Raspbian Package Auto-Building

Build log for kleborate (2.1.0-2) on armhf

kleborate2.1.0-2armhf → 2021-12-03 01:04:33

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01

+==============================================================================+
| kleborate 2.1.0-2 (armhf)                    Fri, 03 Dec 2021 00:42:30 +0000 |
+==============================================================================+

Package: kleborate
Version: 2.1.0-2
Source Version: 2.1.0-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-071f0d84-de57-46fa-8469-4b6cb3f4a865' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.5 MB]
Fetched 26.1 MB in 12s (2219 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

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


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'kleborate' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/kleborate.git
Please use:
git clone https://salsa.debian.org/med-team/kleborate.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 97.3 MB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main kleborate 2.1.0-2 (dsc) [2206 B]
Get:2 http://172.17.4.1/private bookworm-staging/main kleborate 2.1.0-2 (tar) [91.3 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main kleborate 2.1.0-2 (diff) [5996 kB]
Fetched 97.3 MB in 28s (3480 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/kleborate-4j8Ka3/kleborate-2.1.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kleborate-4j8Ka3' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-asLCIA/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-asLCIA/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-asLCIA/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ Packages [429 B]
Fetched 2105 B in 0s (6397 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core 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:
  netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 9 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (42.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12559 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, ncbi-blast+, mash, kaptive
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, ncbi-blast+, mash, kaptive
dpkg-deb: building package 'sbuild-build-depends-kleborate-dummy' in '/<<BUILDDIR>>/resolver-asLCIA/apt_archive/sbuild-build-depends-kleborate-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-kleborate-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ Sources [545 B]
Get:5 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ Packages [613 B]
Fetched 2491 B in 0s (7072 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper
  dh-autoreconf dh-python dh-strip-nondeterminism dwz file fonts-urw-base35
  gettext gettext-base groff-base intltool-debian kaptive libarchive-zip-perl
  libblas3 libbrotli1 libbsd0 libcapnp-0.7.0 libdebhelper-perl libdeflate0
  libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libfribidi0
  libgfortran5 libglib2.0-0 libgraphite2-3 libgsl25 libgslcblas0 libharfbuzz0b
  libicu67 libimagequant0 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2
  liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0
  libmd0 libmpdec3 libmurmurhash2 libopenjp2-7 libpipeline1 libpng16-16
  libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libraqm0
  libsigsegv2 libsub-override-perl libtiff5 libtool libuchardet0 libwebp6
  libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap
  man-db mash media-types mime-support ncbi-blast+ ncbi-data po-debconf
  python3 python3-biopython python3-distutils python3-lib2to3 python3-minimal
  python3-numpy python3-pil python3-pkg-resources python3-renderpm
  python3-reportlab python3-reportlab-accel python3-setuptools python3.9
  python3.9-minimal
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make flit python3-toml
  fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc
  libasprintf-dev libgettextpo-dev groff kaptive-data kaptive-example
  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 muscle phylip phyml
  prank probcons python3-mysqldb python3-matplotlib python3-mmtf
  python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise
  w3-dtd-mathml gfortran python-numpy-doc python3-dev python3-pytest
  python-pil-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc
  python-setuptools-doc python3.9-venv python3.9-doc binfmt-support
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs ca-certificates libltdl-dev libmail-sendmail-perl
  python-biopython-doc python3-olefile
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper
  dh-autoreconf dh-python dh-strip-nondeterminism dwz file fonts-urw-base35
  gettext gettext-base groff-base intltool-debian kaptive libarchive-zip-perl
  libblas3 libbrotli1 libbsd0 libcapnp-0.7.0 libdebhelper-perl libdeflate0
  libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libfribidi0
  libgfortran5 libglib2.0-0 libgraphite2-3 libgsl25 libgslcblas0 libharfbuzz0b
  libicu67 libimagequant0 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2
  liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0
  libmd0 libmpdec3 libmurmurhash2 libopenjp2-7 libpipeline1 libpng16-16
  libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libraqm0
  libsigsegv2 libsub-override-perl libtiff5 libtool libuchardet0 libwebp6
  libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap
  man-db mash media-types mime-support ncbi-blast+ ncbi-data po-debconf
  python3 python3-biopython python3-distutils python3-lib2to3 python3-minimal
  python3-numpy python3-pil python3-pkg-resources python3-renderpm
  python3-reportlab python3-reportlab-accel python3-setuptools python3.9
  python3.9-minimal sbuild-build-depends-kleborate-dummy
0 upgraded, 93 newly installed, 0 to remove and 9 not upgraded.
Need to get 58.0 MB of archives.
After this operation, 228 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-asLCIA/apt_archive ./ sbuild-build-depends-kleborate-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.9-1+rpi1 [795 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-3 [80.1 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.9-1+rpi1 [1582 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.7-1 [38.4 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf mailcap all 3.70 [31.8 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.9-1+rpi1 [1609 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf python3.9 armhf 3.9.9-1+rpi1 [484 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.7-1 [21.6 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.9.7-1 [38.0 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.1-1 [26.5 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.1-1 [15.6 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.9-2 [79.5 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.9.9-2 [146 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20211114 [104 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf fonts-urw-base35 all 20200910-1 [6367 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 58.2.0-1 [192 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.0-1 [108 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-10+rpi1 [234 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.0-1 [1594 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf python3-numpy armhf 1:1.21.4-2 [3438 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.11.0+dfsg-1 [386 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf python3-renderpm armhf 3.6.2-1 [68.4 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf python3-reportlab-accel armhf 3.6.2-1 [38.4 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libimagequant0 armhf 2.12.2-1.1 [27.2 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.12~rc1-2 [121 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libopenjp2-7 armhf 2.4.0-3 [150 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.1-1 [1210 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libraqm0 armhf 0.7.0-4 [9388 B]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libwebp6 armhf 0.6.1-2.1 [225 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.3.0-2 [272 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libwebpdemux2 armhf 0.6.1-2.1 [86.8 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libwebpmux3 armhf 0.6.1-2.1 [94.4 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf python3-pil armhf 8.4.0-1 [419 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf python3-reportlab all 3.6.2-1 [562 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf python3-biopython armhf 1.79+dfsg-1 [1400 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf liblmdb0 armhf 0.9.24-1 [38.7 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libmbedcrypto3 armhf 2.16.11-0.3 [199 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libmbedx509-0 armhf 2.16.11-0.3 [107 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libmbedtls12 armhf 2.16.11-0.3 [134 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf ncbi-blast+ armhf 2.11.0+ds-1 [9360 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf kaptive all 0.7.3-4 [32.8 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libcapnp-0.7.0 armhf 0.7.0-7 [909 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libgslcblas0 armhf 2.6+dfsg-2 [79.5 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libgsl25 armhf 2.6+dfsg-2 [753 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libmurmurhash2 armhf 1.5-3 [5976 B]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf mash armhf 2.2.2+dfsg-1+b1 [123 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 58.2.0-1 [396 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 58.0 MB in 14s (4093 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12559 files and directories currently installed.)
Preparing to unpack .../0-bsdextrautils_2.37.2-4_armhf.deb ...
Unpacking bsdextrautils (2.37.2-4) ...
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Setting up python3-renderpm:armhf (3.6.2-1) ...
Setting up python3-setuptools (58.2.0-1) ...
Setting up debhelper (13.5.2) ...
Setting up python3-pil:armhf (8.4.0-1) ...
Setting up python3-numpy (1:1.21.4-2) ...
Setting up python3-reportlab (3.6.2-1) ...
Setting up python3-biopython (1.79+dfsg-1) ...
Setting up kaptive (0.7.3-4) ...
Setting up sbuild-build-depends-kleborate-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-11_11.2.0-10+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.12 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3.1 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-python_5.20211114 dh-strip-nondeterminism_1.12.1-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.41-2 findutils_4.8.0-1 fonts-urw-base35_20200910-1 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-10+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 kaptive_0.7.3-4 libacl1_2.3.1-1 libapt-pkg6.0_2.3.12 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-5+rpi1 libblas3_3.10.0-1 libblkid1_2.37.2-4 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcapnp-0.7.0_0.7.0-7 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.5.2 libdeflate0_1.8-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.186-1 libexpat1_2.4.1-3 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.1-1 libfreetype6_2.11.0+dfsg-1 libfribidi0_1.0.8-2 libgcc-11-dev_11.2.0-10+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgfortran5_11.2.0-10+rpi1 libglib2.0-0_2.70.1-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgraphite2-3_1.3.14-1 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libgssapi-krb5-2_1.18.3-7 libharfbuzz0b_2.7.4-1 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libimagequant0_2.12.2-1.1 libisl23_0.24-2 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:2.1.2-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack3_3.10.0-1 liblcms2-2_2.12~rc1-2 libldap-2.4-2_2.4.59+dfsg-1 liblmdb0_0.9.24-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmbedcrypto3_2.16.11-0.3 libmbedtls12_2.16.11-0.3 libmbedx509-0_2.16.11-0.3 libmd0_1.0.4-1 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libmurmurhash2_1.5-3 libncursesw6_6.3-1 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopenjp2-7_2.4.0-3 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libpng16-16_1.6.37-3 libpython3-stdlib_3.9.7-1 libpython3.9-minimal_3.9.9-1+rpi1 libpython3.9-stdlib_3.9.9-1+rpi1 libraqm0_0.7.0-4 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg2-2 libsasl2-modules-db_2.1.27+dfsg2-2 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.7-1+rpi1 libtasn1-6_4.18.0-4 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtiff5_4.3.0-2 libtinfo6_6.3-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.7-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libwebp6_0.6.1-2.1 libwebpdemux2_0.6.1-2.1 libwebpmux3_0.6.1-2.1 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.16-1+rpi1 login_1:4.8.1-2 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 mailcap_3.70 make_4.3-4.1 man-db_2.9.4-2 mash_2.2.2+dfsg-1+b1 mawk_1.3.4.20200120-2 media-types_4.0.0 mime-support_3.66 mount_2.37.2-4 ncbi-blast+_2.11.0+ds-1 ncbi-data_6.1.20170106+dfsg1-9 ncurses-base_6.3-1 ncurses-bin_6.3-1 netbase_6.3 passwd_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.7-1 python3-biopython_1.79+dfsg-1 python3-distutils_3.9.9-2 python3-lib2to3_3.9.9-2 python3-minimal_3.9.7-1 python3-numpy_1:1.21.4-2 python3-pil_8.4.0-1 python3-pkg-resources_58.2.0-1 python3-renderpm_3.6.2-1 python3-reportlab_3.6.2-1 python3-reportlab-accel_3.6.2-1 python3-setuptools_58.2.0-1 python3.9_3.9.9-1+rpi1 python3.9-minimal_3.9.9-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-kleborate-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2

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


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.SoFmytHF/trustedkeys.kbx': General error
gpgv: Signature made Wed Sep 22 17:24:46 2021 UTC
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./kleborate_2.1.0-2.dsc
dpkg-source: info: extracting kleborate in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking kleborate_2.1.0.orig.tar.gz
dpkg-source: info: unpacking kleborate_2.1.0-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying python3.patch
dpkg-source: info: applying use_debian_installed_kaptive.patch
dpkg-source: info: applying bigendian.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-071f0d84-de57-46fa-8469-4b6cb3f4a865
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package kleborate
dpkg-buildpackage: info: source version 2.1.0-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean --with python3 --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:237: python3.9 setup.py clean 
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.9' does not exist -- can't clean it
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:237: python3.9 setup.py config 
running config
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:237: /usr/bin/python3 setup.py build 
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/contig_stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/help_formatter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/misc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/mlstBLAST.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/resBLAST.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/rmpA.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/shv_mutations.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/species.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/truncation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/kaptive.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
copying kleborate/blastn.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate
package init file 'kaptive/__init__.py' not found (or not a regular file)
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'
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/AbST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/CARD_AMR_clustered.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/CARD_v3.0.8.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/CbST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/Klebsiella_pneumoniae.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/MgrB_and_PmrB.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/OmpK.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/QRDR_120.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/RmST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/SmST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/YbST_profiles.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/clb_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/iro_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/iuc_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/kpneumoniae.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/rmpA2.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/rmp_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/species_mash_sketches.msh -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/wzi.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/wzi.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
copying kleborate/data/ybt_alleles.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp1.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp10.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp11.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp12.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp13.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp14.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp15.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp16.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp17.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp18.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp19.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp2.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp20.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp21.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp22.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp3.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp4.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp5.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp6.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp7.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp8.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
copying kleborate/data/ICEKp_references/ICEKp9.embl -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/kleborate/data/ICEKp_references
   dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:237: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build; python3.9 -m unittest discover -v 
test_ambiguous_bases_1 (test.test_contig_stats.TestContigStats) ... ok
test_ambiguous_bases_2 (test.test_contig_stats.TestContigStats) ... ok
test_ambiguous_bases_3 (test.test_contig_stats.TestContigStats) ... ok
test_ambiguous_bases_4 (test.test_contig_stats.TestContigStats) ... ok
test_count_1 (test.test_contig_stats.TestContigStats) ... ok
test_count_2 (test.test_contig_stats.TestContigStats) ... ok
test_longest_1 (test.test_contig_stats.TestContigStats) ... ok
test_longest_2 (test.test_contig_stats.TestContigStats) ... ok
test_n50_1 (test.test_contig_stats.TestContigStats) ... ok
test_n50_2 (test.test_contig_stats.TestContigStats) ... ok
test_qc_warnings_1 (test.test_contig_stats.TestContigStats) ... ok
test_qc_warnings_2 (test.test_contig_stats.TestContigStats) ... ok
test_qc_warnings_3 (test.test_contig_stats.TestContigStats) ... ok
test_qc_warnings_4 (test.test_contig_stats.TestContigStats) ... ok
test_qc_warnings_5 (test.test_contig_stats.TestContigStats) ... ok
test_qc_warnings_6 (test.test_contig_stats.TestContigStats) ... ok
test_qc_warnings_7 (test.test_contig_stats.TestContigStats) ... ok
test_qc_warnings_8 (test.test_contig_stats.TestContigStats) ... ok
test_total_size_1 (test.test_contig_stats.TestContigStats) ... ok
test_total_size_2 (test.test_contig_stats.TestContigStats) ... ok
test_total_size_3 (test.test_contig_stats.TestContigStats) ... ok
test_total_size_4 (test.test_contig_stats.TestContigStats) ... ok
test_iro_exact_1 (test.test_iro.TestIro)
This test is an exact match for SmST1. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_iro_exact_33 (test.test_iro.TestIro)
This test is an exact match for SmST33. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_iro_incomplete (test.test_iro.TestIro)
This test is an exact match for only one allele. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_iro_inexact (test.test_iro.TestIro)
This test is an inexact match for SmST33. There are single base changes in iroC and in ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_iro_missing_1 (test.test_iro.TestIro)
This test is a match for SmST1, except that it's missing iroN. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_iro_novel (test.test_iro.TestIro)
This test is an exact match for alleles, but an unknown combination. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_iro_random (test.test_iro.TestIro)
This test has just random sequence and should give no iro call. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_confidence_meets_threshold_01 (test.test_kaptive.TestKaptive) ... ok
test_confidence_meets_threshold_02 (test.test_kaptive.TestKaptive) ... ok
test_confidence_meets_threshold_03 (test.test_kaptive.TestKaptive) ... ok
test_confidence_meets_threshold_04 (test.test_kaptive.TestKaptive) ... ok
test_confidence_meets_threshold_05 (test.test_kaptive.TestKaptive) ... ok
test_confidence_meets_threshold_06 (test.test_kaptive.TestKaptive) ... ok
test_confidence_meets_threshold_07 (test.test_kaptive.TestKaptive) ... ok
test_confidence_meets_threshold_08 (test.test_kaptive.TestKaptive) ... ok
test_confidence_meets_threshold_09 (test.test_kaptive.TestKaptive) ... ok
test_confidence_meets_threshold_10 (test.test_kaptive.TestKaptive) ... ok
test_o_type_01 (test.test_kaptive.TestKaptive) ... ok
test_o_type_02 (test.test_kaptive.TestKaptive) ... ok
test_o_type_03 (test.test_kaptive.TestKaptive) ... ok
test_o_type_04 (test.test_kaptive.TestKaptive) ... ok
test_o_type_05 (test.test_kaptive.TestKaptive) ... ok
test_o_type_06 (test.test_kaptive.TestKaptive) ... ok
test_o_type_07 (test.test_kaptive.TestKaptive) ... ok
test_o_type_08 (test.test_kaptive.TestKaptive) ... ok
test_o_type_09 (test.test_kaptive.TestKaptive) ... ok
test_o_type_10 (test.test_kaptive.TestKaptive) ... ok
test_o_type_11 (test.test_kaptive.TestKaptive) ... ok
test_o_type_12 (test.test_kaptive.TestKaptive) ... ok
test_o_type_13 (test.test_kaptive.TestKaptive) ... ok
test_o_type_14 (test.test_kaptive.TestKaptive) ... ok
test_o_type_15 (test.test_kaptive.TestKaptive) ... ok
test_o_type_16 (test.test_kaptive.TestKaptive) ... ok
test_134 (test.test_mlst.TestMlst) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_83 (test.test_mlst.TestMlst) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_ba779 (test.test_mlst.TestMlst) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_chromosome_exact (test.test_mlst.TestMlst)
This test is an exact match for ST23. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_chromosome_inexact (test.test_mlst.TestMlst)
This test is is one base off from ST23 (single substitution in mdh_1 of G to A). ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_chromosome_random (test.test_mlst.TestMlst)
This test has just random sequence and should give no MLST call. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_kp_subspecies_1 (test.test_mlst.TestMlst) ... ok
test_kp_subspecies_2 (test.test_mlst.TestMlst) ... ok
test_kp_subspecies_3 (test.test_mlst.TestMlst) ... ok
test_kp_subspecies_4 (test.test_mlst.TestMlst) ... ok
test_kp_subspecies_5 (test.test_mlst.TestMlst) ... ok
test_kp_subspecies_6 (test.test_mlst.TestMlst) ... ok
test_kp_subspecies_7 (test.test_mlst.TestMlst) ... ok
test_ozaenae (test.test_mlst.TestMlst) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rhinoscleromatis (test.test_mlst.TestMlst) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_unknown_ST (test.test_mlst.TestMlst)
This test has exact matches for alleles but in an unknown ST combination ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_01 (test.test_res_aac.TestResAac) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/__init__.py:513: 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
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_02 (test.test_res_aac.TestResAac) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_03 (test.test_res_aac.TestResAac) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_04 (test.test_res_aac.TestResAac)
This is a tricky one (and the one which first highlighted the problem). The best bit-score ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_05 (test.test_res_aac.TestResAac)
Same as test_res_04, but with the hit on the other strand. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_exact_aa_match_1 (test.test_res_alleles.TestResAlleles)
Simple case: full protein sequence ending in a stop codon. ... ok
test_exact_aa_match_2 (test.test_res_alleles.TestResAlleles)
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)
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)
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)
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)
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)
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)
The first seq's protein sequence contains the second seq's protein sequence. ... ok
test_res_01 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_02 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_03 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_04 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_05 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_06 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_07 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_08 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_09 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_10 (test.test_res_alleles.TestResAlleles) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_11 (test.test_res_alleles.TestResAlleles)
This test has the ABC-1 gene but with a stop codon in the middle. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_12 (test.test_res_alleles.TestResAlleles)
This test has the ABC-1 gene but missing the first (start) codon. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_13 (test.test_res_alleles.TestResAlleles)
This test has the ABC-1 gene but at only 50% coverage, so it goes to spurious hits. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_14 (test.test_res_alleles.TestResAlleles)
I added this test to catch a weird BLAST-related bug where an exact amino acid match for ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_15 (test.test_res_alleles.TestResAlleles)
Same as the previous test, but with the nucleotide sequence reverse-complemented. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_16 (test.test_res_alleles.TestResAlleles)
I added this test to catch a weird BLAST-related bug where an exact amino acid match for ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_17 (test.test_res_alleles.TestResAlleles)
Same as the previous test, but with the nucleotide sequence reverse-complemented. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_18 (test.test_res_alleles.TestResAlleles)
This is the uncomplicated case for a OKP-B-6^ result (later tests cover more challenging ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_19 (test.test_res_alleles.TestResAlleles)
Same as the previous test, but with the nucleotide sequence reverse-complemented. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_20 (test.test_res_alleles.TestResAlleles)
I added this test to catch a bug where there is an exact amino acid match but inexact ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_21 (test.test_res_alleles.TestResAlleles)
Same as the previous test, but with the nucleotide sequence reverse-complemented. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_22 (test.test_res_alleles.TestResAlleles)
I added this test to catch a bug where there is an exact amino acid match but inexact ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_res_23 (test.test_res_alleles.TestResAlleles)
Same as the previous test, but with the nucleotide sequence reverse-complemented. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_both_genes_intact (test.test_res_mgrb_pmrb.TestResMgrBPmrB) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_mgrb_missing (test.test_res_mgrb_pmrb.TestResMgrBPmrB) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_mgrb_missing_non_kp_complex (test.test_res_mgrb_pmrb.TestResMgrBPmrB)
Setting the Kp complex variable to False should turn off the MgrB/PmrB tests. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_pmrb_early_stop (test.test_res_mgrb_pmrb.TestResMgrBPmrB)
This tests an early stop mutation (without a frameshift) in pmrB. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_pmrb_early_stop_SRR2098701 (test.test_res_mgrb_pmrb.TestResMgrBPmrB) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_pmrb_frameshift (test.test_res_mgrb_pmrb.TestResMgrBPmrB)
A frameshift in pmrB should cause an early stop and lead to a colisitin resistance call. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_both_genes_intact (test.test_res_omp.TestResOmp) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_ompk35_early_stop (test.test_res_omp.TestResOmp)
This tests an early stop mutation (without a frameshift) in OmpK35. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_ompk35_frameshift (test.test_res_omp.TestResOmp)
A frameshift in OmpK35 should cause an early stop and lead to a carbapenem resistance call. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_ompk36_missing (test.test_res_omp.TestResOmp) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_ompk36gd (test.test_res_omp.TestResOmp) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_ompk36td (test.test_res_omp.TestResOmp) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_ompk36td_non_kp_complex (test.test_res_omp.TestResOmp)
Setting the Kp complex variable to False should turn off the OmpK tests. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_gyra (test.test_res_qrdr.TestResGyrAParC) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_gyra_and_parc (test.test_res_qrdr.TestResGyrAParC) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_gyra_and_parc_non_kp_complex (test.test_res_qrdr.TestResGyrAParC)
Setting the Kp complex variable to False should turn off the QRDR tests. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_no_mutations (test.test_res_qrdr.TestResGyrAParC) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_parc (test.test_res_qrdr.TestResGyrAParC) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_tem (test.test_res_tem.TestResTem) ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rmp_19 (test.test_rmp.TestRmp)
This test is an exact match for RmST19, an ST without any truncated alleles. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rmp_21 (test.test_rmp.TestRmp)
This test is an exact match for RmST21, an ST with a truncated allele. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rmp_missing_1 (test.test_rmp.TestRmp)
This test is a match for RmST1, except that it's missing rmpC. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rmp_novel (test.test_rmp.TestRmp)
This test is an exact match for alleles, but an unknown combination. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rmp_random (test.test_rmp.TestRmp)
This test has just random sequence and should give no rmp call. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rmpa2_exact (test.test_rmp.TestRmp)
This test has an exact match for rmpA2_1. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rmpa2_exact_truncated (test.test_rmp.TestRmp)
This test has an exact match for rmpA2_7. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rmpa2_inexact (test.test_rmp.TestRmp)
This test has an inexact match for rmpA2_1. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_rmpa2_random (test.test_rmp.TestRmp)
This test has just random sequence and should give no rmpA2 call. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_bla_class_01 (test.test_shv.TestShvMutations) ... ok
test_bla_class_02 (test.test_shv.TestShvMutations) ... ok
test_bla_class_03 (test.test_shv.TestShvMutations) ... ok
test_bla_class_04 (test.test_shv.TestShvMutations) ... ok
test_get_class_changing_mutations_01 (test.test_shv.TestShvMutations) ... ok
test_get_class_changing_mutations_02 (test.test_shv.TestShvMutations) ... ok
test_get_class_changing_mutations_03 (test.test_shv.TestShvMutations) ... ok
test_get_class_changing_mutations_04 (test.test_shv.TestShvMutations) ... ok
test_get_class_changing_mutations_05 (test.test_shv.TestShvMutations) ... ok
test_get_class_changing_mutations_06 (test.test_shv.TestShvMutations) ... ok
test_get_class_changing_mutations_07 (test.test_shv.TestShvMutations) ... ok
test_get_class_changing_mutations_08 (test.test_shv.TestShvMutations) ... ok
test_shv_01 (test.test_shv.TestShvMutations)
This test has an exact match for SHV-1. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_shv_02 (test.test_shv.TestShvMutations)
This test has a match for SHV-1 with a mutation at site 238 (G -> Y). This changes the ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_shv_03 (test.test_shv.TestShvMutations)
Same as test 2, but the gene is on the reverse strand. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_shv_04 (test.test_shv.TestShvMutations)
This test has a match for SHV-1 with a mutation at site 50 (G -> Y). This doesn't change ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_shv_05 (test.test_shv.TestShvMutations)
This test has an exact match for SHV-29. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_shv_06 (test.test_shv.TestShvMutations)
This test has SHV-29 plus an inhibition mutation. ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_shv_07 (test.test_shv.TestShvMutations)
This test has SHV-1 with position 238 deleted. Since it's not in the omega loop, this isn't ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_shv_08 (test.test_shv.TestShvMutations)
This test has SHV-1 with a synonymous mutation in the omega loop (so not reported). ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_shv_09 (test.test_shv.TestShvMutations)
This test has SHV-1 with a nonsynonymous mutation in the omega loop (so it is reported). ... Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime
ok
test_citrobacter (test.test_species.TestKpComplex) ... ok
test_klebsiella_aerogenes (test.test_species.TestKpComplex) ... ok
test_klebsiella_africanensis (test.test_species.TestKpComplex) ... ok
test_klebsiella_grimontii (test.test_species.TestKpComplex) ... ok
test_klebsiella_michiganensis (test.test_species.TestKpComplex) ... ok
test_klebsiella_oxytoca (test.test_species.TestKpComplex) ... ok
test_klebsiella_pneumoniae (test.test_species.TestKpComplex) ... ok
test_klebsiella_quasipneumoniae_subsp_quasipneumoniae (test.test_species.TestKpComplex) ... ok
test_klebsiella_quasipneumoniae_subsp_similipneumoniae (test.test_species.TestKpComplex) ... ok
test_klebsiella_quasivariicola (test.test_species.TestKpComplex) ... ok
test_klebsiella_variicola_subsp_tropicalensis (test.test_species.TestKpComplex) ... ok
test_klebsiella_variicola_subsp_variicola (test.test_species.TestKpComplex) ... ok
test_raoultella_ornithinolytica (test.test_species.TestKpComplex) ... ok
test_raoultella_planticola (test.test_species.TestKpComplex) ... ok
test_raoultella_terrigena (test.test_species.TestKpComplex) ... ok
test_salmonella (test.test_species.TestKpComplex) ... ok
test_citrobacter (test.test_species.TestSpecies) ... FAIL
test_klebsiella_aerogenes (test.test_species.TestSpecies) ... FAIL
test_klebsiella_africana (test.test_species.TestSpecies) ... FAIL
test_klebsiella_grimontii (test.test_species.TestSpecies) ... FAIL
test_klebsiella_indica (test.test_species.TestSpecies) ... FAIL
test_klebsiella_michiganensis (test.test_species.TestSpecies) ... FAIL
test_klebsiella_oxytoca (test.test_species.TestSpecies) ... FAIL
test_klebsiella_pasteurii (test.test_species.TestSpecies) ... FAIL
test_klebsiella_pneumoniae (test.test_species.TestSpecies) ... FAIL
test_klebsiella_quasipneumoniae_subsp_quasipneumoniae (test.test_species.TestSpecies) ... FAIL
test_klebsiella_quasipneumoniae_subsp_similipneumoniae (test.test_species.TestSpecies) ... FAIL
test_klebsiella_quasivariicola (test.test_species.TestSpecies) ... FAIL
test_klebsiella_spallanzanii (test.test_species.TestSpecies) ... FAIL
test_klebsiella_variicola_subsp_tropicalensis (test.test_species.TestSpecies) ... FAIL
test_klebsiella_variicola_subsp_variicola (test.test_species.TestSpecies) ... FAIL
test_raoultella_ornithinolytica (test.test_species.TestSpecies) ... FAIL
test_raoultella_planticola (test.test_species.TestSpecies) ... FAIL
test_raoultella_terrigena (test.test_species.TestSpecies) ... FAIL
test_salmonella (test.test_species.TestSpecies) ... FAIL
test_yersinia_unknown (test.test_species.TestSpecies) ... FAIL
test_nothing (test.test_summary.TestResScore) ... ok
test_res_counts_1 (test.test_summary.TestResScore) ... ok
test_res_counts_10 (test.test_summary.TestResScore)
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)
Spurious hits should not add to either the gene or class counts. ... ok
test_res_counts_2 (test.test_summary.TestResScore) ... ok
test_res_counts_3 (test.test_summary.TestResScore)
Intrinsic Bla genes should not add to the counts. ... ok
test_res_counts_4 (test.test_summary.TestResScore)
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)
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)
Omp gene truncations should not add to the gene or class counts. ... ok
test_res_counts_7 (test.test_summary.TestResScore)
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)
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)
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) ... ok
test_res_score_2 (test.test_summary.TestResScore) ... ok
test_res_score_3 (test.test_summary.TestResScore) ... ok
test_res_score_4 (test.test_summary.TestResScore) ... ok
test_res_score_5 (test.test_summary.TestResScore) ... ok
test_res_score_6 (test.test_summary.TestResScore) ... ok
test_res_score_7 (test.test_summary.TestResScore) ... ok
test_res_score_8 (test.test_summary.TestResScore) ... ok
test_vir_score_1 (test.test_summary.TestResScore) ... ok
test_vir_score_2 (test.test_summary.TestResScore) ... ok
test_vir_score_3 (test.test_summary.TestResScore) ... ok
test_vir_score_4 (test.test_summary.TestResScore) ... ok
test_vir_score_5 (test.test_summary.TestResScore) ... ok
test_vir_score_6 (test.test_summary.TestResScore) ... ok
test_vir_score_7 (test.test_summary.TestResScore) ... ok

======================================================================
FAIL: test_citrobacter (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 118, in test_citrobacter
    self.assertTrue('Citrobacter' in species)
AssertionError: False is not true

======================================================================
FAIL: test_klebsiella_aerogenes (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 28, in test_klebsiella_aerogenes
    self.assertEqual(species, 'Klebsiella aerogenes')
AssertionError: 'unknown' != 'Klebsiella aerogenes'
- unknown
+ Klebsiella aerogenes


======================================================================
FAIL: test_klebsiella_africana (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 93, in test_klebsiella_africana
    self.assertEqual(species, 'Klebsiella africana')
AssertionError: 'unknown' != 'Klebsiella africana'
- unknown
+ Klebsiella africana


======================================================================
FAIL: test_klebsiella_grimontii (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 33, in test_klebsiella_grimontii
    self.assertEqual(species, 'Klebsiella grimontii')
AssertionError: 'unknown' != 'Klebsiella grimontii'
- unknown
+ Klebsiella grimontii


======================================================================
FAIL: test_klebsiella_indica (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 38, in test_klebsiella_indica
    self.assertEqual(species, 'Klebsiella indica')
AssertionError: 'unknown' != 'Klebsiella indica'
- unknown
+ Klebsiella indica


======================================================================
FAIL: test_klebsiella_michiganensis (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 43, in test_klebsiella_michiganensis
    self.assertEqual(species, 'Klebsiella michiganensis')
AssertionError: 'unknown' != 'Klebsiella michiganensis'
- unknown
+ Klebsiella michiganensis


======================================================================
FAIL: test_klebsiella_oxytoca (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 48, in test_klebsiella_oxytoca
    self.assertEqual(species, 'Klebsiella oxytoca')
AssertionError: 'unknown' != 'Klebsiella oxytoca'
- unknown
+ Klebsiella oxytoca


======================================================================
FAIL: test_klebsiella_pasteurii (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 53, in test_klebsiella_pasteurii
    self.assertEqual(species, 'Klebsiella pasteurii')
AssertionError: 'unknown' != 'Klebsiella pasteurii'
- unknown
+ Klebsiella pasteurii


======================================================================
FAIL: test_klebsiella_pneumoniae (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 58, in test_klebsiella_pneumoniae
    self.assertEqual(species, 'Klebsiella pneumoniae')
AssertionError: 'unknown' != 'Klebsiella pneumoniae'
- unknown
+ Klebsiella pneumoniae


======================================================================
FAIL: test_klebsiella_quasipneumoniae_subsp_quasipneumoniae (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 63, in test_klebsiella_quasipneumoniae_subsp_quasipneumoniae
    self.assertEqual(species, 'Klebsiella quasipneumoniae subsp. quasipneumoniae')
AssertionError: 'unknown' != 'Klebsiella quasipneumoniae subsp. quasipneumoniae'
- unknown
+ Klebsiella quasipneumoniae subsp. quasipneumoniae


======================================================================
FAIL: test_klebsiella_quasipneumoniae_subsp_similipneumoniae (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 68, in test_klebsiella_quasipneumoniae_subsp_similipneumoniae
    self.assertEqual(species, 'Klebsiella quasipneumoniae subsp. similipneumoniae')
AssertionError: 'unknown' != 'Klebsiella quasipneumoniae subsp. similipneumoniae'
- unknown
+ Klebsiella quasipneumoniae subsp. similipneumoniae


======================================================================
FAIL: test_klebsiella_quasivariicola (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 73, in test_klebsiella_quasivariicola
    self.assertEqual(species, 'Klebsiella quasivariicola')
AssertionError: 'unknown' != 'Klebsiella quasivariicola'
- unknown
+ Klebsiella quasivariicola


======================================================================
FAIL: test_klebsiella_spallanzanii (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 78, in test_klebsiella_spallanzanii
    self.assertEqual(species, 'Klebsiella spallanzanii')
AssertionError: 'unknown' != 'Klebsiella spallanzanii'
- unknown
+ Klebsiella spallanzanii


======================================================================
FAIL: test_klebsiella_variicola_subsp_tropicalensis (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 88, in test_klebsiella_variicola_subsp_tropicalensis
    self.assertEqual(species, 'Klebsiella variicola subsp. tropica')
AssertionError: 'unknown' != 'Klebsiella variicola subsp. tropica'
- unknown
+ Klebsiella variicola subsp. tropica


======================================================================
FAIL: test_klebsiella_variicola_subsp_variicola (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 83, in test_klebsiella_variicola_subsp_variicola
    self.assertEqual(species, 'Klebsiella variicola subsp. variicola')
AssertionError: 'unknown' != 'Klebsiella variicola subsp. variicola'
- unknown
+ Klebsiella variicola subsp. variicola


======================================================================
FAIL: test_raoultella_ornithinolytica (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 103, in test_raoultella_ornithinolytica
    self.assertEqual(species, 'Klebsiella ornithinolytica')
AssertionError: 'unknown' != 'Klebsiella ornithinolytica'
- unknown
+ Klebsiella ornithinolytica


======================================================================
FAIL: test_raoultella_planticola (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 98, in test_raoultella_planticola
    self.assertEqual(species, 'Klebsiella planticola')
AssertionError: 'unknown' != 'Klebsiella planticola'
- unknown
+ Klebsiella planticola


======================================================================
FAIL: test_raoultella_terrigena (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 108, in test_raoultella_terrigena
    self.assertEqual(species, 'Klebsiella terrigena')
AssertionError: 'unknown' != 'Klebsiella terrigena'
- unknown
+ Klebsiella terrigena


======================================================================
FAIL: test_salmonella (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 113, in test_salmonella
    self.assertTrue('Salmonella' in species)
AssertionError: False is not true

======================================================================
FAIL: test_yersinia_unknown (test.test_species.TestSpecies)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_species.py", line 123, in test_yersinia_unknown
    self.assertEqual(species, 'Yersinia (unknown species)')
AssertionError: 'unknown' != 'Yersinia (unknown species)'
- unknown
+ Yersinia (unknown species)


----------------------------------------------------------------------
Ran 219 tests in 652.259s

FAILED (failures=20)
{'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': '-'}
E: pybuild pybuild:354: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build; python3.9 -m unittest discover -v 
dh_auto_test: error: pybuild --test -i python{version} -p 3.9 returned exit code 13
make: *** [debian/rules:6: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2021-12-03T01:04:31Z

Finished
--------


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

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

Build Architecture: armhf
Build-Space: 346212
Build-Time: 665
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 602
Job: kleborate_2.1.0-2
Machine Architecture: armhf
Package: kleborate
Package-Time: 1321
Source-Version: 2.1.0-2
Space: 346212
Status: attempted
Version: 2.1.0-2
--------------------------------------------------------------------------------
Finished at 2021-12-03T01:04:31Z
Build needed 00:22:01, 346212k disk space