0s autopkgtest [21:54:52]: starting date and time: 2024-03-17 21:54:52+0000 0s autopkgtest [21:54:52]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [21:54:52]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qaxdfjku/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ncbi-blast+,src:mbedtls --apt-upgrade kleborate --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-14.secgroup --name adt-noble-s390x-kleborate-20240317-215452-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 199s autopkgtest [21:58:11]: testbed dpkg architecture: s390x 199s autopkgtest [21:58:11]: testbed apt version: 2.7.12 199s autopkgtest [21:58:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 200s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 200s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 200s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3676 kB] 201s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [484 kB] 201s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 201s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [639 kB] 201s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 201s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 201s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 201s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3877 kB] 201s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 201s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [33.2 kB] 201s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 203s Fetched 8895 kB in 2s (3938 kB/s) 203s Reading package lists... 205s Reading package lists... 206s Building dependency tree... 206s Reading state information... 206s Calculating upgrade... 206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 206s 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 noble-proposed InRelease 207s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 207s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 207s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 208s Reading package lists... 208s Reading package lists... 208s Building dependency tree... 208s Reading state information... 208s Calculating upgrade... 208s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 208s Reading package lists... 208s Building dependency tree... 208s Reading state information... 209s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 211s autopkgtest [21:58:23]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 211s autopkgtest [21:58:23]: @@@@@@@@@@@@@@@@@@@@ apt-source kleborate 220s Get:1 http://ftpmaster.internal/ubuntu noble/universe kleborate 2.4.1-3 (dsc) [2331 B] 220s Get:2 http://ftpmaster.internal/ubuntu noble/universe kleborate 2.4.1-3 (tar) [91.6 MB] 220s Get:3 http://ftpmaster.internal/ubuntu noble/universe kleborate 2.4.1-3 (diff) [5997 kB] 220s gpgv: Signature made Sun Mar 10 19:05:38 2024 UTC 220s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 220s gpgv: issuer "emollier@debian.org" 220s gpgv: Can't check signature: No public key 220s dpkg-source: warning: cannot verify inline signature for ./kleborate_2.4.1-3.dsc: no acceptable signature found 222s autopkgtest [21:58:34]: testing package kleborate version 2.4.1-3 223s autopkgtest [21:58:35]: build not needed 229s autopkgtest [21:58:41]: test run-unit-test: preparing testbed 231s Reading package lists... 231s Building dependency tree... 231s Reading state information... 231s Starting pkgProblemResolver with broken count: 0 231s Starting 2 pkgProblemResolver with broken count: 0 231s Done 231s The following additional packages will be installed: 231s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 231s fonts-urw-base35 kaptive kaptive-data kleborate kleborate-examples libblas3 231s libcairo2 libcapnp-1.0.1 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 231s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 231s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 231s libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmurmurhash2 231s libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 231s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mash 231s ncbi-blast+ ncbi-data python3-biopython python3-cairo python3-freetype 231s python3-numpy python3-pil python3-reportlab python3-rlpycairo sgml-base 231s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 231s Suggested packages: 231s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre kaptive-example 231s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblcms2-utils 231s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 231s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 231s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 231s gcc gfortran python3-dev python3-pytest python-pil-doc pdf-viewer 231s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 231s sgml-base-doc debhelper 231s Recommended packages: 231s python-biopython-doc python3-olefile 231s The following NEW packages will be installed: 231s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-extra 231s fonts-dejavu-mono fonts-urw-base35 kaptive kaptive-data kleborate 231s kleborate-examples libblas3 libcairo2 libcapnp-1.0.1 libdeflate0 231s libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 231s libgsl27 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 231s libjpeg8 liblapack3 liblcms2-2 libmbedcrypto7t64 libmbedtls14t64 231s libmbedx509-1t64 libmurmurhash2 libopenjp2-7 libpixman-1-0 libraqm0 231s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 231s libxcb-shm0 libxrender1 mash ncbi-blast+ ncbi-data python3-biopython 231s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 231s python3-rlpycairo sgml-base w3c-sgml-lib x11-common xfonts-encodings 231s xfonts-utils xml-core 231s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 231s Need to get 71.7 MB/71.7 MB of archives. 231s After this operation, 277 MB of additional disk space will be used. 231s Get:1 /tmp/autopkgtest.3GEnxs/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 231s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x sgml-base all 1.31 [11.4 kB] 231s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 232s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 232s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libfontenc1 s390x 1:1.1.8-1 [14.8 kB] 232s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 232s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] 232s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 232s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-utils s390x 1:7.7+6build2 [94.8 kB] 232s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 233s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 233s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-extra all 2.37-8 [1947 kB] 233s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 233s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 233s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 233s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB] 233s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 233s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libimagequant0 s390x 2.18.0-1 [42.9 kB] 233s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 233s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 233s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB] 233s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libopenjp2-7 s390x 2.5.0-2 [169 kB] 233s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 233s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 233s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libraqm0 s390x 0.10.1-1 [14.4 kB] 233s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 233s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 233s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 233s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 233s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 233s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libwebpdemux2 s390x 1.3.2-0.4 [12.4 kB] 233s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libwebpmux3 s390x 1.3.2-0.4 [25.4 kB] 233s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x python3-pil s390x 10.2.0-1 [519 kB] 233s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 233s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 233s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 233s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 233s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 233s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 233s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x python3-cairo s390x 1.25.1-2 [150 kB] 233s Get:41 http://ftpmaster.internal/ubuntu noble/universe s390x python3-freetype all 2.4.0-1 [83.1 kB] 233s Get:42 http://ftpmaster.internal/ubuntu noble/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 233s Get:43 http://ftpmaster.internal/ubuntu noble/universe s390x python3-reportlab all 4.1.0-1 [683 kB] 233s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x xml-core all 0.19 [20.3 kB] 233s Get:45 http://ftpmaster.internal/ubuntu noble/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 233s Get:46 http://ftpmaster.internal/ubuntu noble/universe s390x python3-biopython s390x 1.81+dfsg-3 [2234 kB] 233s Get:47 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 234s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedcrypto7t64 s390x 2.28.7-1.1ubuntu1 [216 kB] 234s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedx509-1t64 s390x 2.28.7-1.1ubuntu1 [46.2 kB] 234s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedtls14t64 s390x 2.28.7-1.1ubuntu1 [84.7 kB] 234s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x ncbi-blast+ s390x 2.12.0+ds-4build1 [12.8 MB] 234s Get:52 http://ftpmaster.internal/ubuntu noble/universe s390x kaptive all 2.0.8-1 [28.1 kB] 234s Get:53 http://ftpmaster.internal/ubuntu noble/universe s390x kaptive-data all 2.0.8-1 [5432 kB] 234s Get:54 http://ftpmaster.internal/ubuntu noble/universe s390x libcapnp-1.0.1 s390x 1.0.1-3 [1405 kB] 234s Get:55 http://ftpmaster.internal/ubuntu noble/universe s390x libgslcblas0 s390x 2.7.1+dfsg-6ubuntu1 [147 kB] 234s Get:56 http://ftpmaster.internal/ubuntu noble/universe s390x libgsl27 s390x 2.7.1+dfsg-6ubuntu1 [1069 kB] 235s Get:57 http://ftpmaster.internal/ubuntu noble/universe s390x libmurmurhash2 s390x 1.6-1 [6162 B] 235s Get:58 http://ftpmaster.internal/ubuntu noble/universe s390x mash s390x 2.3+dfsg-6 [191 kB] 235s Get:59 http://ftpmaster.internal/ubuntu noble/universe s390x kleborate s390x 2.4.1-3 [8730 kB] 235s Get:60 http://ftpmaster.internal/ubuntu noble/universe s390x kleborate-examples all 2.4.1-3 [5990 kB] 235s Fetched 71.7 MB in 4s (18.6 MB/s) 235s Selecting previously unselected package sgml-base. 235s (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 ... 52171 files and directories currently installed.) 235s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 235s Unpacking sgml-base (1.31) ... 235s Selecting previously unselected package fonts-dejavu-mono. 235s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 235s Unpacking fonts-dejavu-mono (2.37-8) ... 235s Selecting previously unselected package fonts-dejavu-core. 236s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 236s Unpacking fonts-dejavu-core (2.37-8) ... 236s Selecting previously unselected package libfontenc1:s390x. 236s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1_s390x.deb ... 236s Unpacking libfontenc1:s390x (1:1.1.8-1) ... 236s Selecting previously unselected package libfreetype6:s390x. 236s Preparing to unpack .../04-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 236s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 236s Selecting previously unselected package x11-common. 236s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu2_all.deb ... 236s Unpacking x11-common (1:7.7+23ubuntu2) ... 236s Selecting previously unselected package xfonts-encodings. 236s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 236s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 236s Selecting previously unselected package xfonts-utils. 236s Preparing to unpack .../07-xfonts-utils_1%3a7.7+6build2_s390x.deb ... 236s Unpacking xfonts-utils (1:7.7+6build2) ... 236s Selecting previously unselected package fonts-urw-base35. 236s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 236s Unpacking fonts-urw-base35 (20200910-8) ... 236s Selecting previously unselected package fontconfig-config. 236s Preparing to unpack .../09-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 236s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 236s Selecting previously unselected package fonts-dejavu-extra. 236s Preparing to unpack .../10-fonts-dejavu-extra_2.37-8_all.deb ... 236s Unpacking fonts-dejavu-extra (2.37-8) ... 236s Selecting previously unselected package libblas3:s390x. 236s Preparing to unpack .../11-libblas3_3.12.0-3_s390x.deb ... 236s Unpacking libblas3:s390x (3.12.0-3) ... 236s Selecting previously unselected package libgfortran5:s390x. 236s Preparing to unpack .../12-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 236s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 236s Selecting previously unselected package liblapack3:s390x. 236s Preparing to unpack .../13-liblapack3_3.12.0-3_s390x.deb ... 236s Unpacking liblapack3:s390x (3.12.0-3) ... 236s Selecting previously unselected package python3-numpy. 236s Preparing to unpack .../14-python3-numpy_1%3a1.24.2-2_s390x.deb ... 236s Unpacking python3-numpy (1:1.24.2-2) ... 236s Selecting previously unselected package libgomp1:s390x. 236s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 236s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 236s Selecting previously unselected package libimagequant0:s390x. 236s Preparing to unpack .../16-libimagequant0_2.18.0-1_s390x.deb ... 236s Unpacking libimagequant0:s390x (2.18.0-1) ... 236s Selecting previously unselected package libjpeg-turbo8:s390x. 236s Preparing to unpack .../17-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 236s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 236s Selecting previously unselected package libjpeg8:s390x. 236s Preparing to unpack .../18-libjpeg8_8c-2ubuntu11_s390x.deb ... 236s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 236s Selecting previously unselected package liblcms2-2:s390x. 236s Preparing to unpack .../19-liblcms2-2_2.14-2_s390x.deb ... 236s Unpacking liblcms2-2:s390x (2.14-2) ... 236s Selecting previously unselected package libopenjp2-7:s390x. 236s Preparing to unpack .../20-libopenjp2-7_2.5.0-2_s390x.deb ... 236s Unpacking libopenjp2-7:s390x (2.5.0-2) ... 236s Selecting previously unselected package libgraphite2-3:s390x. 236s Preparing to unpack .../21-libgraphite2-3_1.3.14-2_s390x.deb ... 236s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 236s Selecting previously unselected package libharfbuzz0b:s390x. 236s Preparing to unpack .../22-libharfbuzz0b_8.3.0-2_s390x.deb ... 236s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 236s Selecting previously unselected package libraqm0:s390x. 236s Preparing to unpack .../23-libraqm0_0.10.1-1_s390x.deb ... 236s Unpacking libraqm0:s390x (0.10.1-1) ... 236s Selecting previously unselected package libdeflate0:s390x. 236s Preparing to unpack .../24-libdeflate0_1.19-1_s390x.deb ... 236s Unpacking libdeflate0:s390x (1.19-1) ... 236s Selecting previously unselected package libjbig0:s390x. 236s Preparing to unpack .../25-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 236s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 236s Selecting previously unselected package libsharpyuv0:s390x. 237s Preparing to unpack .../26-libsharpyuv0_1.3.2-0.4_s390x.deb ... 237s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ... 237s Selecting previously unselected package libwebp7:s390x. 237s Preparing to unpack .../27-libwebp7_1.3.2-0.4_s390x.deb ... 237s Unpacking libwebp7:s390x (1.3.2-0.4) ... 237s Selecting previously unselected package libtiff6:s390x. 237s Preparing to unpack .../28-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ... 237s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 237s Selecting previously unselected package libwebpdemux2:s390x. 237s Preparing to unpack .../29-libwebpdemux2_1.3.2-0.4_s390x.deb ... 237s Unpacking libwebpdemux2:s390x (1.3.2-0.4) ... 237s Selecting previously unselected package libwebpmux3:s390x. 237s Preparing to unpack .../30-libwebpmux3_1.3.2-0.4_s390x.deb ... 237s Unpacking libwebpmux3:s390x (1.3.2-0.4) ... 237s Selecting previously unselected package python3-pil:s390x. 237s Preparing to unpack .../31-python3-pil_10.2.0-1_s390x.deb ... 237s Unpacking python3-pil:s390x (10.2.0-1) ... 237s Selecting previously unselected package libfontconfig1:s390x. 237s Preparing to unpack .../32-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 237s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 237s Selecting previously unselected package libpixman-1-0:s390x. 237s Preparing to unpack .../33-libpixman-1-0_0.42.2-1_s390x.deb ... 237s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 237s Selecting previously unselected package libxcb-render0:s390x. 237s Preparing to unpack .../34-libxcb-render0_1.15-1_s390x.deb ... 237s Unpacking 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to unpack .../40-python3-rlpycairo_0.3.0-3_all.deb ... 237s Unpacking python3-rlpycairo (0.3.0-3) ... 237s Selecting previously unselected package python3-reportlab. 237s Preparing to unpack .../41-python3-reportlab_4.1.0-1_all.deb ... 237s Unpacking python3-reportlab (4.1.0-1) ... 237s Selecting previously unselected package xml-core. 237s Preparing to unpack .../42-xml-core_0.19_all.deb ... 237s Unpacking xml-core (0.19) ... 237s Selecting previously unselected package w3c-sgml-lib. 237s Preparing to unpack .../43-w3c-sgml-lib_1.3-3_all.deb ... 237s Unpacking w3c-sgml-lib (1.3-3) ... 237s Selecting previously unselected package python3-biopython. 237s Preparing to unpack .../44-python3-biopython_1.81+dfsg-3_s390x.deb ... 237s Unpacking python3-biopython (1.81+dfsg-3) ... 237s Selecting previously unselected package ncbi-data. 237s Preparing to unpack .../45-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 237s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 237s Selecting previously 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238s Unpacking mash (2.3+dfsg-6) ... 238s Selecting previously unselected package kleborate. 238s Preparing to unpack .../57-kleborate_2.4.1-3_s390x.deb ... 238s Unpacking kleborate (2.4.1-3) ... 238s Selecting previously unselected package kleborate-examples. 238s Preparing to unpack .../58-kleborate-examples_2.4.1-3_all.deb ... 238s Unpacking kleborate-examples (2.4.1-3) ... 238s Selecting previously unselected package autopkgtest-satdep. 238s Preparing to unpack .../59-1-autopkgtest-satdep.deb ... 238s Unpacking autopkgtest-satdep (0) ... 238s Setting up libgraphite2-3:s390x (1.3.14-2) ... 238s Setting up liblcms2-2:s390x (2.14-2) ... 238s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 238s Setting up libpixman-1-0:s390x (0.42.2-1) ... 238s Setting up libsharpyuv0:s390x (1.3.2-0.4) ... 238s Setting up libmbedcrypto7t64:s390x (2.28.7-1.1ubuntu1) ... 238s Setting up libxrender1:s390x (1:0.9.10-1.1) ... 238s Setting up libgslcblas0:s390x (2.7.1+dfsg-6ubuntu1) ... 238s Setting up 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... 239s Setting up fonts-dejavu-core (2.37-8) ... 239s Setting up kaptive-data (2.0.8-1) ... 239s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 239s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 239s Setting up libwebp7:s390x (1.3.2-0.4) ... 239s Setting up fonts-dejavu-extra (2.37-8) ... 239s Setting up libopenjp2-7:s390x (2.5.0-2) ... 239s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 239s Setting up sgml-base (1.31) ... 239s Setting up libwebpmux3:s390x (1.3.2-0.4) ... 239s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 239s Setting up liblapack3:s390x (3.12.0-3) ... 239s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 239s Setting up libmbedx509-1t64:s390x (2.28.7-1.1ubuntu1) ... 239s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 239s Setting up libwebpdemux2:s390x (1.3.2-0.4) ... 239s Setting up python3-freetype (2.4.0-1) ... 239s Setting up xfonts-utils (1:7.7+6build2) ... 239s Setting up libraqm0:s390x (0.10.1-1) ... 239s Setting up python3-numpy (1:1.24.2-2) ... 241s Setting up libmbedtls14t64:s390x (2.28.7-1.1ubuntu1) ... 241s Setting up libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 241s Setting up xml-core (0.19) ... 241s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 241s Setting up fonts-urw-base35 (20200910-8) ... 241s Setting up libcairo2:s390x (1.18.0-1) ... 241s Setting up ncbi-blast+ (2.12.0+ds-4build1) ... 241s Setting up python3-pil:s390x (10.2.0-1) ... 241s Setting up python3-cairo (1.25.1-2) ... 241s Setting up python3-rlpycairo (0.3.0-3) ... 241s Setting up python3-reportlab (4.1.0-1) ... 242s Processing triggers for libc-bin (2.39-0ubuntu2) ... 242s Processing triggers for man-db (2.12.0-3) ... 243s Processing triggers for sgml-base (1.31) ... 243s Setting up w3c-sgml-lib (1.3-3) ... 265s Setting up python3-biopython (1.81+dfsg-3) ... 266s Setting up kaptive (2.0.8-1) ... 266s Setting up kleborate (2.4.1-3) ... 267s Setting up autopkgtest-satdep (0) ... 270s (Reading database ... 55855 files and directories currently installed.) 270s Removing autopkgtest-satdep (0) ... 271s autopkgtest [21:59:23]: test run-unit-test: [----------------------- 271s /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. 271s warnings.warn( 272s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 281s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 281s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 281s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 284s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 293s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 293s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 293s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 296s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 298s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 298s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 298s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 301s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 310s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 310s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 310s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 311s strain species ST virulence_score Yersiniabactin YbST Colibactin CbST Aerobactin AbST Salmochelin SmST RmpADC RmST rmpA2 wzi K_locus 311s Klebs_HS11286 Klebsiella pneumoniae 0 1 ybt 9; ICEKp3 15 - 0 - 0 - 0 - 0 - wzi74 KL103 311s Klebs_Kp1084 Klebsiella pneumoniae 0 2 ybt 1; ICEKp10 47 clb 2 37 - 0 - 0 - 0 - wzi172 KL1 311s MGH78578 Klebsiella pneumoniae 0 0 - 0 - 0 - 0 - 0 - 0 - wzi50 KL15 (KL17,KL51,KL52) 311s NTUH-K2044 Klebsiella pneumoniae 0 1 ybt 2; ICEKp1 326 - 0 - 0 - 0 - 0 rmpA2_3-47% wzi1 KL1 312s /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. 312s warnings.warn( 313s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 321s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 321s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 321s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 323s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ndb 327s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 336s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 336s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 336s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 338s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ndb 341s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 342s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 342s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 343s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 344s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ndb 348s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 356s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 356s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 356s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 358s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ndb 360s 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 360s Klebs_HS11286 Klebsiella pneumoniae 0 1 0 ybt 9; ICEKp3 15 - 0 - 0 - 0 - 0 - wzi74 KL103 - - - - - - - - - - - - - - - - - - - OmpK35-40% PmrB-10% GyrA-83I;ParC-80I - - 360s Klebs_Kp1084 Klebsiella pneumoniae 0 2 0 ybt 1; ICEKp10 47 clb 2 37 - 0 - 0 - 0 - wzi172 KL1 - - - - - - - - - - - - - - - - - - - - - - - - 360s MGH78578 Klebsiella pneumoniae 0 0 0 - 0 - 0 - 0 - 0 - 0 - wzi50 KL15 (KL17,KL51,KL52) - - - - - - - - - - - - - - - - - - - OmpK35-86% - GyrA-83Y - - 360s NTUH-K2044 Klebsiella pneumoniae 0 1 0 ybt 2; ICEKp1 326 - 0 - 0 - 0 - 0 rmpA2_3-47% wzi1 KL1 - - - - - - - - - - - - - - - - - - - - - - - - 361s /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. 361s warnings.warn( 362s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 370s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 370s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 370s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 372s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ndb 533s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 542s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 542s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 542s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 544s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ndb 699s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 701s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 701s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 701s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 703s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ndb 865s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb 873s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb 873s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb 873s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb 875s BLAST Database error: Invalid db file : /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ndb 1030s 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 1030s Klebs_HS11286 Klebsiella pneumoniae 0 1 0 ybt 9; ICEKp3 15 - 0 - 0 - 0 - 0 - wzi74 KL103 Very high O1/O2v1 Very high - - - - - - - - - - - - - - - - - - - OmpK35-40% PmrB-10% GyrA-83I;ParC-80I - - 1030s Klebs_Kp1084 Klebsiella pneumoniae 0 2 0 ybt 1; ICEKp10 47 clb 2 37 - 0 - 0 - 0 - wzi172 unknown (KL1) None O1/O2v2 High - - - - - - - - - - - - - - - - - - - - - - - - 1030s MGH78578 Klebsiella pneumoniae 0 0 0 - 0 - 0 - 0 - 0 - 0 - wzi50 KL52 Perfect OL13 High - - - - - - - - - - - - - - - - - - - OmpK35-86% - GyrA-83Y - - 1030s NTUH-K2044 Klebsiella pneumoniae 0 1 0 ybt 2; ICEKp1 326 - 0 - 0 - 0 - 0 rmpA2_3-47% wzi1 KL1 Perfect O1/O2v2 Very high - - - - - - - - - - - - - - - - - - - - - - - - 1030s autopkgtest [22:12:02]: test run-unit-test: -----------------------] 1031s autopkgtest [22:12:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1031s run-unit-test PASS 1031s autopkgtest [22:12:03]: @@@@@@@@@@@@@@@@@@@@ summary 1031s run-unit-test PASS 1042s Creating nova instance adt-noble-s390x-kleborate-20240317-215452-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240316.img (UUID 7afe023c-7cb8-41b6-91a7-c69e7d1e7c0d)...