0s autopkgtest [22:04:37]: starting date and time: 2024-05-05 22:04:37+0000
  0s autopkgtest [22:04:37]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init
  0s autopkgtest [22:04:37]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b2ksuppa/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-biopython --apt-upgrade kleborate --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-biopython/1.83+dfsg1-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-25.secgroup --name adt-oracular-ppc64el-kleborate-20240505-220437-juju-7f2275-prod-proposed-migration-environment-3-0d490a1c-b84a-431b-b628-5c9f88380ef0 --image adt/ubuntu-oracular-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
182s autopkgtest [22:07:39]: testbed dpkg architecture: ppc64el
182s autopkgtest [22:07:39]: testbed apt version: 2.7.14build2
182s autopkgtest [22:07:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup
184s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB]
184s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B]
184s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1641 kB]
185s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [108 kB]
185s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [23.5 kB]
185s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [180 kB]
185s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1260 B]
185s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [1272 kB]
185s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [22.6 kB]
187s Fetched 3315 kB in 3s (995 kB/s)
187s Reading package lists...
193s Reading package lists...
195s Building dependency tree...
195s Reading state information...
195s Calculating upgrade...
195s The following packages will be upgraded:
195s   ed hdparm libnfnetlink0 libudisks2-0 lsof lto-disabled-list udisks2
196s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
196s Need to get 974 kB of archives.
196s After this operation, 2048 B disk space will be freed.
196s Get:1 http://ftpmaster.internal/ubuntu oracular/main ppc64el ed ppc64el 1.20.2-2 [63.6 kB]
196s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el hdparm ppc64el 9.65+ds-1.1 [105 kB]
196s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnfnetlink0 ppc64el 1.0.2-3 [16.4 kB]
196s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el lsof ppc64el 4.95.0-1.1 [255 kB]
196s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el udisks2 ppc64el 2.10.1-7 [341 kB]
196s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el libudisks2-0 ppc64el 2.10.1-7 [180 kB]
196s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el lto-disabled-list all 48 [12.3 kB]
197s Fetched 974 kB in 1s (1651 kB/s)
198s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 72142 files and directories currently installed.)
198s Preparing to unpack .../0-ed_1.20.2-2_ppc64el.deb ...
198s Unpacking ed (1.20.2-2) over (1.20.1-1) ...
198s Preparing to unpack .../1-hdparm_9.65+ds-1.1_ppc64el.deb ...
198s Unpacking hdparm (9.65+ds-1.1) over (9.65+ds-1build1) ...
198s dpkg: warning: unable to delete old directory '/lib/systemd/system-sleep': Directory not empty
198s dpkg: warning: unable to delete old directory '/lib/hdparm': Directory not empty
198s Preparing to unpack .../2-libnfnetlink0_1.0.2-3_ppc64el.deb ...
198s Unpacking libnfnetlink0:ppc64el (1.0.2-3) over (1.0.2-2build1) ...
198s Preparing to unpack .../3-lsof_4.95.0-1.1_ppc64el.deb ...
198s Unpacking lsof (4.95.0-1.1) over (4.95.0-1build3) ...
198s Preparing to unpack .../4-udisks2_2.10.1-7_ppc64el.deb ...
198s Unpacking udisks2 (2.10.1-7) over (2.10.1-6build1) ...
198s Preparing to unpack .../5-libudisks2-0_2.10.1-7_ppc64el.deb ...
198s Unpacking libudisks2-0:ppc64el (2.10.1-7) over (2.10.1-6build1) ...
198s Preparing to unpack .../6-lto-disabled-list_48_all.deb ...
198s Unpacking lto-disabled-list (48) over (47) ...
198s Setting up lto-disabled-list (48) ...
198s Setting up hdparm (9.65+ds-1.1) ...
198s Installing new version of config file /etc/hdparm.conf ...
198s Setting up ed (1.20.2-2) ...
198s Setting up lsof (4.95.0-1.1) ...
198s Setting up libnfnetlink0:ppc64el (1.0.2-3) ...
198s Setting up libudisks2-0:ppc64el (2.10.1-7) ...
198s Setting up udisks2 (2.10.1-7) ...
201s Processing triggers for man-db (2.12.0-4build2) ...
204s Processing triggers for dbus (1.14.10-4ubuntu4) ...
204s Processing triggers for install-info (7.1-3build2) ...
205s Processing triggers for libc-bin (2.39-0ubuntu8) ...
205s Reading package lists...
206s Building dependency tree...
206s Reading state information...
206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
207s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
207s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease
207s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease
207s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease
211s Reading package lists...
211s Reading package lists...
212s Building dependency tree...
212s Reading state information...
212s Calculating upgrade...
213s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
213s Reading package lists...
213s Building dependency tree...
213s Reading state information...
214s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
215s autopkgtest [22:08:12]: rebooting testbed after setup commands that affected boot
220s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
253s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
286s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
311s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
319s autopkgtest [22:09:56]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024
322s autopkgtest [22:09:59]: @@@@@@@@@@@@@@@@@@@@ apt-source kleborate
334s Get:1 http://ftpmaster.internal/ubuntu oracular/universe kleborate 2.4.1-3build1 (dsc) [2290 B]
334s Get:2 http://ftpmaster.internal/ubuntu oracular/universe kleborate 2.4.1-3build1 (tar) [91.6 MB]
334s Get:3 http://ftpmaster.internal/ubuntu oracular/universe kleborate 2.4.1-3build1 (diff) [5997 kB]
334s gpgv: Signature made Mon Apr  1 06:04:16 2024 UTC
334s gpgv:                using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984
334s gpgv: Can't check signature: No public key
335s dpkg-source: warning: cannot verify inline signature for ./kleborate_2.4.1-3build1.dsc: no acceptable signature found
343s autopkgtest [22:10:20]: testing package kleborate version 2.4.1-3build1
344s autopkgtest [22:10:21]: build not needed
350s autopkgtest [22:10:27]: test run-unit-test: preparing testbed
351s Reading package lists...
352s Building dependency tree...
352s Reading state information...
353s Starting pkgProblemResolver with broken count: 0
353s Starting 2 pkgProblemResolver with broken count: 0
353s Done
353s The following additional packages will be installed:
353s   fonts-urw-base35 kaptive kaptive-data kleborate kleborate-examples libblas3
353s   libcairo2 libcapnp-1.0.1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3
353s   libgsl27 libgslcblas0 libharfbuzz0b libimagequant0 liblapack3 liblcms2-2
353s   libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmurmurhash2
353s   libopenjp2-7 libpixman-1-0 libraqm0 libwebpdemux2 libwebpmux3 libxcb-render0
353s   libxcb-shm0 libxrender1 mash ncbi-blast+ ncbi-data python3-biopython
353s   python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab
353s   python3-rlpycairo sgml-base w3c-sgml-lib x11-common xfonts-encodings
353s   xfonts-utils xml-core
353s Suggested packages:
353s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre kaptive-example
353s   gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblcms2-utils
353s   python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3
353s   phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf
353s   python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise
353s   gcc gfortran python3-dev python3-pytest python-pil-doc pdf-viewer
353s   python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm
353s   sgml-base-doc debhelper
353s Recommended packages:
353s   python-biopython-doc python3-olefile fonts-dejavu-extra
353s The following NEW packages will be installed:
353s   autopkgtest-satdep fonts-urw-base35 kaptive kaptive-data kleborate
353s   kleborate-examples libblas3 libcairo2 libcapnp-1.0.1 libfontenc1
353s   libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b
353s   libimagequant0 liblapack3 liblcms2-2 libmbedcrypto7t64 libmbedtls14t64
353s   libmbedx509-1t64 libmurmurhash2 libopenjp2-7 libpixman-1-0 libraqm0
353s   libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mash
353s   ncbi-blast+ ncbi-data python3-biopython python3-cairo python3-freetype
353s   python3-numpy python3-pil python3-reportlab python3-rlpycairo sgml-base
353s   w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
354s 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded.
354s Need to get 67.4 MB/67.4 MB of archives.
354s After this operation, 273 MB of additional disk space will be used.
354s Get:1 /tmp/autopkgtest.V5UIsv/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B]
354s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el sgml-base all 1.31 [11.4 kB]
355s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB]
355s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB]
355s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
355s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el xfonts-utils ppc64el 1:7.7+6build3 [113 kB]
355s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB]
356s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB]
356s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14-20240412-0ubuntu1 [574 kB]
356s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB]
356s Get:11 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-6ubuntu1 [4446 kB]
357s Get:12 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgomp1 ppc64el 14-20240412-0ubuntu1 [161 kB]
357s Get:13 http://ftpmaster.internal/ubuntu oracular/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB]
357s Get:14 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblcms2-2 ppc64el 2.14-2build1 [233 kB]
357s Get:15 http://ftpmaster.internal/ubuntu oracular/main ppc64el libopenjp2-7 ppc64el 2.5.0-2build3 [239 kB]
357s Get:16 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgraphite2-3 ppc64el 1.3.14-2build1 [84.6 kB]
357s Get:17 http://ftpmaster.internal/ubuntu oracular/main ppc64el libharfbuzz0b ppc64el 8.3.0-2build2 [580 kB]
357s Get:18 http://ftpmaster.internal/ubuntu oracular/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB]
357s Get:19 http://ftpmaster.internal/ubuntu oracular/main ppc64el libwebpdemux2 ppc64el 1.3.2-0.4build3 [14.4 kB]
357s Get:20 http://ftpmaster.internal/ubuntu oracular/main ppc64el libwebpmux3 ppc64el 1.3.2-0.4build3 [31.2 kB]
357s Get:21 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-pil ppc64el 10.2.0-1build1 [485 kB]
357s Get:22 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpixman-1-0 ppc64el 0.42.2-1build1 [336 kB]
357s Get:23 http://ftpmaster.internal/ubuntu oracular/main ppc64el libxcb-render0 ppc64el 1.15-1ubuntu2 [17.7 kB]
357s Get:24 http://ftpmaster.internal/ubuntu oracular/main ppc64el libxcb-shm0 ppc64el 1.15-1ubuntu2 [6184 B]
357s Get:25 http://ftpmaster.internal/ubuntu oracular/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB]
357s Get:26 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcairo2 ppc64el 1.18.0-3build1 [751 kB]
357s Get:27 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-cairo ppc64el 1.25.1-2build2 [129 kB]
357s Get:28 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-freetype all 2.4.0-1 [83.1 kB]
357s Get:29 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B]
357s Get:30 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-reportlab all 4.1.0-4 [1105 kB]
357s Get:31 http://ftpmaster.internal/ubuntu oracular/main ppc64el xml-core all 0.19 [20.3 kB]
357s Get:32 http://ftpmaster.internal/ubuntu oracular/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB]
357s Get:33 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-biopython ppc64el 1.83+dfsg1-2 [1696 kB]
357s Get:34 http://ftpmaster.internal/ubuntu oracular/universe ppc64el ncbi-data all 6.1.20170106+dfsg2-2 [4281 kB]
358s Get:35 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libmbedcrypto7t64 ppc64el 2.28.8-1 [267 kB]
358s Get:36 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libmbedx509-1t64 ppc64el 2.28.8-1 [51.7 kB]
358s Get:37 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libmbedtls14t64 ppc64el 2.28.8-1 [90.6 kB]
358s Get:38 http://ftpmaster.internal/ubuntu oracular/universe ppc64el ncbi-blast+ ppc64el 2.12.0+ds-4build2 [13.5 MB]
359s Get:39 http://ftpmaster.internal/ubuntu oracular/universe ppc64el kaptive all 2.0.8-1 [28.1 kB]
359s Get:40 http://ftpmaster.internal/ubuntu oracular/universe ppc64el kaptive-data all 2.0.8-1 [5432 kB]
359s Get:41 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libcapnp-1.0.1 ppc64el 1.0.1-4 [1561 kB]
359s Get:42 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu2 [86.6 kB]
359s Get:43 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu2 [1090 kB]
359s Get:44 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libmurmurhash2 ppc64el 1.6-1 [6626 B]
359s Get:45 http://ftpmaster.internal/ubuntu oracular/universe ppc64el mash ppc64el 2.3+dfsg-6 [159 kB]
359s Get:46 http://ftpmaster.internal/ubuntu oracular/universe ppc64el kleborate ppc64el 2.4.1-3build1 [8742 kB]
360s Get:47 http://ftpmaster.internal/ubuntu oracular/universe ppc64el kleborate-examples all 2.4.1-3build1 [5990 kB]
361s Fetched 67.4 MB in 7s (10.3 MB/s)
362s Selecting previously unselected package sgml-base.
362s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 72141 files and directories currently installed.)
362s Preparing to unpack .../00-sgml-base_1.31_all.deb ...
362s Unpacking sgml-base (1.31) ...
362s Selecting previously unselected package libfontenc1:ppc64el.
362s Preparing to unpack .../01-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ...
362s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ...
362s Selecting previously unselected package x11-common.
362s Preparing to unpack .../02-x11-common_1%3a7.7+23ubuntu3_all.deb ...
362s Unpacking x11-common (1:7.7+23ubuntu3) ...
362s Selecting previously unselected package xfonts-encodings.
362s Preparing to unpack .../03-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
362s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
363s Selecting previously unselected package xfonts-utils.
363s Preparing to unpack .../04-xfonts-utils_1%3a7.7+6build3_ppc64el.deb ...
363s Unpacking xfonts-utils (1:7.7+6build3) ...
363s Selecting previously unselected package fonts-urw-base35.
363s Preparing to unpack .../05-fonts-urw-base35_20200910-8_all.deb ...
363s Unpacking fonts-urw-base35 (20200910-8) ...
364s Selecting previously unselected package libblas3:ppc64el.
364s Preparing to unpack .../06-libblas3_3.12.0-3build1_ppc64el.deb ...
364s Unpacking libblas3:ppc64el (3.12.0-3build1) ...
364s Selecting previously unselected package libgfortran5:ppc64el.
364s Preparing to unpack .../07-libgfortran5_14-20240412-0ubuntu1_ppc64el.deb ...
364s Unpacking libgfortran5:ppc64el (14-20240412-0ubuntu1) ...
364s Selecting previously unselected package liblapack3:ppc64el.
364s Preparing to unpack .../08-liblapack3_3.12.0-3build1_ppc64el.deb ...
364s Unpacking liblapack3:ppc64el (3.12.0-3build1) ...
364s Selecting previously unselected package python3-numpy.
364s Preparing to unpack .../09-python3-numpy_1%3a1.26.4+ds-6ubuntu1_ppc64el.deb ...
364s Unpacking python3-numpy (1:1.26.4+ds-6ubuntu1) ...
365s Selecting previously unselected package libgomp1:ppc64el.
365s Preparing to unpack .../10-libgomp1_14-20240412-0ubuntu1_ppc64el.deb ...
365s Unpacking libgomp1:ppc64el (14-20240412-0ubuntu1) ...
365s Selecting previously unselected package libimagequant0:ppc64el.
365s Preparing to unpack .../11-libimagequant0_2.18.0-1build1_ppc64el.deb ...
365s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ...
365s Selecting previously unselected package liblcms2-2:ppc64el.
365s Preparing to unpack .../12-liblcms2-2_2.14-2build1_ppc64el.deb ...
365s Unpacking liblcms2-2:ppc64el (2.14-2build1) ...
365s Selecting previously unselected package libopenjp2-7:ppc64el.
365s Preparing to unpack .../13-libopenjp2-7_2.5.0-2build3_ppc64el.deb ...
365s Unpacking libopenjp2-7:ppc64el (2.5.0-2build3) ...
366s Selecting previously unselected package libgraphite2-3:ppc64el.
366s Preparing to unpack .../14-libgraphite2-3_1.3.14-2build1_ppc64el.deb ...
366s Unpacking libgraphite2-3:ppc64el (1.3.14-2build1) ...
366s Selecting previously unselected package libharfbuzz0b:ppc64el.
366s Preparing to unpack .../15-libharfbuzz0b_8.3.0-2build2_ppc64el.deb ...
366s Unpacking libharfbuzz0b:ppc64el (8.3.0-2build2) ...
366s Selecting previously unselected package libraqm0:ppc64el.
366s Preparing to unpack .../16-libraqm0_0.10.1-1build1_ppc64el.deb ...
366s Unpacking libraqm0:ppc64el (0.10.1-1build1) ...
366s Selecting previously unselected package libwebpdemux2:ppc64el.
366s Preparing to unpack .../17-libwebpdemux2_1.3.2-0.4build3_ppc64el.deb ...
366s Unpacking libwebpdemux2:ppc64el (1.3.2-0.4build3) ...
366s Selecting previously unselected package libwebpmux3:ppc64el.
366s Preparing to unpack .../18-libwebpmux3_1.3.2-0.4build3_ppc64el.deb ...
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367s Selecting previously unselected package python3-cairo.
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372s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu2) ...
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372s Setting up libwebpdemux2:ppc64el (1.3.2-0.4build3) ...
372s Setting up x11-common (1:7.7+23ubuntu3) ...
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374s Setting up libgomp1:ppc64el (14-20240412-0ubuntu1) ...
374s Setting up python3-freetype (2.4.0-1) ...
374s Setting up libcairo2:ppc64el (1.18.0-3build1) ...
374s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ...
374s Setting up libblas3:ppc64el (3.12.0-3build1) ...
375s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
375s Setting up kleborate-examples (2.4.1-3build1) ...
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375s Setting up libimagequant0:ppc64el (2.18.0-1build1) ...
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375s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
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376s Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ...
383s Setting up libmbedtls14t64:ppc64el (2.28.8-1) ...
383s Setting up xml-core (0.19) ...
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384s Setting up ncbi-blast+ (2.12.0+ds-4build2) ...
384s Setting up python3-pil:ppc64el (10.2.0-1build1) ...
386s Setting up python3-reportlab (4.1.0-4) ...
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393s Setting up w3c-sgml-lib (1.3-3) ...
507s Setting up python3-biopython (1.83+dfsg1-2) ...
511s Setting up kaptive (2.0.8-1) ...
511s Setting up kleborate (2.4.1-3build1) ...
515s Setting up autopkgtest-satdep (0) ...
523s (Reading database ... 75638 files and directories currently installed.)
523s Removing autopkgtest-satdep (0) ...
524s autopkgtest [22:13:21]: test run-unit-test: [-----------------------
527s /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
527s   warnings.warn(
653s strain	species	ST	virulence_score	Yersiniabactin	YbST	Colibactin	CbST	Aerobactin	AbST	Salmochelin	SmST	RmpADC	RmST	rmpA2	wzi	K_locus
653s Klebs_HS11286	Klebsiella pneumoniae	ST11	1	ybt 9; ICEKp3	15	-	0	-	0	-	0	-	0	-	wzi74	KL103
653s Klebs_Kp1084	Klebsiella pneumoniae	ST23	2	ybt 1; ICEKp10	47	clb 2	37	-	0	-	0	-	0	-	wzi172	KL1
653s MGH78578	Klebsiella pneumoniae	ST38	0	-	0	-	0	-	0	-	0	-	0	-	wzi50	KL15 (KL17,KL51,KL52)
653s NTUH-K2044	Klebsiella pneumoniae	ST23	4	ybt 2; ICEKp1	326	-	0	iuc 1	1	iro 1,iro 3	19,18	rmp 1; KpVP-1 (truncated),rmp 3; ICEKp1 (truncated)	26-1LV,119	rmpA2_3-47%	wzi1	KL1
653s /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
653s   warnings.warn(
918s strain	species	ST	virulence_score	resistance_score	Yersiniabactin	YbST	Colibactin	CbST	Aerobactin	AbST	Salmochelin	SmST	RmpADC	RmST	rmpA2	wzi	K_locus	AGly_acquired	Col_acquired	Fcyn_acquired	Flq_acquired	Gly_acquired	MLS_acquired	Phe_acquired	Rif_acquired	Sul_acquired	Tet_acquired	Tgc_acquired	Tmt_acquired	Bla_acquired	Bla_inhR_acquired	Bla_ESBL_acquired	Bla_ESBL_inhR_acquired	Bla_Carb_acquired	Bla_chr	SHV_mutations	Omp_mutations	Col_mutations	Flq_mutations	truncated_resistance_hits	spurious_resistance_hits
918s Klebs_HS11286	Klebsiella pneumoniae	ST11	1	3	ybt 9; ICEKp3	15	-	0	-	0	-	0	-	0	-	wzi74	KL103	aadA2^;rmtB;strA.v1^;strB.v1	-	-	-	-	-	-	-	sul2	tet(G).v1	-	dfrA12*	TEM-1;TEM-1;TEM-1	-	CTX-M-14;CTX-M-14	-	KPC-2	SHV-11	35Q	OmpK35-40%	PmrB-10%	GyrA-83I;ParC-80I	aac(3)-IId*?-0%	floR.v2*?;sul1?-63%
918s Klebs_Kp1084	Klebsiella pneumoniae	ST23	2	0	ybt 1; ICEKp10	47	clb 2	37	-	0	-	0	-	0	-	wzi172	KL1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	SHV-11^	35Q	-	-	-	-	-
918s MGH78578	Klebsiella pneumoniae	ST38	0	1	-	0	-	0	-	0	-	0	-	0	-	wzi50	KL15 (KL17,KL51,KL52)	aac(6')-Ib'.v1;aadA*;ant(2'')-Ia;aph(3')-Ia;strA.v1;strB.v1	-	-	-	-	-	catA1*;cmlA5	-	sul1;sul2	tet(D)	-	-	TEM-1D.v1^;TEM-1D.v1^	-	SHV-12	-	-	SHV-11^	238S;240K;35Q;35Q	OmpK35-86%	-	GyrA-83Y	OXA-9.v1*-42%	-
918s NTUH-K2044	Klebsiella pneumoniae	ST23	4	0	ybt 2; ICEKp1	326	-	0	iuc 1	1	iro 1,iro 3	19,18	rmp 1; KpVP-1 (truncated),rmp 3; ICEKp1 (truncated)	26-1LV,119	rmpA2_3-47%	wzi1	KL1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	SHV-11^	35Q	-	-	-	-	-
919s /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
919s   warnings.warn(
2998s strain	species	ST	virulence_score	resistance_score	Yersiniabactin	YbST	Colibactin	CbST	Aerobactin	AbST	Salmochelin	SmST	RmpADC	RmST	rmpA2	wzi	K_locus	K_locus_confidence	O_locus	O_locus_confidence	AGly_acquired	Col_acquired	Fcyn_acquired	Flq_acquired	Gly_acquired	MLS_acquired	Phe_acquired	Rif_acquired	Sul_acquired	Tet_acquired	Tgc_acquired	Tmt_acquired	Bla_acquired	Bla_inhR_acquired	Bla_ESBL_acquired	Bla_ESBL_inhR_acquired	Bla_Carb_acquired	Bla_chr	SHV_mutations	Omp_mutations	Col_mutations	Flq_mutations	truncated_resistance_hits	spurious_resistance_hits
2998s Klebs_HS11286	Klebsiella pneumoniae	ST11	1	3	ybt 9; ICEKp3	15	-	0	-	0	-	0	-	0	-	wzi74	KL103	Very high	O1/O2v1	Very high	aadA2^;rmtB;strA.v1^;strB.v1	-	-	-	-	-	-	-	sul2	tet(G).v1	-	dfrA12*	TEM-1;TEM-1;TEM-1	-	CTX-M-14;CTX-M-14	-	KPC-2	SHV-11	35Q	OmpK35-40%	PmrB-10%	GyrA-83I;ParC-80I	aac(3)-IId*?-0%	floR.v2*?;sul1?-63%
2998s Klebs_Kp1084	Klebsiella pneumoniae	ST23	2	0	ybt 1; ICEKp10	47	clb 2	37	-	0	-	0	-	0	-	wzi172	unknown (KL1)	None	O1/O2v2	High	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	SHV-11^	35Q	-	-	-	-	-
2998s MGH78578	Klebsiella pneumoniae	ST38	0	1	-	0	-	0	-	0	-	0	-	0	-	wzi50	KL52	Perfect	OL13	High	aac(6')-Ib'.v1;aadA*;ant(2'')-Ia;aph(3')-Ia;strA.v1;strB.v1	-	-	-	-	-	catA1*;cmlA5	-	sul1;sul2	tet(D)	-	-	TEM-1D.v1^;TEM-1D.v1^	-	SHV-12	-	-	SHV-11^	238S;240K;35Q;35Q	OmpK35-86%	-	GyrA-83Y	OXA-9.v1*-42%	-
2998s NTUH-K2044	Klebsiella pneumoniae	ST23	4	0	ybt 2; ICEKp1	326	-	0	iuc 1	1	iro 1,iro 3	19,18	rmp 1; KpVP-1 (truncated),rmp 3; ICEKp1 (truncated)	26-1LV,119	rmpA2_3-47%	wzi1	KL1	Perfect	O1/O2v2	Very high	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	SHV-11^	35Q	-	-	-	-	-
2998s autopkgtest [22:54:35]: test run-unit-test: -----------------------]
2999s autopkgtest [22:54:36]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
2999s run-unit-test        PASS
2999s autopkgtest [22:54:36]: @@@@@@@@@@@@@@@@@@@@ summary
2999s run-unit-test        PASS
3010s Creating nova instance adt-oracular-ppc64el-kleborate-20240505-220437-juju-7f2275-prod-proposed-migration-environment-3-0d490a1c-b84a-431b-b628-5c9f88380ef0 from image adt/ubuntu-oracular-ppc64el-server-20240504.img (UUID f8235939-8f4e-46c0-affb-4b5e32764d3a)...