https://launchpad.net/ubuntu/+source/kleborate/2.3.2-1/+build/26436014
RUN: /usr/share/launchpad-buildd/bin/builder-prep 
Kernel version: Linux bos03-amd64-011 5.4.0-153-generic #170-Ubuntu SMP Fri Jun 16 13:43:31 UTC 2023 x86_64
Buildd toolchain package versions: launchpad-buildd_234~642~ubuntu20.04.1 python3-lpbuildd_234~642~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_0.1.36ubuntu1.1.
Syncing the system clock with the buildd NTP service...
20 Jul 05:11:11 ntpdate[2036]: adjust time server 10.211.37.1 offset 0.001035 sec
RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26436014 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3
Creating target for build PACKAGEBUILD-26436014
RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26436014
Starting target for build PACKAGEBUILD-26436014
RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26436014 '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-26436014
RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26436014
Updating target for build PACKAGEBUILD-26436014
Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB]
Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB]
Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB]
Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB]
Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 Packages [1406 kB]
Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [515 kB]
Get:7 http://ftpmaster.internal/ubuntu mantic/universe amd64 Packages [14.8 MB]
Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5957 kB]
Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 Packages [121 kB]
Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [40.3 kB]
Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 Packages [375 kB]
Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [142 kB]
Fetched 23.9 MB in 3s (8238 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
  g++-12 libstdc++-12-dev
Use 'sudo apt autoremove' to remove them.
The following NEW packages will be installed:
  cpp-13 g++-13 gcc-13 gcc-13-base libgcc-13-dev libhwasan0 libproc2-0
  libsframe1 libstdc++-13-dev systemd-dev
The following packages will be upgraded:
  adduser advancecomp apt base-files bash binutils binutils-common
  binutils-x86-64-linux-gnu bsdutils build-essential ca-certificates coreutils
  cpp cpp-12 dash debconf debianutils diffutils dpkg dpkg-dev e2fsprogs
  fakeroot findutils g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf
  gpgv grep hostname init init-system-helpers 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
  libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libfdisk1
  libgcc-12-dev libgcc-s1 libgcrypt20 libgmp10 libgnutls30 libgomp1
  libgprofng0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1
  libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmd0
  libmount1 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpam-modules
  libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36
  libpng16-16 libquadmath0 libreadline8 libseccomp2 libselinux1
  libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2
  libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6
  libtinfo6 libtsan2 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev
  logsave lsb-base lto-disabled-list mawk 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
147 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
Need to get 313 MB of archives.
After this operation, 638 MB of additional disk space will be used.
Get:1 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt-dev amd64 1:4.4.35-1 [112 kB]
Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6-dev amd64 2.37-0ubuntu2 [2092 kB]
Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-dev-bin amd64 2.37-0ubuntu2 [20.0 kB]
Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt1 amd64 1:4.4.35-1 [82.1 kB]
Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 linux-libc-dev amd64 6.3.0-7.7 [1544 kB]
Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6 amd64 2.37-0ubuntu2 [3179 kB]
Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-bin amd64 2.37-0ubuntu2 [669 kB]
Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-13-base amd64 13.1.0-8ubuntu1 [42.3 kB]
Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-s1 amd64 13.1.0-8ubuntu1 [62.5 kB]
Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 base-files amd64 13ubuntu1 [74.0 kB]
Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 debianutils amd64 5.8-1 [103 kB]
Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB]
Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdutils amd64 1:2.38.1-5ubuntu2 [91.5 kB]
Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB]
Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 liblzma5 amd64 5.4.1-0.2 [125 kB]
Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libzstd1 amd64 1.5.5+dfsg2-1ubuntu2 [295 kB]
Get:17 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgcrypt20 amd64 1.10.2-2ubuntu1 [531 kB]
Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++6 amd64 13.1.0-8ubuntu1 [772 kB]
Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB]
Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libapparmor1 amd64 3.0.8-1ubuntu4 [46.2 kB]
Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit-common all 1:3.1.1-1 [5426 B]
Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap-ng0 amd64 0.8.3-1build2 [15.3 kB]
Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit1 amd64 1:3.1.1-1 [46.1 kB]
Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libblkid1 amd64 2.38.1-5ubuntu2 [111 kB]
Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap2 amd64 1:2.66-4ubuntu1 [29.4 kB]
Get:26 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libip4tc2 amd64 1.8.9-2ubuntu1 [22.1 kB]
Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 libperl5.36 amd64 5.36.0-7ubuntu1 [4834 kB]
Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 perl amd64 5.36.0-7ubuntu1 [235 kB]
Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-base amd64 5.36.0-7ubuntu1 [1784 kB]
Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB]
Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [742 kB]
Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu4 [61.2 kB]
Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 debconf all 1.5.82 [125 kB]
Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libssl3 amd64 3.0.9-1ubuntu1 [1901 kB]
Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 libkmod2 amd64 30+20221128-1ubuntu1 [49.5 kB]
Get:36 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libpcre2-8-0 amd64 10.42-2 [229 kB]
Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libselinux1 amd64 3.5-1 [78.2 kB]
Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 libmount1 amd64 2.38.1-5ubuntu2 [121 kB]
Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam0g amd64 1.5.2-6ubuntu1 [65.9 kB]
Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 libseccomp2 amd64 2.5.4-1ubuntu3 [49.1 kB]
Get:41 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 systemd-sysv amd64 253.5-1ubuntu1 [11.5 kB]
Get:42 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 systemd amd64 253.5-1ubuntu1 [3071 kB]
Get:43 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libsystemd-shared amd64 253.5-1ubuntu1 [1870 kB]
Get:44 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 systemd-dev all 253.5-1ubuntu1 [78.5 kB]
Get:45 http://ftpmaster.internal/ubuntu mantic/main amd64 libargon2-1 amd64 0~20190702+dfsg-3 [20.3 kB]
Get:46 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libudev1 amd64 253.5-1ubuntu1 [159 kB]
Get:47 http://ftpmaster.internal/ubuntu mantic/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-2ubuntu1 [139 kB]
Get:48 http://ftpmaster.internal/ubuntu mantic/main amd64 libuuid1 amd64 2.38.1-5ubuntu2 [32.7 kB]
Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 libcryptsetup12 amd64 2:2.6.1-4ubuntu1 [243 kB]
Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 libfdisk1 amd64 2.38.1-5ubuntu2 [144 kB]
Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 libp11-kit0 amd64 0.24.1-2ubuntu1 [248 kB]
Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 mount amd64 2.38.1-5ubuntu2 [114 kB]
Get:53 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libsystemd0 amd64 253.5-1ubuntu1 [407 kB]
Get:54 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libapt-pkg6.0 amd64 2.7.2 [933 kB]
Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 tar amd64 1.34+dfsg-1.2ubuntu1 [293 kB]
Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg amd64 1.21.22ubuntu1 [1393 kB]
Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 dash amd64 0.5.12-2ubuntu1 [88.2 kB]
Get:58 http://ftpmaster.internal/ubuntu mantic/main amd64 diffutils amd64 1:3.8-4 [176 kB]
Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 findutils amd64 4.9.0-5 [299 kB]
Get:60 http://ftpmaster.internal/ubuntu mantic/main amd64 grep amd64 3.11-1 [161 kB]
Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 hostname amd64 3.23+nmu1ubuntu1 [11.0 kB]
Get:62 http://ftpmaster.internal/ubuntu mantic/main amd64 libncurses6 amd64 6.4+20230625-1 [112 kB]
Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 libncursesw6 amd64 6.4+20230625-1 [149 kB]
Get:64 http://ftpmaster.internal/ubuntu mantic/main amd64 libtinfo6 amd64 6.4+20230625-1 [107 kB]
Get:65 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-bin amd64 6.4+20230625-1 [185 kB]
Get:66 http://ftpmaster.internal/ubuntu mantic/main amd64 sed amd64 4.9-1 [193 kB]
Get:67 http://ftpmaster.internal/ubuntu mantic/main amd64 libsmartcols1 amd64 2.38.1-5ubuntu2 [59.5 kB]
Get:68 http://ftpmaster.internal/ubuntu mantic/main amd64 util-linux-extra amd64 2.38.1-5ubuntu2 [83.8 kB]
Get:69 http://ftpmaster.internal/ubuntu mantic/main amd64 util-linux amd64 2.38.1-5ubuntu2 [1075 kB]
Get:70 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 init-system-helpers all 1.65.2ubuntu1 [38.7 kB]
Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-base all 6.4+20230625-1 [24.1 kB]
Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 sysvinit-utils amd64 3.06-4ubuntu1 [33.0 kB]
Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 lsb-base all 11.6 [4606 B]
Get:74 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 adduser all 3.137ubuntu1 [101 kB]
Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgv amd64 2.2.40-1.1ubuntu1 [140 kB]
Get:76 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgmp10 amd64 2:6.2.1+dfsg1-1.1ubuntu2 [252 kB]
Get:77 http://ftpmaster.internal/ubuntu mantic/main amd64 libidn2-0 amd64 2.3.4-1 [108 kB]
Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 libtasn1-6 amd64 4.19.0-3 [44.5 kB]
Get:79 http://ftpmaster.internal/ubuntu mantic/main amd64 libgnutls30 amd64 3.7.9-2ubuntu1 [999 kB]
Get:80 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 apt amd64 2.7.2 [1357 kB]
Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules-bin amd64 1.5.2-6ubuntu1 [47.3 kB]
Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules amd64 1.5.2-6ubuntu1 [284 kB]
Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 logsave amd64 1.47.0-1ubuntu2 [21.8 kB]
Get:84 http://ftpmaster.internal/ubuntu mantic/main amd64 libext2fs2 amd64 1.47.0-1ubuntu2 [219 kB]
Get:85 http://ftpmaster.internal/ubuntu mantic/main amd64 e2fsprogs amd64 1.47.0-1ubuntu2 [598 kB]
Get:86 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 init amd64 1.65.2ubuntu1 [5508 B]
Get:87 http://ftpmaster.internal/ubuntu mantic/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB]
Get:88 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libdebconfclient0 amd64 0.270ubuntu1 [11.1 kB]
Get:89 http://ftpmaster.internal/ubuntu mantic/main amd64 libmd0 amd64 1.1.0-1 [26.9 kB]
Get:90 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB]
Get:91 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage-common all 3.5-1 [9890 B]
Get:92 http://ftpmaster.internal/ubuntu mantic/main amd64 libsepol2 amd64 3.5-1 [301 kB]
Get:93 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage2 amd64 3.5-1 [93.3 kB]
Get:94 http://ftpmaster.internal/ubuntu mantic/main amd64 usrmerge all 35ubuntu1 [58.2 kB]
Get:95 http://ftpmaster.internal/ubuntu mantic/main amd64 libcom-err2 amd64 1.47.0-1ubuntu2 [22.1 kB]
Get:96 http://ftpmaster.internal/ubuntu mantic/main amd64 libproc2-0 amd64 2:4.0.3-1ubuntu1 [55.9 kB]
Get:97 http://ftpmaster.internal/ubuntu mantic/main amd64 libss2 amd64 1.47.0-1ubuntu2 [16.8 kB]
Get:98 http://ftpmaster.internal/ubuntu mantic/main amd64 mawk amd64 1.3.4.20230525-1 [113 kB]
Get:99 http://ftpmaster.internal/ubuntu mantic/main amd64 procps amd64 2:4.0.3-1ubuntu1 [609 kB]
Get:100 http://ftpmaster.internal/ubuntu mantic/main amd64 sensible-utils all 0.0.20 [19.6 kB]
Get:101 http://ftpmaster.internal/ubuntu mantic/main amd64 openssl amd64 3.0.9-1ubuntu1 [1189 kB]
Get:102 http://ftpmaster.internal/ubuntu mantic/main amd64 ca-certificates all 20230311ubuntu1 [152 kB]
Get:103 http://ftpmaster.internal/ubuntu mantic/main amd64 libgssapi-krb5-2 amd64 1.20.1-2 [142 kB]
Get:104 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5-3 amd64 1.20.1-2 [346 kB]
Get:105 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5support0 amd64 1.20.1-2 [32.7 kB]
Get:106 http://ftpmaster.internal/ubuntu mantic/main amd64 libk5crypto3 amd64 1.20.1-2 [81.1 kB]
Get:107 http://ftpmaster.internal/ubuntu mantic/main amd64 readline-common all 8.2-1.3 [55.7 kB]
Get:108 http://ftpmaster.internal/ubuntu mantic/main amd64 libreadline8 amd64 8.2-1.3 [151 kB]
Get:109 http://ftpmaster.internal/ubuntu mantic/main amd64 libsqlite3-0 amd64 3.42.0-1 [668 kB]
Get:110 http://ftpmaster.internal/ubuntu mantic/main amd64 tzdata all 2023c-7ubuntu1 [272 kB]
Get:111 http://ftpmaster.internal/ubuntu mantic/main amd64 libpng16-16 amd64 1.6.40-1 [186 kB]
Get:112 http://ftpmaster.internal/ubuntu mantic/main amd64 xz-utils amd64 5.4.1-0.2 [270 kB]
Get:113 http://ftpmaster.internal/ubuntu mantic/main amd64 advancecomp amd64 2.5-1 [180 kB]
Get:114 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgprofng0 amd64 2.40.90.20230714-2ubuntu1 [848 kB]
Get:115 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libctf0 amd64 2.40.90.20230714-2ubuntu1 [94.1 kB]
Get:116 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libctf-nobfd0 amd64 2.40.90.20230714-2ubuntu1 [96.2 kB]
Get:117 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.40.90.20230714-2ubuntu1 [2477 kB]
Get:118 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libbinutils amd64 2.40.90.20230714-2ubuntu1 [562 kB]
Get:119 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 binutils amd64 2.40.90.20230714-2ubuntu1 [18.6 kB]
Get:120 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 binutils-common amd64 2.40.90.20230714-2ubuntu1 [253 kB]
Get:121 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libsframe1 amd64 2.40.90.20230714-2ubuntu1 [14.5 kB]
Get:122 http://ftpmaster.internal/ubuntu mantic/main amd64 libisl23 amd64 0.26-3 [741 kB]
Get:123 http://ftpmaster.internal/ubuntu mantic/main amd64 libmpfr6 amd64 4.2.0-1 [352 kB]
Get:124 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp-13 amd64 13.1.0-8ubuntu1 [60.2 MB]
Get:125 http://ftpmaster.internal/ubuntu mantic/main amd64 g++ amd64 4:13.1.0-4ubuntu2 [1122 B]
Get:126 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc amd64 4:13.1.0-4ubuntu2 [5162 B]
Get:127 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp amd64 4:13.1.0-4ubuntu2 [28.9 kB]
Get:128 http://ftpmaster.internal/ubuntu mantic/main amd64 libcc1-0 amd64 13.1.0-8ubuntu1 [48.0 kB]
Get:129 http://ftpmaster.internal/ubuntu mantic/main amd64 libgomp1 amd64 13.1.0-8ubuntu1 [142 kB]
Get:130 http://ftpmaster.internal/ubuntu mantic/main amd64 libitm1 amd64 13.1.0-8ubuntu1 [29.4 kB]
Get:131 http://ftpmaster.internal/ubuntu mantic/main amd64 libatomic1 amd64 13.1.0-8ubuntu1 [10.4 kB]
Get:132 http://ftpmaster.internal/ubuntu mantic/main amd64 libasan8 amd64 13.1.0-8ubuntu1 [2826 kB]
Get:133 http://ftpmaster.internal/ubuntu mantic/main amd64 liblsan0 amd64 13.1.0-8ubuntu1 [1203 kB]
Get:134 http://ftpmaster.internal/ubuntu mantic/universe amd64 g++-12 amd64 12.3.0-6ubuntu1 [12.1 MB]
Get:135 http://ftpmaster.internal/ubuntu mantic/universe amd64 gcc-12 amd64 12.3.0-6ubuntu1 [21.6 MB]
Get:136 http://ftpmaster.internal/ubuntu mantic/universe amd64 cpp-12 amd64 12.3.0-6ubuntu1 [10.7 MB]
Get:137 http://ftpmaster.internal/ubuntu mantic/main amd64 libubsan1 amd64 13.1.0-8ubuntu1 [1104 kB]
Get:138 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++-12-dev amd64 12.3.0-6ubuntu1 [2180 kB]
Get:139 http://ftpmaster.internal/ubuntu mantic/main amd64 libquadmath0 amd64 13.1.0-8ubuntu1 [153 kB]
Get:140 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-12-dev amd64 12.3.0-6ubuntu1 [2574 kB]
Get:141 http://ftpmaster.internal/ubuntu mantic/main amd64 libtsan2 amd64 13.1.0-8ubuntu1 [2595 kB]
Get:142 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12-base amd64 12.3.0-6ubuntu1 [43.0 kB]
Get:143 http://ftpmaster.internal/ubuntu mantic/main amd64 libhwasan0 amd64 13.1.0-8ubuntu1 [1262 kB]
Get:144 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-13-dev amd64 13.1.0-8ubuntu1 [2686 kB]
Get:145 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-13 amd64 13.1.0-8ubuntu1 [69.6 MB]
Get:146 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++-13-dev amd64 13.1.0-8ubuntu1 [2347 kB]
Get:147 http://ftpmaster.internal/ubuntu mantic/main amd64 g++-13 amd64 13.1.0-8ubuntu1 [65.2 MB]
Get:148 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg-dev all 1.21.22ubuntu1 [1118 kB]
Get:149 http://ftpmaster.internal/ubuntu mantic/main amd64 libdpkg-perl all 1.21.22ubuntu1 [247 kB]
Get:150 http://ftpmaster.internal/ubuntu mantic/main amd64 lto-disabled-list all 41 [12.4 kB]
Get:151 http://ftpmaster.internal/ubuntu mantic/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
Get:152 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libfakeroot amd64 1.32.1-1 [31.9 kB]
Get:153 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 fakeroot amd64 1.32.1-1 [60.1 kB]
Get:154 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg amd64 2.2.40-1.1ubuntu1 [523 kB]
Get:155 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgconf amd64 2.2.40-1.1ubuntu1 [96.3 kB]
Get:156 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg-agent amd64 2.2.40-1.1ubuntu1 [216 kB]
Get:157 http://ftpmaster.internal/ubuntu mantic/main amd64 pkgbinarymangler all 153 [16.3 kB]
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Local time is now:      Thu Jul 20 05:11:40 UTC 2023.
Universal Time is now:  Thu Jul 20 05:11:40 UTC 2023.
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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26436014 amd64 mantic-proposed -c chroot:build-PACKAGEBUILD-26436014 --arch=amd64 --dist=mantic-proposed --nolog -A kleborate_2.3.2-1.dsc
Initiating build PACKAGEBUILD-26436014 with 4 jobs across 4 processor cores.
Kernel reported to sbuild: 5.4.0-153-generic #170-Ubuntu SMP Fri Jun 16 13:43:31 UTC 2023 x86_64
sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-amd64-011.buildd

+==============================================================================+
| kleborate 2.3.2-1 (amd64)                    Thu, 20 Jul 2023 05:11:43 +0000 |
+==============================================================================+

Package: kleborate
Version: 2.3.2-1
Source Version: 2.3.2-1
Distribution: mantic-proposed
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: binary

I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26436014/chroot-autobuild' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/kleborate-WBUppw/resolver-vh7kNL' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

kleborate_2.3.2-1.dsc exists in .; copying to chroot
I: NOTICE: Log filtering will replace 'build/kleborate-WBUppw/kleborate-2.3.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kleborate-WBUppw' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| 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 '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
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Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [419 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [492 B]
Fetched 1868 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  g++-12 libstdc++-12-dev
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit
  dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig-config
  fonts-dejavu-core fonts-urw-base35 gettext gettext-base groff-base
  intltool-debian kaptive libarchive-zip-perl libblas3 libbrotli1 libbsd0
  libcairo2 libcapnp-0.9.2 libdebhelper-perl libdeflate0 libdw1 libelf1
  libexpat1 libfile-stripnondeterminism-perl libfontconfig1 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 libpixman-1-0 libpython3-stdlib libpython3.11-minimal
  libpython3.11-stdlib libraqm0 libsub-override-perl libtiff6 libtool
  libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 m4
  mailcap man-db mash media-types mime-support ncbi-blast+ ncbi-data
  po-debconf python3 python3-biopython python3-cairo python3-distutils
  python3-freetype python3-lib2to3 python3-minimal python3-numpy python3-pil
  python3-pkg-resources python3-reportlab python3-rlpycairo python3-setuptools
  python3.11 python3.11-minimal sgml-base ttf-bitstream-vera 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 fontconfig-config
  fonts-dejavu-core fonts-urw-base35 gettext gettext-base groff-base
  intltool-debian kaptive libarchive-zip-perl libblas3 libbrotli1 libbsd0
  libcairo2 libcapnp-0.9.2 libdebhelper-perl libdeflate0 libdw1 libelf1
  libexpat1 libfile-stripnondeterminism-perl libfontconfig1 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 libpixman-1-0 libpython3-stdlib libpython3.11-minimal
  libpython3.11-stdlib libraqm0 libsub-override-perl libtiff6 libtool
  libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 m4
  mailcap man-db mash media-types mime-support ncbi-blast+ ncbi-data
  po-debconf python3 python3-biopython python3-cairo python3-distutils
  python3-freetype python3-lib2to3 python3-minimal python3-numpy python3-pil
  python3-pkg-resources python3-reportlab python3-rlpycairo python3-setuptools
  python3.11 python3.11-minimal sbuild-build-depends-main-dummy sgml-base
  ttf-bitstream-vera w3c-sgml-lib x11-common xfonts-encodings xfonts-utils
  xml-core
0 upgraded, 114 newly installed, 0 to remove and 0 not upgraded.
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Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11-minimal amd64 3.11.4-1 [839 kB]
Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libexpat1 amd64 2.5.0-2 [85.2 kB]
Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 python3.11-minimal amd64 3.11.4-1 [2228 kB]
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Get:6 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 media-types all 10.1.0 [27.5 kB]
Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 mailcap all 3.70+nmu1ubuntu1 [23.8 kB]
Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 mime-support all 3.66 [3696 B]
Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11-stdlib amd64 3.11.4-1 [1908 kB]
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Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 sgml-base all 1.31 [11.4 kB]
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Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 libelf1 amd64 0.189-4 [56.3 kB]
Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libfribidi0 amd64 1.0.13-3 [26.1 kB]
Get:17 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libglib2.0-0 amd64 2.77.0-0ubuntu2 [1522 kB]
Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 libicu72 amd64 72.1-3ubuntu2 [10.8 MB]
Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 libxml2 amd64 2.9.14+dfsg-1.3 [764 kB]
Get:20 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-pkg-resources all 68.0.0-1 [167 kB]
Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdextrautils amd64 2.38.1-5ubuntu2 [71.0 kB]
Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic-mgc amd64 1:5.44-3 [293 kB]
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Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB]
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Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 m4 amd64 1.4.19-3 [243 kB]
Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 autoconf all 2.71-3 [339 kB]
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Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 dwz amd64 0.15-1 [112 kB]
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Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-distutils all 3.11.4-1 [131 kB]
Get:58 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 dh-python all 6.20230603 [107 kB]
Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 fonts-dejavu-core all 2.37-6 [1137 kB]
Get:60 http://ftpmaster.internal/ubuntu mantic/universe amd64 ttf-bitstream-vera all 1.10-8.2 [244 kB]
Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 libfontenc1 amd64 1:1.1.4-1build3 [14.7 kB]
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Get:79 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libharfbuzz0b amd64 8.0.1-1 [456 kB]
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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 libcairo2:amd64 (1.17.8-2) ...
Setting up python3-pil:amd64 (10.0.0-1) ...
Setting up python3-numpy (1:1.24.2-1) ...
Setting up python3-cairo:amd64 (1.24.0-1) ...
Setting up debhelper (13.11.4ubuntu3) ...
Setting up python3-rlpycairo (0.3.0-2) ...
Setting up python3-reportlab (4.0.4-9) ...
Processing triggers for libc-bin (2.37-0ubuntu2) ...
Processing triggers for systemd (253.5-1ubuntu1) ...
Processing triggers for sgml-base (1.31) ...
Setting up w3c-sgml-lib (1.3-3) ...
Setting up python3-biopython (1.81+dfsg-1) ...
Setting up kaptive (2.0.4-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in any all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 5.4.0-153-generic #170-Ubuntu SMP Fri Jun 16 13:43:31 UTC 2023 amd64 (x86_64)
Toolchain package versions: binutils_2.40.90.20230714-2ubuntu1 dpkg-dev_1.21.22ubuntu1 g++-12_12.3.0-6ubuntu1 g++-13_13.1.0-8ubuntu1 gcc-12_12.3.0-6ubuntu1 gcc-13_13.1.0-8ubuntu1 libc6-dev_2.37-0ubuntu2 libstdc++-12-dev_12.3.0-6ubuntu1 libstdc++-13-dev_13.1.0-8ubuntu1 libstdc++6_13.1.0-8ubuntu1 linux-libc-dev_6.3.0-7.7
Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.2 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40.90.20230714-2ubuntu1 binutils-common_2.40.90.20230714-2ubuntu1 binutils-x86-64-linux-gnu_2.40.90.20230714-2ubuntu1 bsdextrautils_2.38.1-5ubuntu2 bsdutils_1:2.38.1-5ubuntu2 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:13.1.0-4ubuntu2 cpp-12_12.3.0-6ubuntu1 cpp-13_13.1.0-8ubuntu1 dash_0.5.12-2ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.8-1 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_6.20230603 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_1.47.0-1ubuntu2 fakeroot_1.32.1-1 file_1:5.44-3 findutils_4.9.0-5 fontconfig-config_2.14.1-4ubuntu1 fonts-dejavu-core_2.37-6 fonts-urw-base35_20200910-7 g++_4:13.1.0-4ubuntu2 g++-12_12.3.0-6ubuntu1 g++-13_13.1.0-8ubuntu1 gcc_4:13.1.0-4ubuntu2 gcc-12_12.3.0-6ubuntu1 gcc-12-base_12.3.0-6ubuntu1 gcc-13_13.1.0-8ubuntu1 gcc-13-base_13.1.0-8ubuntu1 gettext_0.21-13 gettext-base_0.21-13 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_3.11-1 groff-base_1.23.0-2 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.65.2ubuntu1 init-system-helpers_1.65.2ubuntu1 intltool-debian_0.35.0+20060710.6 kaptive_2.0.4-1 libacl1_2.3.1-3 libapparmor1_3.0.8-1ubuntu4 libapt-pkg6.0_2.7.2 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libasan8_13.1.0-8ubuntu1 libassuan0_2.5.5-5 libatomic1_13.1.0-8ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.40.90.20230714-2ubuntu1 libblas3_3.11.0-2 libblkid1_2.38.1-5ubuntu2 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 libcairo2_1.17.8-2 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-4ubuntu1 libcapnp-0.9.2_0.9.2-3 libcc1-0_13.1.0-8ubuntu1 libcom-err2_1.47.0-1ubuntu2 libcrypt-dev_1:4.4.35-1 libcrypt1_1:4.4.35-1 libcryptsetup12_2:2.6.1-4ubuntu1 libctf-nobfd0_2.40.90.20230714-2ubuntu1 libctf0_2.40.90.20230714-2ubuntu1 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.270ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate0_1.15-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.21.22ubuntu1 libdw1_0.189-4 libelf1_0.189-4 libexpat1_2.5.0-2 libext2fs2_1.47.0-1ubuntu2 libfakeroot_1.32.1-1 libfdisk1_2.38.1-5ubuntu2 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libfontconfig1_2.14.1-4ubuntu1 libfontenc1_1:1.1.4-1build3 libfreetype6_2.13.0+dfsg-1 libfribidi0_1.0.13-3 libgcc-12-dev_12.3.0-6ubuntu1 libgcc-13-dev_13.1.0-8ubuntu1 libgcc-s1_13.1.0-8ubuntu1 libgcrypt20_1.10.2-2ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13.1.0-8ubuntu1 libglib2.0-0_2.77.0-0ubuntu2 libgmp10_2:6.2.1+dfsg1-1.1ubuntu2 libgnutls30_3.7.9-2ubuntu1 libgomp1_13.1.0-8ubuntu1 libgpg-error0_1.46-1 libgprofng0_2.40.90.20230714-2ubuntu1 libgraphite2-3_1.3.14-1build2 libgsl27_2.7.1+dfsg-5 libgslcblas0_2.7.1+dfsg-5 libgssapi-krb5-2_1.20.1-2 libharfbuzz0b_8.0.1-1 libhogweed6_3.8.1-2 libhwasan0_13.1.0-8ubuntu1 libicu72_72.1-3ubuntu2 libidn2-0_2.3.4-1 libimagequant0_2.17.0-1 libip4tc2_1.8.9-2ubuntu1 libisl23_0.26-3 libitm1_13.1.0-8ubuntu1 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_13.1.0-8ubuntu1 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_1.1.0-1 libmount1_2.38.1-5ubuntu2 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libmurmurhash2_1.5-3 libncurses6_6.4+20230625-1 libncursesw6_6.4+20230625-1 libnettle8_3.8.1-2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libopenjp2-7_2.5.0-2 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_10.42-2 libpcre3_2:8.39-15 libperl5.36_5.36.0-7ubuntu1 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpng16-16_1.6.40-1 libproc2-0_2:4.0.3-1ubuntu1 libprocps8_2:3.3.17-7ubuntu1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.4-1 libpython3.11-stdlib_3.11.4-1 libquadmath0_13.1.0-8ubuntu1 libraqm0_0.10.1-1 libreadline8_8.2-1.3 libseccomp2_2.5.4-1ubuntu3 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.40.90.20230714-2ubuntu1 libsmartcols1_2.38.1-5ubuntu2 libsqlite3-0_3.42.0-1 libss2_1.47.0-1ubuntu2 libssl3_3.0.9-1ubuntu1 libstdc++-12-dev_12.3.0-6ubuntu1 libstdc++-13-dev_13.1.0-8ubuntu1 libstdc++6_13.1.0-8ubuntu1 libsub-override-perl_0.09-4 libsystemd-shared_253.5-1ubuntu1 libsystemd0_253.5-1ubuntu1 libtasn1-6_4.19.0-3 libtiff6_4.5.0-6ubuntu1 libtinfo6_6.4+20230625-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-6 libtsan2_13.1.0-8ubuntu1 libubsan1_13.1.0-8ubuntu1 libuchardet0_0.0.7-1build2 libudev1_253.5-1ubuntu1 libunistring2_1.0-2 libuuid1_2.38.1-5ubuntu2 libwebp7_1.2.4-0.2 libwebpdemux2_1.2.4-0.2 libwebpmux3_1.2.4-0.2 libx11-6_2:1.8.6-1 libx11-data_2:1.8.6-1 libxau6_1:1.0.9-1build5 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.3-0ubuntu5 libxext6_2:1.3.4-1build1 libxml2_2.9.14+dfsg-1.3 libxrender1_1:0.9.10-1.1 libxxhash0_0.8.1-1 libzstd1_1.5.5+dfsg2-1ubuntu2 linux-libc-dev_6.3.0-7.7 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-1ubuntu2 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_1.3.4.20230525-1 media-types_10.1.0 mime-support_3.66 mount_2.38.1-5ubuntu2 ncbi-blast+_2.12.0+ds-3build1 ncbi-data_6.1.20170106+dfsg1-10 ncurses-base_6.4+20230625-1 ncurses-bin_6.4+20230625-1 openssl_3.0.9-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7ubuntu1 perl-base_5.36.0-7ubuntu1 perl-modules-5.36_5.36.0-7ubuntu1 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_3.11.4-5 python3-biopython_1.81+dfsg-1 python3-cairo_1.24.0-1 python3-distutils_3.11.4-1 python3-freetype_2.4.0-1 python3-lib2to3_3.11.4-1 python3-minimal_3.11.4-5 python3-numpy_1:1.24.2-1 python3-pil_10.0.0-1 python3-pkg-resources_68.0.0-1 python3-reportlab_4.0.4-9 python3-rlpycairo_0.3.0-2 python3-setuptools_68.0.0-1 python3.11_3.11.4-1 python3.11-minimal_3.11.4-1 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_0.0.20 sgml-base_1.31 systemd_253.5-1ubuntu1 systemd-dev_253.5-1ubuntu1 systemd-sysv_253.5-1ubuntu1 sysvinit-utils_3.06-4ubuntu1 tar_1.34+dfsg-1.2ubuntu1 ttf-bitstream-vera_1.10-8.2 tzdata_2023c-7ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.38.1-5ubuntu2 util-linux-extra_2.38.1-5ubuntu2 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: 2.3.2-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
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+ <!nocheck>, mash <!nocheck>, kaptive <!nocheck>
Package-List:
 kleborate deb science optional arch=any
 kleborate-examples deb science optional arch=all
Checksums-Sha1:
 9c5e25aeaf6b2b176a93b00166227be180d2e7d1 91569258 kleborate_2.3.2.orig.tar.gz
 42be28ec6de2accf612da54d2b1e322a9d5e1fc4 5996420 kleborate_2.3.2-1.debian.tar.xz
Checksums-Sha256:
 da7cb9a27ddba4e5440063e2d4a0c4a9f9e668a65ae9f019db126dc5b10d7002 91569258 kleborate_2.3.2.orig.tar.gz
 8634dc2a19e455e447dadd3f9ca7a1cdb580bfd58c640639b64c99a77fb02e50 5996420 kleborate_2.3.2-1.debian.tar.xz
Files:
 9772fb524841a8415e80ec9a95563562 91569258 kleborate_2.3.2.orig.tar.gz
 abbbe47c15159e1a3441977e3944a72e 5996420 kleborate_2.3.2-1.debian.tar.xz
Dgit: 28e362323f6114a0f21907c814384c377db2f165 debian archive/debian/2.3.2-1 https://git.dgit.debian.org/kleborate

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gpgv: Signature made Wed Jul 19 22:39:20 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_2.3.2-1.dsc: no acceptable signature found
dpkg-source: info: extracting kleborate in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking kleborate_2.3.2.orig.tar.gz
dpkg-source: info: unpacking kleborate_2.3.2-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying python3.patch
dpkg-source: info: applying use_debian_installed_kaptive.patch
dpkg-source: info: applying bigendian.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26436014
SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26436014
SCHROOT_COMMAND=env
SCHROOT_GID=2501
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=build-PACKAGEBUILD-26436014
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 <buildd@bos03-amd64-011.buildd> -b -rfakeroot
dpkg-buildpackage: info: source package kleborate
dpkg-buildpackage: info: source version 2.3.2-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --with python3 --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:275: python3.11 setup.py clean 
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --with python3 --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:275: python3.11 setup.py config 
running config
   dh_auto_build -O--buildsystem=pybuild
I: pybuild base:275: /usr/bin/python3 setup.py build 
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/misc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/blastn.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/contig_stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/help_formatter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/resBLAST.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/truncation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/kaptive.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/species.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/shv_mutations.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/mlstBLAST.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate
copying kleborate/rmpA.py -> /<<PKGBUILDDIR>>/.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:201: _Warning: Package 'kleborate.data' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'kleborate.data' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'kleborate.data' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'kleborate.data' to be distributed and are
        already explicitly excluding 'kleborate.data' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'kleborate.data.ICEKp_references' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'kleborate.data.ICEKp_references' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'kleborate.data.ICEKp_references' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'kleborate.data.ICEKp_references' to be distributed and are
        already explicitly excluding 'kleborate.data.ICEKp_references' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/AbST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/CARD_AMR_clustered.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/CARD_v3.1.13.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/CbST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/Klebsiella_pneumoniae.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/MgrB_and_PmrB.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/OmpK.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/QRDR_120.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/RmST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/SmST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/YbST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/clb_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/iro_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/iuc_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/kpneumoniae.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/rmpA2.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/rmp_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/species_mash_sketches.msh -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/wzi.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/wzi.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
copying kleborate/data/ybt_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp1.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp10.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp11.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp12.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp13.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp14.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp15.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp16.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp17.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp18.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp19.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp2.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp20.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp21.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp22.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp3.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp4.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp5.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp6.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp7.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp8.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp9.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references
   dh_auto_test -O--buildsystem=pybuild
I: pybuild base:275: cd /<<PKGBUILDDIR>>/.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 25.642s

OK
{'Sul_acquired': 'sul2^', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': '-', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'}
{'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'}
{'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'}
{'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'}
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=pybuild
   dh_prep -O--buildsystem=pybuild
   dh_auto_install -O--buildsystem=pybuild
I: pybuild base:275: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/tmp 
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running build
running build_py
running egg_info
writing Kleborate.egg-info/PKG-INFO
writing dependency_links to Kleborate.egg-info/dependency_links.txt
writing entry points to Kleborate.egg-info/entry_points.txt
writing requirements to Kleborate.egg-info/requires.txt
writing top-level names to Kleborate.egg-info/top_level.txt
reading manifest file 'Kleborate.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no directories found matching 'kleborate/ICEKp_references'
warning: no directories found matching 'kaptive/reference_database'
warning: no directories found matching 'kaptive/sample_data'
adding license file 'LICENSE'
writing manifest file 'Kleborate.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'kleborate.data' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'kleborate.data' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'kleborate.data' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'kleborate.data' to be distributed and are
        already explicitly excluding 'kleborate.data' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'kleborate.data.ICEKp_references' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'kleborate.data.ICEKp_references' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'kleborate.data.ICEKp_references' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'kleborate.data.ICEKp_references' to be distributed and are
        already explicitly excluding 'kleborate.data.ICEKp_references' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
running install_lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/misc.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/blastn.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/contig_stats.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/help_formatter.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/resBLAST.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/truncation.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/MgrB_and_PmrB.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/iuc_alleles.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/CARD_v3.1.13.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/rmpA2.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/CbST_profiles.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/QRDR_120.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/kpneumoniae.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/SmST_profiles.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/AbST_profiles.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/rmp_alleles.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/CARD_AMR_clustered.csv -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/wzi.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/RmST_profiles.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/species_mash_sketches.msh -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp20.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp11.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp22.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp18.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp15.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp19.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp3.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp2.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp7.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp4.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp5.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp13.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp8.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp10.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp9.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp1.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp17.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp12.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp14.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp16.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp6.embl -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp21.gff -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/ybt_alleles.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/iro_alleles.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/clb_alleles.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/Klebsiella_pneumoniae.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/OmpK.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/wzi.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/data/YbST_profiles.txt -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/kaptive.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__main__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/shv_mutations.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/__main__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/mlstBLAST.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/help_formatter.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/contig_stats.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/version.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/resBLAST.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/rmpA.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/misc.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/blastn.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/truncation.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/kaptive.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__pycache__/species.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/version.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/species.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/shv_mutations.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/mlstBLAST.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/kleborate/rmpA.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/misc.py to misc.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/blastn.py to blastn.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/contig_stats.py to contig_stats.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/help_formatter.py to help_formatter.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/resBLAST.py to resBLAST.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/truncation.py to truncation.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/kaptive.py to kaptive.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__main__.py to __main__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/version.py to version.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/species.py to species.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/shv_mutations.py to shv_mutations.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/mlstBLAST.py to mlstBLAST.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/rmpA.py to rmpA.cpython-311.pyc
running install_egg_info
Copying Kleborate.egg-info to /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/Kleborate-2.3.2.egg-info
Skipping SOURCES.txt
running install_scripts
Installing kleborate script to /<<PKGBUILDDIR>>/debian/tmp/usr/bin

Building BLAST databases with makeblastdb:
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/CARD_v3.1.13.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/clb_alleles.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/rmpA2.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/iro_alleles.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/iuc_alleles.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/rmp_alleles.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/wzi.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ybt_alleles.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/MgrB_and_PmrB.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/OmpK.fasta
  makeblastdb -dbtype nucl -in /<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
   dh_installdocs -O--buildsystem=pybuild
   dh_installchangelogs -O--buildsystem=pybuild
   dh_installman -O--buildsystem=pybuild
   dh_python3 -O--buildsystem=pybuild
   dh_installsystemduser -O--buildsystem=pybuild
   dh_perl -O--buildsystem=pybuild
   dh_link -O--buildsystem=pybuild
   dh_strip_nondeterminism -O--buildsystem=pybuild
   dh_compress -O--buildsystem=pybuild
   debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian -name "*.msh" -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_missing -O--buildsystem=pybuild
   dh_dwz -a -O--buildsystem=pybuild
   dh_strip -a -O--buildsystem=pybuild
   dh_makeshlibs -a -O--buildsystem=pybuild
   dh_shlibdeps -a -O--buildsystem=pybuild
   dh_installdeb -O--buildsystem=pybuild
   dh_gencontrol -O--buildsystem=pybuild
   dh_md5sums -O--buildsystem=pybuild
   dh_builddeb -O--buildsystem=pybuild
INFO: pkgstriptranslations version 153
INFO: pkgstriptranslations version 153
pkgstriptranslations: processing kleborate (in debian/kleborate); do_strip: , oemstrip: 
pkgstriptranslations: processing kleborate-examples (in debian/kleborate-examples); do_strip: , oemstrip: 
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
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.
pkgstripfiles: processing control file: debian/kleborate-examples/DEBIAN/control, package kleborate-examples, directory debian/kleborate-examples
dpkg-deb: building package 'kleborate' in '../kleborate_2.3.2-1_amd64.deb'.
pkgstripfiles: Truncating usr/share/doc/kleborate-examples/changelog.Debian.gz to topmost ten records
pkgstripfiles: Running PNG optimization (using 4 cpus) for package kleborate-examples ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'kleborate-examples' in '../kleborate-examples_2.3.2-1_all.deb'.
 dpkg-genbuildinfo --build=binary -O../kleborate_2.3.2-1_amd64.buildinfo
 dpkg-genchanges --build=binary -mLaunchpad Build Daemon <buildd@bos03-amd64-011.buildd> -O../kleborate_2.3.2-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-07-20T05:12:57Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


kleborate_2.3.2-1_amd64.changes:
--------------------------------

Format: 1.8
Date: Thu, 20 Jul 2023 00:23:19 +0200
Source: kleborate
Binary: kleborate kleborate-examples
Built-For-Profiles: noudeb
Architecture: all amd64
Version: 2.3.2-1
Distribution: mantic-proposed
Urgency: medium
Maintainer: Launchpad Build Daemon <buildd@bos03-amd64-011.buildd>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
 kleborate  - tool to screen Klebsiella genome assemblies
 kleborate-examples - tool to screen Klebsiella genome assemblies (example data)
Changes:
 kleborate (2.3.2-1) unstable; urgency=medium
 .
   * New upstream version
   * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
     Repository-Browse.
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Files:
 166ec478015ec5604d18f9b6f07b85cc 5989340 science optional kleborate-examples_2.3.2-1_all.deb
 beba2474d0722367d2abad1d65b68aba 8510 science optional kleborate_2.3.2-1_amd64.buildinfo
 f0cfab6b7c7a579a08d136704bde6454 8738346 science optional kleborate_2.3.2-1_amd64.deb
/<<BUILDDIR>>/kleborate_2.3.2-1_amd64.changes.new could not be renamed to /<<BUILDDIR>>/kleborate_2.3.2-1_amd64.changes: Illegal seek
Distribution field may be wrong!!!
+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: kleborate
Binary: kleborate kleborate-examples
Architecture: all amd64
Version: 2.3.2-1
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 0f5b3f84e6c06aedef6e10e67f8a38ae7e37138c7a2b610abb89746362fea889 8738346 kleborate_2.3.2-1_amd64.deb
Build-Origin: Ubuntu
Build-Architecture: amd64
Build-Date: Thu, 20 Jul 2023 05:12:57 +0000
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+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


kleborate-examples_2.3.2-1_all.deb
----------------------------------

 new Debian package, version 2.0.
 size 5989340 bytes: control archive=1064 bytes.
    1094 bytes,    27 lines      control              
     680 bytes,     8 lines      md5sums              
 Package: kleborate-examples
 Source: kleborate
 Version: 2.3.2-1
 Architecture: all
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5863
 Recommends: kleborate
 Section: science
 Priority: optional
 Multi-Arch: foreign
 Homepage: https://github.com/katholt/Kleborate
 Description: tool to screen Klebsiella genome assemblies (example data)
  Kleborate is a tool to screen Klebsiella genome assemblies for:
  .
   * MLST sequence type
   * species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
   * ICEKp associated virulence loci: yersiniabactin (ybt),
     colibactin (clb)
   * virulence plasmid associated loci: salmochelin (iro), aerobactin
     (iuc), hypermucoidy (rmpA, rmpA2)
   * antimicrobial resistance genes, including quinolone resistance SNPs
     and colistin resistance truncations
   * K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles
     and Kaptive
  .
  This package provides example data end tests that are used in autopkgtest.

drwxr-xr-x root/root         0 2023-07-19 22:23 ./
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/share/
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/share/doc/
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/share/doc/kleborate-examples/
-rw-r--r-- root/root      1243 2023-07-19 22:23 ./usr/share/doc/kleborate-examples/changelog.Debian.gz
-rw-r--r-- root/root      1146 2023-07-19 22:23 ./usr/share/doc/kleborate-examples/copyright
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/share/doc/kleborate/
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/share/doc/kleborate/examples/
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/share/doc/kleborate/examples/data/
-rw-r--r-- root/root   1529920 2023-07-19 22:23 ./usr/share/doc/kleborate/examples/data/Klebs_HS11286.fna.xz
-rw-r--r-- root/root   1455464 2023-07-19 22:23 ./usr/share/doc/kleborate/examples/data/Klebs_Kp1084.fna.xz
-rw-r--r-- root/root   1521788 2023-07-19 22:23 ./usr/share/doc/kleborate/examples/data/MGH78578.fna.xz
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-rw-r--r-- root/root       454 2023-07-19 22:23 ./usr/share/doc/kleborate/run-unit-test


kleborate_2.3.2-1_amd64.deb
---------------------------

 new Debian package, version 2.0.
 size 8738346 bytes: control archive=4269 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: 2.3.2-1
 Architecture: amd64
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 62140
 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 2023-07-19 22:23 ./
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/bin/
-rwxr-xr-x root/root       968 2023-07-19 22:23 ./usr/bin/kleborate
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/lib/
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/lib/python3/
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drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/lib/python3/dist-packages/Kleborate-2.3.2.egg-info/
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-rw-r--r-- root/root        54 2023-07-19 22:23 ./usr/lib/python3/dist-packages/Kleborate-2.3.2.egg-info/entry_points.txt
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-rw-r--r-- root/root        18 2023-07-19 22:23 ./usr/lib/python3/dist-packages/Kleborate-2.3.2.egg-info/top_level.txt
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-rw-r--r-- root/root         0 2023-03-07 02:48 ./usr/lib/python3/dist-packages/kleborate/__init__.py
-rw-r--r-- root/root     27543 2023-07-19 22:23 ./usr/lib/python3/dist-packages/kleborate/__main__.py
-rw-r--r-- root/root      5846 2023-07-19 22:23 ./usr/lib/python3/dist-packages/kleborate/blastn.py
-rw-r--r-- root/root      2916 2023-03-07 02:48 ./usr/lib/python3/dist-packages/kleborate/contig_stats.py
drwxr-xr-x root/root         0 2023-07-19 22:23 ./usr/lib/python3/dist-packages/kleborate/data/
-rw-r--r-- root/root      2034 2023-03-07 02:48 ./usr/lib/python3/dist-packages/kleborate/data/AbST_profiles.txt
-rw-r--r-- root/root    246517 2023-03-07 02:48 ./usr/lib/python3/dist-packages/kleborate/data/CARD_AMR_clustered.csv
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-rw-r--r-- root/root    607403 2023-07-19 22:23 ./usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.nsq
-rw-r--r-- root/root     10776 2023-07-19 22:23 ./usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.nto
-rw-r--r-- root/root      3178 2023-03-07 02:48 ./usr/lib/python3/dist-packages/kleborate/data/CbST_profiles.txt
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+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not removing build depends: as requested

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: binary
Build-Space: 377592
Build-Time: 41
Distribution: mantic-proposed
Host Architecture: amd64
Install-Time: 31
Job: kleborate_2.3.2-1.dsc
Machine Architecture: amd64
Package: kleborate
Package-Time: 74
Source-Version: 2.3.2-1
Space: 377592
Status: successful
Version: 2.3.2-1
--------------------------------------------------------------------------------
Finished at 2023-07-20T05:12:57Z
Build needed 00:01:14, 377592k disk space
RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26436014
Scanning for processes to kill in build PACKAGEBUILD-26436014