/ICEKp5.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp14.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp9.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/ICEKp4.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp2.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp7.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp8.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp15.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp10.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/ICEKp6.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp11.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp13.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/ICEKp16.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp20.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp1.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp12.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp19.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/OmpK.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/CbST_profiles.txt -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/clb_alleles.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data creating /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/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/__pycache__/help_formatter.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__/resBLAST.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__/mlstBLAST.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__/species.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__/__init__.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/misc.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/kaptive.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/blastn.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/version.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/help_formatter.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/resBLAST.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/mlstBLAST.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/truncation.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/__main__.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate 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/contig_stats.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate 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/species.py to species.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/blastn.py to blastn.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/rmpA.py to rmpA.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/__init__.py to __init__.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/kaptive.py to kaptive.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/mlstBLAST.py to mlstBLAST.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/truncation.py to truncation.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__main__.py to __main__.cpython-311.pyc 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/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. Other fasta.* are rebuilt by makeblastdb and may # cause inconsistencies in the package itself when makeblastdb is # upgraded and changes format, e.g. during a major operating system # upgrade. See Bug#1036743. find debian -name "*.fasta.nin" -delete find debian -name "*.fasta.ndb" -delete find debian -name "*.fasta.ntf" -delete make[1]: Leaving directory '/<>' 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 153 INFO: pkgstriptranslations version 153 pkgstriptranslations: processing kleborate (in debian/kleborate); do_strip: , oemstrip: pkgstriptranslations: processing kleborate-examples (in debian/kleborate-examples); 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: Truncating usr/share/doc/kleborate/changelog.Debian.gz to topmost ten records pkgstripfiles: processing control file: debian/kleborate-examples/DEBIAN/control, package kleborate-examples, directory debian/kleborate-examples 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_2.3.1-2_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_2.3.1-2_all.deb'. dpkg-genbuildinfo --build=binary -O../kleborate_2.3.1-2_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../kleborate_2.3.1-2_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 2023-05-25T17:16:00Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kleborate_2.3.1-2_amd64.changes: -------------------------------- Format: 1.8 Date: Thu, 25 May 2023 14:48:18 +0200 Source: kleborate Binary: kleborate kleborate-examples Built-For-Profiles: noudeb Architecture: all amd64 Version: 2.3.1-2 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: kleborate - tool to screen Klebsiella genome assemblies kleborate-examples - tool to screen Klebsiella genome assemblies (example data) Closes: 1036743 Changes: kleborate (2.3.1-2) unstable; urgency=medium . * d/{rules,*.prerm}: cleanup .fasta.{ndb,ntf} files kleborate binary package used to embed autogenerated files depending on makeblastdb version at both build time and postinst time. When there is a discrepancy of makeblastdb version between the package build and the package installation, for instance during a major operating system upgrade, there can be a mismatch of int the .fasta.ndb and .fasta.ntf files produced and expected. This change gets rid of the build time artifacts to solely rely on the post-installation artifacts, which will be more consistent and won't break the package consistency. (Closes: #1036743) Checksums-Sha1: f96494fc2d7c6a81f907b4a37a06d0b3064ba7a8 5989310 kleborate-examples_2.3.1-2_all.deb d0658b0c2dc8cb42ab0f41191f12f9c7836be305 7895 kleborate_2.3.1-2_amd64.buildinfo 1b783395e3891d82342becc6718900fdfabc14d1 8740304 kleborate_2.3.1-2_amd64.deb Checksums-Sha256: dd3d765abb799f6590cecd4fc4a25e1ef9ca15d96ec6be7b5aa0d56f2b264015 5989310 kleborate-examples_2.3.1-2_all.deb 5f2436d34b620a81c5000908bc94a6e782a47b66229536f20fbe0227c3816c99 7895 kleborate_2.3.1-2_amd64.buildinfo 7c088bd74da5c4b395833bc17fc8bbec9394181e832460e79e172cf1058c7be3 8740304 kleborate_2.3.1-2_amd64.deb Files: 7de18fb3b18cf4214bf025ca7f5ac149 5989310 science optional kleborate-examples_2.3.1-2_all.deb 546ae12f47dc5ec488ee06d2b7083aff 7895 science optional kleborate_2.3.1-2_amd64.buildinfo b06f360e8c9a0a36bc35d87ab57b1862 8740304 science optional kleborate_2.3.1-2_amd64.deb /<>/kleborate_2.3.1-2_amd64.changes.new could not be renamed to /<>/kleborate_2.3.1-2_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: kleborate Binary: kleborate kleborate-examples Architecture: all amd64 Version: 2.3.1-2 Checksums-Md5: 7de18fb3b18cf4214bf025ca7f5ac149 5989310 kleborate-examples_2.3.1-2_all.deb b06f360e8c9a0a36bc35d87ab57b1862 8740304 kleborate_2.3.1-2_amd64.deb Checksums-Sha1: f96494fc2d7c6a81f907b4a37a06d0b3064ba7a8 5989310 kleborate-examples_2.3.1-2_all.deb 1b783395e3891d82342becc6718900fdfabc14d1 8740304 kleborate_2.3.1-2_amd64.deb Checksums-Sha256: dd3d765abb799f6590cecd4fc4a25e1ef9ca15d96ec6be7b5aa0d56f2b264015 5989310 kleborate-examples_2.3.1-2_all.deb 7c088bd74da5c4b395833bc17fc8bbec9394181e832460e79e172cf1058c7be3 8740304 kleborate_2.3.1-2_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 25 May 2023 17:16:00 +0000 Build-Path: /<> 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libwebp7 (= 1.2.4-0.2), libwebpdemux2 (= 1.2.4-0.2), libwebpmux3 (= 1.2.4-0.2), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxml2 (= 2.9.14+dfsg-1.2), libzstd1 (= 1.5.4+dfsg2-5), linux-libc-dev (= 6.3.0-4.4), login (= 1:4.13+dfsg1-1ubuntu1), lsb-base (= 11.6), lto-disabled-list (= 41), m4 (= 1.4.19-3), mailcap (= 3.70+nmu1ubuntu1), make (= 4.3-4.1build1), man-db (= 2.11.2-2), mash (= 2.3+dfsg-3build1), mawk (= 1.3.4.20200120-3.1), media-types (= 10.0.0), mime-support (= 3.66), ncbi-blast+ (= 2.12.0+ds-3build1), ncbi-data (= 6.1.20170106+dfsg1-10), ncurses-base (= 6.4-4), ncurses-bin (= 6.4-4), 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 (= 3.11.2-1), python3-biopython (= 1.80+dfsg-4build1), python3-distutils (= 3.11.3-2), python3-lib2to3 (= 3.11.3-2), python3-minimal (= 3.11.2-1), python3-numpy (= 1:1.24.2-1), python3-pil (= 9.4.0-1.1build1), python3-pkg-resources (= 66.1.1-1), python3-renderpm (= 3.6.12-1build1), python3-reportlab (= 3.6.12-1build1), python3-reportlab-accel (= 3.6.12-1build1), python3-setuptools (= 66.1.1-1), python3.11 (= 3.11.3-1), python3.11-minimal (= 3.11.3-1), 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 (= 3.06-4ubuntu1), tar (= 1.34+dfsg-1.2), usrmerge (= 35ubuntu1), util-linux (= 2.38.1-5ubuntu1), util-linux-extra (= 2.38.1-5ubuntu1), 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 (= 5.4.1-0.2), 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="1685018898" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ kleborate-examples_2.3.1-2_all.deb ---------------------------------- new Debian package, version 2.0. size 5989310 bytes: control archive=1061 bytes. 1094 bytes, 27 lines control 680 bytes, 8 lines md5sums Package: kleborate-examples Source: kleborate Version: 2.3.1-2 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 5863 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 2023-05-25 12:48 ./ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/share/ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/share/doc/kleborate-examples/ -rw-r--r-- root/root 1212 2023-05-25 12:48 ./usr/share/doc/kleborate-examples/changelog.Debian.gz -rw-r--r-- root/root 1146 2023-05-25 12:48 ./usr/share/doc/kleborate-examples/copyright drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/share/doc/kleborate/ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/share/doc/kleborate/examples/ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/share/doc/kleborate/examples/data/ -rw-r--r-- root/root 1529920 2023-05-25 12:48 ./usr/share/doc/kleborate/examples/data/Klebs_HS11286.fna.xz -rw-r--r-- root/root 1455464 2023-05-25 12:48 ./usr/share/doc/kleborate/examples/data/Klebs_Kp1084.fna.xz -rw-r--r-- root/root 1521788 2023-05-25 12:48 ./usr/share/doc/kleborate/examples/data/MGH78578.fna.xz -rw-r--r-- root/root 1477412 2023-05-25 12:48 ./usr/share/doc/kleborate/examples/data/NTUH-K2044.fna.xz -rwxr-xr-x root/root 1144 2023-05-25 12:48 ./usr/share/doc/kleborate/examples/data/get-data -rw-r--r-- root/root 454 2023-05-25 12:48 ./usr/share/doc/kleborate/run-unit-test kleborate_2.3.1-2_amd64.deb --------------------------- new Debian package, version 2.0. size 8740304 bytes: control archive=4266 bytes. 1035 bytes, 23 lines control 11446 bytes, 117 lines md5sums 717 bytes, 36 lines * postinst #!/bin/sh 768 bytes, 34 lines * prerm #!/bin/sh Package: kleborate Version: 2.3.1-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 62139 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 2023-05-25 12:48 ./ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/bin/ -rwxr-xr-x root/root 968 2023-05-25 12:48 ./usr/bin/kleborate drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/lib/ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/lib/python3/ drwxr-xr-x root/root 0 2023-05-25 12:48 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2023-05-25 12:48 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+------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 377352 Build-Time: 54 Distribution: mantic-proposed Host Architecture: amd64 Install-Time: 38 Job: kleborate_2.3.1-2.dsc Machine Architecture: amd64 Package: kleborate Package-Time: 94 Source-Version: 2.3.1-2 Space: 377352 Status: successful Version: 2.3.1-2 -------------------------------------------------------------------------------- Finished at 2023-05-25T17:16:00Z Build needed 00:01:34, 377352k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26218145 Scanning for processes to kill in build PACKAGEBUILD-26218145