https://launchpad.net/ubuntu/+source/kleborate/2.3.1-2/+build/26218146 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-003 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:52:10 UTC 2023 aarch64 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 17:14:03 ntpdate[1841]: adjust time server 10.211.37.1 offset 0.005650 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26218146 --image-type chroot /home/buildd/filecache-default/f16216f5497f1f0724e8a3a0f3bd4b5063e2189b Creating target for build PACKAGEBUILD-26218146 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26218146 Starting target for build PACKAGEBUILD-26218146 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26218146 '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-26218146 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26218146 Updating target for build PACKAGEBUILD-26218146 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 arm64 Packages [1374 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [514 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe arm64 Packages [14.8 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5928 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 Packages [67.2 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [23.2 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe arm64 Packages [102 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [47.8 kB] Fetched 23.4 MB in 8s (2842 kB/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-aarch64-linux-gnu binutils-common 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 libhwasan0 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 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 103 MB of archives. After this operation, 4793 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu mantic/main arm64 libcrypt-dev arm64 1:4.4.33-2 [118 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main arm64 libc6-dev arm64 2.37-0ubuntu2 [1544 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main arm64 libc-dev-bin arm64 2.37-0ubuntu2 [19.3 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main arm64 libcrypt1 arm64 1:4.4.33-2 [83.8 kB] Get:5 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 linux-libc-dev arm64 6.3.0-4.4 [1482 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main arm64 libc6 arm64 2.37-0ubuntu2 [2723 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main arm64 libc-bin arm64 2.37-0ubuntu2 [584 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main arm64 gcc-13-base arm64 13.1.0-2ubuntu2 [41.2 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main arm64 libgcc-s1 arm64 13.1.0-2ubuntu2 [46.6 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main arm64 base-files arm64 12.3ubuntu3 [76.2 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main arm64 bash arm64 5.2.15-2ubuntu1 [780 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 bsdutils arm64 1:2.38.1-5ubuntu1 [94.4 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main arm64 coreutils arm64 9.1-1ubuntu2 [1347 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main arm64 liblzma5 arm64 5.4.1-0.2 [122 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main arm64 libgcrypt20 arm64 1.10.1-3ubuntu1 [465 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main arm64 libstdc++6 arm64 13.1.0-2ubuntu2 [731 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main arm64 libacl1 arm64 2.3.1-3 [16.3 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main arm64 libapparmor1 arm64 3.0.8-1ubuntu2 [46.4 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main arm64 libaudit-common all 1:3.0.9-1 [5142 B] Get:20 http://ftpmaster.internal/ubuntu mantic/main arm64 libcap-ng0 arm64 0.8.3-1build2 [14.6 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main arm64 libaudit1 arm64 1:3.0.9-1 [46.1 kB] Get:22 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libblkid1 arm64 2.38.1-5ubuntu1 [110 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main arm64 libcap2 arm64 1:2.66-3ubuntu2 [27.9 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main arm64 libperl5.36 arm64 5.36.0-7 [4674 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main arm64 perl arm64 5.36.0-7 [235 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main arm64 perl-base arm64 5.36.0-7 [1726 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main arm64 perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main arm64 libdb5.3 arm64 5.3.28+dfsg2-1 [732 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main arm64 zlib1g arm64 1:1.2.13.dfsg-1ubuntu4 [59.3 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main arm64 debconf all 1.5.82 [125 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main arm64 libssl3 arm64 3.0.8-1ubuntu2 [1764 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main arm64 libzstd1 arm64 1.5.4+dfsg2-5 [265 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main arm64 libkmod2 arm64 30+20221128-1ubuntu1 [47.7 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main arm64 libpcre2-8-0 arm64 10.42-1 [210 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main arm64 libselinux1 arm64 3.4-1build4 [77.6 kB] Get:36 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libmount1 arm64 2.38.1-5ubuntu1 [119 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main arm64 libpam0g arm64 1.5.2-6ubuntu1 [65.8 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main arm64 libseccomp2 arm64 2.5.4-1ubuntu3 [49.3 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main arm64 systemd-sysv arm64 252.5-2ubuntu3 [11.5 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main arm64 systemd arm64 252.5-2ubuntu3 [2906 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main arm64 libsystemd-shared arm64 252.5-2ubuntu3 [1750 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main arm64 libargon2-1 arm64 0~20190702+dfsg-3 [18.9 kB] Get:43 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libuuid1 arm64 2.38.1-5ubuntu1 [32.4 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main arm64 libcryptsetup12 arm64 2:2.6.1-4ubuntu1 [238 kB] Get:45 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libfdisk1 arm64 2.38.1-5ubuntu1 [140 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main arm64 libp11-kit0 arm64 0.24.1-2ubuntu1 [226 kB] Get:47 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 mount arm64 2.38.1-5ubuntu1 [112 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main arm64 libsystemd0 arm64 252.5-2ubuntu3 [382 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main arm64 libudev1 arm64 252.5-2ubuntu3 [148 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main arm64 libapt-pkg6.0 arm64 2.7.0 [878 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main arm64 tar arm64 1.34+dfsg-1.2 [283 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main arm64 dpkg arm64 1.21.22ubuntu1 [1390 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main arm64 dash arm64 0.5.12-2ubuntu1 [87.8 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main arm64 diffutils arm64 1:3.8-4 [172 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main arm64 findutils arm64 4.9.0-4ubuntu1 [300 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main arm64 grep arm64 3.8-5 [156 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main arm64 hostname arm64 3.23+nmu1ubuntu1 [10.7 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main arm64 ncurses-bin arm64 6.4-4 [183 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main arm64 sed arm64 4.9-1 [191 kB] Get:60 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libsmartcols1 arm64 2.38.1-5ubuntu1 [58.1 kB] Get:61 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 util-linux-extra arm64 2.38.1-5ubuntu1 [81.3 kB] Get:62 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 util-linux arm64 2.38.1-5ubuntu1 [1073 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main arm64 ncurses-base all 6.4-4 [23.3 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main arm64 sysvinit-utils arm64 3.06-4ubuntu1 [32.4 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main arm64 lsb-base all 11.6 [4606 B] Get:66 http://ftpmaster.internal/ubuntu mantic/main arm64 adduser all 3.129ubuntu1 [59.0 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/main arm64 gpgv arm64 2.2.40-1.1ubuntu1 [135 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main arm64 libgnutls30 arm64 3.7.9-2ubuntu1 [946 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main arm64 apt arm64 2.7.0 [1314 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main arm64 libpam-modules-bin arm64 1.5.2-6ubuntu1 [46.1 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main arm64 libpam-modules arm64 1.5.2-6ubuntu1 [283 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main arm64 logsave arm64 1.47.0-1ubuntu1 [14.0 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main arm64 libext2fs2 arm64 1.47.0-1ubuntu1 [213 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main arm64 e2fsprogs arm64 1.47.0-1ubuntu1 [591 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main arm64 libattr1 arm64 1:2.5.1-4 [12.2 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main arm64 libdebconfclient0 arm64 0.267ubuntu1 [7842 B] Get:77 http://ftpmaster.internal/ubuntu mantic/main arm64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main arm64 libsemanage-common all 3.4-1build4 [9852 B] Get:79 http://ftpmaster.internal/ubuntu mantic/main arm64 libsemanage2 arm64 3.4-1build4 [89.3 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main arm64 libncurses6 arm64 6.4-4 [108 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main arm64 libncursesw6 arm64 6.4-4 [141 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main arm64 libtinfo6 arm64 6.4-4 [99.7 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main arm64 usrmerge all 35ubuntu1 [58.2 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main arm64 libcom-err2 arm64 1.47.0-1ubuntu1 [14.0 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main arm64 libproc2-0 arm64 2:4.0.3-1ubuntu1 [53.1 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main arm64 libss2 arm64 1.47.0-1ubuntu1 [16.1 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main arm64 procps arm64 2:4.0.3-1ubuntu1 [606 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main arm64 sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main arm64 openssl arm64 3.0.8-1ubuntu2 [1161 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main arm64 ca-certificates all 20230311ubuntu1 [152 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main arm64 libgssapi-krb5-2 arm64 1.20.1-2 [139 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main arm64 libkrb5-3 arm64 1.20.1-2 [345 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main arm64 libkrb5support0 arm64 1.20.1-2 [32.6 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main arm64 libk5crypto3 arm64 1.20.1-2 [84.8 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main arm64 readline-common all 8.2-1.3 [55.7 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/main arm64 libreadline8 arm64 8.2-1.3 [150 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main arm64 libsqlite3-0 arm64 3.40.1-2 [663 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main arm64 tzdata all 2023c-4exp1ubuntu1 [271 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main arm64 xz-utils arm64 5.4.1-0.2 [271 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main arm64 advancecomp arm64 2.5-1 [171 kB] Get:101 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libgprofng0 arm64 2.40-2ubuntu6 [792 kB] Get:102 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libctf0 arm64 2.40-2ubuntu6 [93.1 kB] Get:103 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libctf-nobfd0 arm64 2.40-2ubuntu6 [98.0 kB] Get:104 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.40-2ubuntu6 [3138 kB] Get:105 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libbinutils arm64 2.40-2ubuntu6 [767 kB] Get:106 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 binutils arm64 2.40-2ubuntu6 [18.5 kB] Get:107 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 binutils-common arm64 2.40-2ubuntu6 [239 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/main arm64 libmpfr6 arm64 4.2.0-1 [256 kB] Get:109 http://ftpmaster.internal/ubuntu mantic/main arm64 g++-12 arm64 12.3.0-1ubuntu1 [10.9 MB] Get:110 http://ftpmaster.internal/ubuntu mantic/main arm64 gcc-12 arm64 12.3.0-1ubuntu1 [19.1 MB] Get:111 http://ftpmaster.internal/ubuntu mantic/main arm64 cpp-12 arm64 12.3.0-1ubuntu1 [9590 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main arm64 libubsan1 arm64 13.1.0-2ubuntu2 [1089 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main arm64 libstdc++-12-dev arm64 12.3.0-1ubuntu1 [2164 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/main arm64 libgomp1 arm64 13.1.0-2ubuntu2 [134 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/main arm64 libitm1 arm64 13.1.0-2ubuntu2 [27.9 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/main arm64 libatomic1 arm64 13.1.0-2ubuntu2 [11.7 kB] Get:117 http://ftpmaster.internal/ubuntu mantic/main arm64 libasan8 arm64 13.1.0-2ubuntu2 [2739 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main arm64 liblsan0 arm64 13.1.0-2ubuntu2 [1183 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main arm64 libhwasan0 arm64 13.1.0-2ubuntu2 [1241 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main arm64 libgcc-12-dev arm64 12.3.0-1ubuntu1 [1156 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main arm64 libtsan2 arm64 13.1.0-2ubuntu2 [2618 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main arm64 libcc1-0 arm64 13.1.0-2ubuntu2 [49.5 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main arm64 gcc-12-base arm64 12.3.0-1ubuntu1 [42.3 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main arm64 g++ arm64 4:12.2.0-3ubuntu1 [1106 B] Get:125 http://ftpmaster.internal/ubuntu mantic/main arm64 gcc arm64 4:12.2.0-3ubuntu1 [5184 B] Get:126 http://ftpmaster.internal/ubuntu mantic/main arm64 cpp arm64 4:12.2.0-3ubuntu1 [27.8 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/main arm64 dpkg-dev all 1.21.22ubuntu1 [1118 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main arm64 libdpkg-perl all 1.21.22ubuntu1 [247 kB] Get:129 http://ftpmaster.internal/ubuntu mantic/main arm64 lto-disabled-list all 41 [12.4 kB] Get:130 http://ftpmaster.internal/ubuntu mantic/main arm64 libfakeroot arm64 1.31-1.2 [31.9 kB] Get:131 http://ftpmaster.internal/ubuntu mantic/main arm64 fakeroot arm64 1.31-1.2 [59.6 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main arm64 gpg arm64 2.2.40-1.1ubuntu1 [509 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main arm64 gpgconf arm64 2.2.40-1.1ubuntu1 [95.3 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main arm64 gpg-agent arm64 2.2.40-1.1ubuntu1 [211 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main arm64 pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 103 MB in 9s (11.3 MB/s) (Reading database ... 13115 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.33-2_arm64.deb ... Unpacking libcrypt-dev:arm64 (1:4.4.33-2) over (1:4.4.33-1) ... Preparing to unpack .../libc6-dev_2.37-0ubuntu2_arm64.deb ... Unpacking libc6-dev:arm64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.37-0ubuntu2_arm64.deb ... Unpacking libc-dev-bin (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libcrypt1_1%3a4.4.33-2_arm64.deb ... Unpacking libcrypt1:arm64 (1:4.4.33-2) over (1:4.4.33-1) ... Setting up libcrypt1:arm64 (1:4.4.33-2) ... (Reading database ... 13115 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.3.0-4.4_arm64.deb ... Unpacking linux-libc-dev:arm64 (6.3.0-4.4) over (5.19.0-21.21) ... Preparing to unpack .../libc6_2.37-0ubuntu2_arm64.deb ... Unpacking libc6:arm64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Setting up libc6:arm64 (2.37-0ubuntu2) ... (Reading database ... 13117 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:arm64 (2.40-2ubuntu6) ... Setting up libgcc-12-dev:arm64 (12.3.0-1ubuntu1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-2) ... Setting up libsystemd-shared:arm64 (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:arm64 (2.37-0ubuntu2) ... Setting up gpg (2.2.40-1.1ubuntu1) ... Setting up gpg-agent (2.2.40-1.1ubuntu1) ... Setting up libstdc++-12-dev:arm64 (12.3.0-1ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.40-2ubuntu6) ... 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-26218146 arm64 mantic-proposed -c chroot:build-PACKAGEBUILD-26218146 --arch=arm64 --dist=mantic-proposed --nolog kleborate_2.3.1-2.dsc Initiating build PACKAGEBUILD-26218146 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:52:10 UTC 2023 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-003.buildd +==============================================================================+ | kleborate 2.3.1-2 (arm64) Thu, 25 May 2023 17:15:34 +0000 | +==============================================================================+ Package: kleborate Version: 2.3.1-2 Source Version: 2.3.1-2 Distribution: mantic-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26218146/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/kleborate-tcYf32/resolver-aJgzKm' 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-tcYf32/kleborate-2.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/kleborate-tcYf32' 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 [488 B] Fetched 1864 B in 0s (49.5 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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70.7 MB in 4s (17.9 MB/s) Selecting previously unselected package libpython3.11-minimal:arm64. 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Setting up libmurmurhash2:arm64 (1.5-3) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.76.2-1ubuntu1) ... No schema files found: doing nothing. Setting up libpython3.11-stdlib:arm64 (3.11.3-1) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:arm64 (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:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.15-1) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:arm64 (2.7.1+dfsg-4) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... Setting up libpcre3:arm64 (2:8.39-15) ... Setting up libfontenc1:arm64 (1:1.1.4-1build3) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libfreetype6:arm64 (2.12.1+dfsg-5) ... Setting up libmbedcrypto7:arm64 (2.28.3-1) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up libfribidi0:arm64 (1.0.8-2.1ubuntu1) ... Setting up libimagequant0:arm64 (2.17.0-1) ... Setting up autopoint (0.21-12) ... Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... Setting up libgfortran5:arm64 (13.1.0-2ubuntu2) ... Setting up libcapnp-0.9.2:arm64 (0.9.2-2) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.2.4-0.2) ... Setting up libuchardet0:arm64 (0.0.7-1build2) ... Setting up libopenjp2-7:arm64 (2.5.0-1build1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3build1) ... Setting up sgml-base (1.31) ... Setting up libwebpmux3:arm64 (1.2.4-0.2) ... Setting up libbsd0:arm64 (0.11.7-4) ... Setting up mailcap (3.70+nmu1ubuntu1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up libpython3-stdlib:arm64 (3.11.2-1) ... Setting up libjpeg8:arm64 (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:arm64 (0.188-2.1) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up mime-support (3.66) ... Setting up libmbedx509-1:arm64 (2.28.3-1) ... Setting up libmbedtls14:arm64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up libwebpdemux2:arm64 (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:arm64 (0.10.1-1) ... Setting up python3-reportlab-accel:arm64 (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:arm64 (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:arm64 (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:arm64 (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 (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:52:10 UTC 2023 arm64 (aarch64) 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-aarch64-linux-gnu_2.40-2ubuntu6 binutils-common_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 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.22ubuntu1 libdw1_0.188-2.1 libelf1_0.188-2.1 libexpat1_2.5.0-1 libext2fs2_1.47.0-1ubuntu1 libfakeroot_1.31-1.2 libfdisk1_2.38.1-5ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libfontenc1_1:1.1.4-1build3 libfreetype6_2.12.1+dfsg-5 libfribidi0_1.0.8-2.1ubuntu1 libgcc-12-dev_12.3.0-1ubuntu1 libgcc-s1_13.1.0-2ubuntu2 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13.1.0-2ubuntu2 libglib2.0-0_2.76.2-1ubuntu1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.9-2ubuntu1 libgomp1_13.1.0-2ubuntu2 libgpg-error0_1.46-1 libgprofng0_2.40-2ubuntu6 libgraphite2-3_1.3.14-1build2 libgsl27_2.7.1+dfsg-4 libgslcblas0_2.7.1+dfsg-4 libgssapi-krb5-2_1.20.1-2 libharfbuzz0b_6.0.0+dfsg-3build1 libhogweed6_3.8.1-2 libhwasan0_13.1.0-2ubuntu2 libicu72_72.1-3ubuntu2 libidn2-0_2.3.3-1build1 libimagequant0_2.17.0-1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libitm1_13.1.0-2ubuntu2 libjansson4_2.14-2 libjbig0_2.1-6.1ubuntu1 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjson-c5_0.16-2 libk5crypto3_1.20.1-2 libkeyutils1_1.6.3-2 libkmod2_30+20221128-1ubuntu1 libkrb5-3_1.20.1-2 libkrb5support0_1.20.1-2 liblapack3_3.11.0-2 liblcms2-2_2.14-2 liblerc4_4.0.0+ds-2ubuntu2 liblmdb0_0.9.24-1build2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_13.1.0-2ubuntu2 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmbedcrypto7_2.28.3-1 libmbedtls14_2.28.3-1 libmbedx509-1_2.28.3-1 libmd0_1.0.4-2 libmount1_2.38.1-5ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libmurmurhash2_1.5-3 libncurses6_6.4-4 libncursesw6_6.4-4 libnettle8_3.8.1-2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libopenjp2-7_2.5.0-1build1 libp11-kit0_0.24.1-2ubuntu1 libpam-modules_1.5.2-6ubuntu1 libpam-modules-bin_1.5.2-6ubuntu1 libpam-runtime_1.5.2-6ubuntu1 libpam0g_1.5.2-6ubuntu1 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 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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-26218146 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26218146 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26218146 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 arm64 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-arm64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:275: python3.11 setup.py config running config dh_auto_build -a -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/help_formatter.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/blastn.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/mlstBLAST.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/rmpA.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/species.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/truncation.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/misc.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/resBLAST.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/kaptive.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/shv_mutations.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__main__.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__init__.py -> /<>/.pybuild/cpython3_3.11/build/kleborate copying kleborate/version.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 -a -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 137.179s OK {'Sul_acquired': 'sul2^', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': '-', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base: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/help_formatter.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/blastn.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/mlstBLAST.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/rmpA.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/species.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/truncation.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/misc.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/resBLAST.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/Klebsiella_pneumoniae.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/QRDR_120.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/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 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/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/iro_alleles.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ybt_alleles.fasta -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/iuc_alleles.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/OmpK.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/CARD_AMR_clustered.csv -> /<>/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/rmpA2.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/MgrB_and_PmrB.fasta -> /<>/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/ICEKp5.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp6.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp7.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp19.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp13.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp10.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp15.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp8.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp1.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp16.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp2.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp9.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp21.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp3.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp20.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp17.gff -> /<>/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/ICEKp14.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp22.gff -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /<>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp4.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/ICEKp11.embl -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references 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/kaptive.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/shv_mutations.py -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /<>/.pybuild/cpython3_3.11/build/kleborate/__main__.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/version.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 creating /<>/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__/species.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__/shv_mutations.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__/version.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/kaptive.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/misc.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/rmpA.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/blastn.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__/resBLAST.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/contig_stats.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /<>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/__init__.cpython-311.pyc -> /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ 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/blastn.py to blastn.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/mlstBLAST.py to mlstBLAST.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/rmpA.py to rmpA.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/truncation.py to truncation.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/misc.py to misc.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/resBLAST.py to resBLAST.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/kaptive.py to kaptive.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/shv_mutations.py to shv_mutations.cpython-311.pyc byte-compiling /<>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__main__.py to __main__.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/version.py to version.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 -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian -name "*.msh" -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 153 pkgstriptranslations: processing kleborate (in debian/kleborate); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/kleborate/DEBIAN/control, package kleborate, directory debian/kleborate pkgstripfiles: Truncating usr/share/doc/kleborate/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package kleborate ... pkgstripfiles: No PNG files. dpkg-deb: building package 'kleborate' in '../kleborate_2.3.1-2_arm64.deb'. dpkg-genbuildinfo --build=any -O../kleborate_2.3.1-2_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../kleborate_2.3.1-2_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-05-25T17:21:57Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kleborate_2.3.1-2_arm64.changes: -------------------------------- Format: 1.8 Date: Thu, 25 May 2023 14:48:18 +0200 Source: kleborate Binary: kleborate Built-For-Profiles: noudeb Architecture: arm64 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 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: adaa139dbf876404e8c893a974ea7cbd0e7f5780 7600 kleborate_2.3.1-2_arm64.buildinfo 29cba78b466ccc28ff1b80722630eb18e7351724 8740304 kleborate_2.3.1-2_arm64.deb Checksums-Sha256: c20c4cdd6b98794749301365b472a009b380671e88cdfdfe160f00660f2b7c06 7600 kleborate_2.3.1-2_arm64.buildinfo f6e1a77c334f33ef0104db56b7d111f47393d1d0b2471aa120126dda4226d4ac 8740304 kleborate_2.3.1-2_arm64.deb Files: 67d311f279f44f309de1a81d7f26879a 7600 science optional kleborate_2.3.1-2_arm64.buildinfo 2ae27a244c8266727561d6e166365823 8740304 science optional kleborate_2.3.1-2_arm64.deb /<>/kleborate_2.3.1-2_arm64.changes.new could not be renamed to /<>/kleborate_2.3.1-2_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: kleborate Binary: kleborate Architecture: arm64 Version: 2.3.1-2 Checksums-Md5: 2ae27a244c8266727561d6e166365823 8740304 kleborate_2.3.1-2_arm64.deb Checksums-Sha1: 29cba78b466ccc28ff1b80722630eb18e7351724 8740304 kleborate_2.3.1-2_arm64.deb Checksums-Sha256: f6e1a77c334f33ef0104db56b7d111f47393d1d0b2471aa120126dda4226d4ac 8740304 kleborate_2.3.1-2_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Thu, 25 May 2023 17:21:56 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-12), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu3), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.40-2ubuntu6), binutils-aarch64-linux-gnu (= 2.40-2ubuntu6), binutils-common (= 2.40-2ubuntu6), bsdextrautils (= 2.38.1-5ubuntu1), bsdutils (= 1:2.38.1-5ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), 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), 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), grep (= 3.8-5), groff-base (= 1.22.4-10), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), kaptive (= 2.0.4-1), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.1.0-2ubuntu2), 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), 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), libdpkg-perl (= 1.21.22ubuntu1), libdw1 (= 0.188-2.1), libelf1 (= 0.188-2.1), libexpat1 (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontenc1 (= 1:1.1.4-1build3), libfreetype6 (= 2.12.1+dfsg-5), libfribidi0 (= 1.0.8-2.1ubuntu1), libgcc-12-dev (= 12.3.0-1ubuntu1), libgcc-s1 (= 13.1.0-2ubuntu2), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 13.1.0-2ubuntu2), libglib2.0-0 (= 2.76.2-1ubuntu1), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgomp1 (= 13.1.0-2ubuntu2), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.40-2ubuntu6), libgraphite2-3 (= 1.3.14-1build2), libgsl27 (= 2.7.1+dfsg-4), libgslcblas0 (= 2.7.1+dfsg-4), libgssapi-krb5-2 (= 1.20.1-2), libharfbuzz0b (= 6.0.0+dfsg-3build1), libhwasan0 (= 13.1.0-2ubuntu2), libicu72 (= 72.1-3ubuntu2), libimagequant0 (= 2.17.0-1), libisl23 (= 0.25-1), libitm1 (= 13.1.0-2ubuntu2), libjansson4 (= 2.14-2), libjbig0 (= 2.1-6.1ubuntu1), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libk5crypto3 (= 1.20.1-2), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-2), libkrb5support0 (= 1.20.1-2), liblapack3 (= 3.11.0-2), liblcms2-2 (= 2.14-2), liblerc4 (= 4.0.0+ds-2ubuntu2), liblmdb0 (= 0.9.24-1build2), liblsan0 (= 13.1.0-2ubuntu2), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmbedcrypto7 (= 2.28.3-1), libmbedtls14 (= 2.28.3-1), libmbedx509-1 (= 2.28.3-1), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-5ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libmurmurhash2 (= 1.5-3), libncursesw6 (= 6.4-4), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libopenjp2-7 (= 2.5.0-1build1), libpam-modules (= 1.5.2-6ubuntu1), libpam-modules-bin (= 1.5.2-6ubuntu1), libpam-runtime (= 1.5.2-6ubuntu1), libpam0g (= 1.5.2-6ubuntu1), libpcre2-8-0 (= 10.42-1), libpcre3 (= 2:8.39-15), libperl5.36 (= 5.36.0-7), libpipeline1 (= 1.5.7-1), libpng16-16 (= 1.6.39-2), libpython3-stdlib (= 3.11.2-1), libpython3.11-minimal (= 3.11.3-1), libpython3.11-stdlib (= 3.11.3-1), libraqm0 (= 0.10.1-1), libreadline8 (= 8.2-1.3), libseccomp2 (= 2.5.4-1ubuntu3), libselinux1 (= 3.4-1build4), libsmartcols1 (= 2.38.1-5ubuntu1), libsqlite3-0 (= 3.40.1-2), libssl3 (= 3.0.8-1ubuntu2), libstdc++-12-dev (= 12.3.0-1ubuntu1), libstdc++6 (= 13.1.0-2ubuntu2), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.5-2ubuntu3), libtiff6 (= 4.5.0-6ubuntu1), libtinfo6 (= 6.4-4), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan2 (= 13.1.0-2ubuntu2), libubsan1 (= 13.1.0-2ubuntu2), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.5-2ubuntu3), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-5ubuntu1), 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_2.3.1-2_arm64.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: arm64 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/ 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+------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 365576 Build-Time: 212 Distribution: mantic-proposed Host Architecture: arm64 Install-Time: 164 Job: kleborate_2.3.1-2.dsc Machine Architecture: arm64 Package: kleborate Package-Time: 383 Source-Version: 2.3.1-2 Space: 365576 Status: successful Version: 2.3.1-2 -------------------------------------------------------------------------------- Finished at 2023-05-25T17:21:57Z Build needed 00:06:23, 365576k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26218146 Scanning for processes to kill in build PACKAGEBUILD-26218146