I: pbuilder: network access will be disabled during build I: Current time: Fri Jul 5 13:58:35 +14 2024 I: pbuilder-time-stamp: 1720137515 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [kleborate_2.3.1-2.dsc] I: copying [./kleborate_2.3.1.orig.tar.gz] I: copying [./kleborate_2.3.1-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri May 26 03:36:00 2023 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kleborate_2.3.1-2.dsc: no acceptable signature found dpkg-source: info: extracting kleborate in kleborate-2.3.1 dpkg-source: info: unpacking kleborate_2.3.1.orig.tar.gz dpkg-source: info: unpacking kleborate_2.3.1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3.patch dpkg-source: info: applying use_debian_installed_kaptive.patch dpkg-source: info: applying bigendian.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5082/tmp/hooks/D01_modify_environment starting debug: Running on codethink11-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jul 5 13:58 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/5082/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/5082/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=5082 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.5hDObzcR/pbuilderrc_A7z4 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5hDObzcR/b2 --logfile b2/build.log --extrapackages usrmerge kleborate_2.3.1-2.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 2 2023 /bin -> usr/bin I: user script /srv/workspace/pbuilder/5082/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, ncbi-blast+, mash, kaptive dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19611 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on mash; however: Package mash is not installed. pbuilder-satisfydepends-dummy depends on kaptive; however: Package kaptive is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} kaptive{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcapnp-0.9.2{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgsl27{a} libgslcblas0{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblcms2-2{a} liblerc4{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmurmurhash2{a} libopenjp2-7{a} libpcre3{a} libpipeline1{a} libpng16-16{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} libreadline8{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} mash{a} media-types{a} mime-support{a} ncbi-blast+{a} ncbi-data{a} po-debconf{a} python3{a} python3-biopython{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx python-biopython-doc python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 70.2 MB of archives. After unpacking 279 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 mailcap all 3.70+nmu1 [32.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 mime-support all 3.66 [10.9 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 13 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-3 [131 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libfontenc1 arm64 1:1.1.4-1 [23.6 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-5 [369 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 python3-numpy arm64 1:1.24.2-1 [4751 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 python3-renderpm arm64 3.6.12-1+b1 [73.5 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 python3-reportlab-accel arm64 3.6.12-1+b1 [38.4 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libimagequant0 arm64 2.17.0-1 [31.3 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libopenjp2-7 arm64 2.5.0-2 [175 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libfribidi0 arm64 1.0.8-2.1 [64.9 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-2 [1310 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libraqm0 arm64 0.7.0-4.1 [10.4 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.2 [259 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-6 [300 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libwebpdemux2 arm64 1.2.4-0.2 [99.2 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libwebpmux3 arm64 1.2.4-0.2 [109 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 python3-pil arm64 9.4.0-1.1+b1 [452 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 python3-reportlab all 3.6.12-1 [564 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 python3-biopython arm64 1.80+dfsg-4+b1 [1580 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 liblmdb0 arm64 0.9.24-1 [43.7 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 libmbedcrypto7 arm64 2.28.3-1 [263 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libmbedx509-1 arm64 2.28.3-1 [127 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 libmbedtls14 arm64 2.28.3-1 [156 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libpcre3 arm64 2:8.39-15 [313 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 ncbi-blast+ arm64 2.12.0+ds-3+b1 [10.9 MB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 kaptive all 2.0.4-1 [23.9 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libcapnp-0.9.2 arm64 0.9.2-2 [1127 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libgslcblas0 arm64 2.7.1+dfsg-3+b1 [82.3 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libgsl27 arm64 2.7.1+dfsg-3+b1 [824 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 libmurmurhash2 arm64 1.5-3 [6112 B] Get: 100 http://deb.debian.org/debian bookworm/main arm64 mash arm64 2.3+dfsg-3+b1 [165 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Fetched 70.2 MB in 5s (14.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19611 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19927 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.70+nmu1_all.deb ... Unpacking mailcap (3.70+nmu1) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../5-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... 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Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:arm64 (2.7.1+dfsg-3+b1) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libjbig0:arm64 (2.1-6.1) ... Setting up libpcre3:arm64 (2:8.39-15) ... Setting up libfontenc1:arm64 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ... Setting up libmbedcrypto7:arm64 (2.28.3-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.8-2.1) ... Setting up libimagequant0:arm64 (2.17.0-1) ... Setting up libpng16-16:arm64 (1.6.39-2) ... Setting up autopoint (0.21-12) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up libcapnp-0.9.2:arm64 (0.9.2-2) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.2.4-0.2) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:arm64 (4.5.0-6) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libopenjp2-7:arm64 (2.5.0-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up sgml-base (1.31) ... Setting up libwebpmux3:arm64 (1.2.4-0.2) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up mailcap (3.70+nmu1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up mime-support (3.66) ... Setting up libmbedx509-1:arm64 (2.28.3-1) ... Setting up libmbedtls14:arm64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up libwebpdemux2:arm64 (1.2.4-0.2) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:arm64 (2.12.1+dfsg-5) ... Setting up mash (2.3+dfsg-3+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libraqm0:arm64 (0.7.0-4.1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up ncbi-blast+ (2.12.0+ds-3+b1) ... Setting up python3-pil:arm64 (9.4.0-1.1+b1) ... Setting up python3-reportlab-accel:arm64 (3.6.12-1+b1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up python3-renderpm:arm64 (3.6.12-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-numpy (1:1.24.2-1) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Setting up kaptive (2.0.4-1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/5082/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... I: user script /srv/workspace/pbuilder/5082/tmp/hooks/A99_set_merged_usr finished hostname: Temporary failure in name resolution I: Running cd /build/kleborate-2.3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../kleborate_2.3.1-2_source.changes dpkg-buildpackage: info: source package kleborate dpkg-buildpackage: info: source version 2.3.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/kleborate-2.3.1/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/blastn.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__main__.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/kaptive.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/version.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/truncation.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/species.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/shv_mutations.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/rmpA.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/resBLAST.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/mlstBLAST.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/misc.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/help_formatter.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/contig_stats.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate copying kleborate/__init__.py -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate running egg_info creating Kleborate.egg-info writing Kleborate.egg-info/PKG-INFO writing dependency_links to Kleborate.egg-info/dependency_links.txt writing entry points to Kleborate.egg-info/entry_points.txt writing requirements to Kleborate.egg-info/requires.txt writing top-level names to Kleborate.egg-info/top_level.txt writing manifest file 'Kleborate.egg-info/SOURCES.txt' reading manifest file 'Kleborate.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'kleborate/ICEKp_references' warning: no directories found matching 'kaptive/reference_database' warning: no directories found matching 'kaptive/sample_data' adding license file 'LICENSE' writing manifest file 'Kleborate.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'kleborate.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'kleborate.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'kleborate.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'kleborate.data.ICEKp_references' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data.ICEKp_references' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'kleborate.data.ICEKp_references' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'kleborate.data.ICEKp_references' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) creating /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/AbST_profiles.txt -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/CARD_AMR_clustered.csv -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/CARD_v3.1.13.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/CbST_profiles.txt -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/Klebsiella_pneumoniae.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/MgrB_and_PmrB.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/OmpK.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/QRDR_120.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/RmST_profiles.txt -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/SmST_profiles.txt -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/YbST_profiles.txt -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/clb_alleles.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/iro_alleles.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/iuc_alleles.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/kpneumoniae.txt -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/rmpA2.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/rmp_alleles.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/species_mash_sketches.msh -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/wzi.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/wzi.txt -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data copying kleborate/data/ybt_alleles.fasta -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data creating /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp1.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp10.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp11.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp12.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp13.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp14.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp15.gff -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp16.gff -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp17.gff -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp18.gff -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp19.gff -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp2.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp20.gff -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp21.gff -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp22.gff -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp3.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp4.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp5.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp6.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp7.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp8.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references copying kleborate/data/ICEKp_references/ICEKp9.embl -> /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references dh_auto_test -O--buildsystem=pybuild I: pybuild base:240: cd /build/kleborate-2.3.1/.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 177.780s OK {'Sul_acquired': 'sul2^', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': '-', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} {'Sul_acquired': '-', 'Tet_acquired': '-', 'Bla_acquired': '-', 'Bla_inhR_acquired': '-', 'Bla_ESBL_acquired': '-', 'Bla_ESBL_inhR_acquired': '-', 'Bla_Carb_acquired': '-', 'Bla_chr': 'OKP-B-6^', 'SHV_mutations': '-', 'Omp_mutations': 'OmpK35-0%;OmpK36-0%', 'Col_mutations': 'MgrB-0%;PmrB-0%', 'Flq_mutations': '-', 'truncated_resistance_hits': '-', 'spurious_resistance_hits': '-'} create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/kleborate-2.3.1/debian/tmp running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing Kleborate.egg-info/PKG-INFO writing dependency_links to Kleborate.egg-info/dependency_links.txt writing entry points to Kleborate.egg-info/entry_points.txt writing requirements to Kleborate.egg-info/requires.txt writing top-level names to Kleborate.egg-info/top_level.txt reading manifest file 'Kleborate.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'kleborate/ICEKp_references' warning: no directories found matching 'kaptive/reference_database' warning: no directories found matching 'kaptive/sample_data' adding license file 'LICENSE' writing manifest file 'Kleborate.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'kleborate.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'kleborate.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'kleborate.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'kleborate.data.ICEKp_references' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'kleborate.data.ICEKp_references' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'kleborate.data.ICEKp_references' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'kleborate.data.ICEKp_references' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running install_lib creating /build/kleborate-2.3.1/debian/tmp/usr creating /build/kleborate-2.3.1/debian/tmp/usr/lib creating /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11 creating /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages creating /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate creating /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/version.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/rmpA.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/shv_mutations.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/resBLAST.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/truncation.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/blastn.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/mlstBLAST.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/species.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/kaptive.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/help_formatter.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/__main__.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/misc.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/contig_stats.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__pycache__/__init__.cpython-311.pyc -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__pycache__ creating /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data creating /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp9.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp8.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp7.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp6.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp5.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp4.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp3.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp22.gff -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp21.gff -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp20.gff -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp2.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp19.gff -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp18.gff -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp17.gff -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp16.gff -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp15.gff -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp14.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp13.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp12.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp11.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp10.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ICEKp_references/ICEKp1.embl -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ICEKp_references copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/ybt_alleles.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/wzi.txt -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/wzi.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/species_mash_sketches.msh -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/rmp_alleles.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/rmpA2.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/kpneumoniae.txt -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/iuc_alleles.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/iro_alleles.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/clb_alleles.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/YbST_profiles.txt -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/SmST_profiles.txt -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/RmST_profiles.txt -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/QRDR_120.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/OmpK.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/MgrB_and_PmrB.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/Klebsiella_pneumoniae.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/CbST_profiles.txt -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/CARD_v3.1.13.fasta -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/CARD_AMR_clustered.csv -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/data/AbST_profiles.txt -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__init__.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/contig_stats.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/help_formatter.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/misc.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/mlstBLAST.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/resBLAST.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/rmpA.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/shv_mutations.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/species.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/truncation.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/version.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/kaptive.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/__main__.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate copying /build/kleborate-2.3.1/.pybuild/cpython3_3.11/build/kleborate/blastn.py -> /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__init__.py to __init__.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/contig_stats.py to contig_stats.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/help_formatter.py to help_formatter.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/misc.py to misc.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/mlstBLAST.py to mlstBLAST.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/resBLAST.py to resBLAST.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/rmpA.py to rmpA.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/shv_mutations.py to shv_mutations.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/species.py to species.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/truncation.py to truncation.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/version.py to version.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/kaptive.py to kaptive.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/__main__.py to __main__.cpython-311.pyc byte-compiling /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/blastn.py to blastn.cpython-311.pyc running install_egg_info Copying Kleborate.egg-info to /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/Kleborate-2.2.0.egg-info Skipping SOURCES.txt running install_scripts Installing kleborate script to /build/kleborate-2.3.1/debian/tmp/usr/bin Building BLAST databases with makeblastdb: makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/CARD_v3.1.13.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/clb_alleles.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/rmpA2.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/iro_alleles.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/iuc_alleles.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/rmp_alleles.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/wzi.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/ybt_alleles.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/MgrB_and_PmrB.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/kleborate/data/OmpK.fasta makeblastdb -dbtype nucl -in /build/kleborate-2.3.1/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 '/build/kleborate-2.3.1' 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 '/build/kleborate-2.3.1' 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 '/build/kleborate-2.3.1' dh_fixperms find debian -name "*.msh" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/kleborate-2.3.1' 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 dpkg-deb: building package 'kleborate' in '../kleborate_2.3.1-2_arm64.deb'. dpkg-deb: building package 'kleborate-examples' in '../kleborate-examples_2.3.1-2_all.deb'. dpkg-genbuildinfo --build=binary -O../kleborate_2.3.1-2_arm64.buildinfo dpkg-genchanges --build=binary -O../kleborate_2.3.1-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/5082/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/5082/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/5082 and its subdirectories I: Current time: Fri Jul 5 14:05:57 +14 2024 I: pbuilder-time-stamp: 1720137957