0s autopkgtest [02:21:31]: starting date and time: 2024-07-27 02:21:31+0000 0s autopkgtest [02:21:31]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [02:21:31]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yk_iedvz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ncbi-blast+ --apt-upgrade kleborate --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=ncbi-blast+/2.16.0+ds-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-4.secgroup --name adt-oracular-ppc64el-kleborate-20240727-022131-juju-7f2275-prod-proposed-migration-environment-2-bb36eda3-2c9e-4a09-b732-1e3934647278 --image adt/ubuntu-oracular-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -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/ 76s autopkgtest [02:22:47]: testbed dpkg architecture: ppc64el 76s autopkgtest [02:22:47]: testbed apt version: 2.9.6 76s autopkgtest [02:22:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 77s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 77s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4288 B] 77s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [51.2 kB] 77s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 77s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [401 kB] 77s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [75.9 kB] 77s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el c-n-f Metadata [2116 B] 77s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1368 B] 77s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el c-n-f Metadata [120 B] 77s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [355 kB] 78s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el c-n-f Metadata [8952 B] 78s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [1448 B] 78s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el c-n-f Metadata [120 B] 80s Fetched 1035 kB in 1s (1267 kB/s) 80s Reading package lists... 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Calculating upgrade... 83s The following packages will be upgraded: 83s binutils binutils-common binutils-powerpc64le-linux-gnu bpftrace libbinutils 83s libclang-cpp18 libclang1-18 libctf-nobfd0 libctf0 libllvm18 libsframe1 83s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 68.3 MB of archives. 83s After this operation, 73.7 kB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu oracular/main ppc64el libctf0 ppc64el 2.42.90.20240720-2ubuntu1 [113 kB] 83s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el libctf-nobfd0 ppc64el 2.42.90.20240720-2ubuntu1 [113 kB] 84s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.42.90.20240720-2ubuntu1 [2493 kB] 84s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el libbinutils ppc64el 2.42.90.20240720-2ubuntu1 [702 kB] 84s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el binutils ppc64el 2.42.90.20240720-2ubuntu1 [3090 B] 84s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el binutils-common ppc64el 2.42.90.20240720-2ubuntu1 [221 kB] 84s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsframe1 ppc64el 2.42.90.20240720-2ubuntu1 [15.8 kB] 84s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el libclang-cpp18 ppc64el 1:18.1.8-4ubuntu1 [14.4 MB] 84s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libllvm18 ppc64el 1:18.1.8-4ubuntu1 [28.6 MB] 85s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el libclang1-18 ppc64el 1:18.1.8-4ubuntu1 [8653 kB] 86s Get:11 http://ftpmaster.internal/ubuntu oracular/main ppc64el bpftrace ppc64el 0.21.2-1ubuntu1 [12.9 MB] 86s Fetched 68.3 MB in 3s (22.4 MB/s) 87s (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 ... 72808 files and directories currently installed.) 87s Preparing to unpack .../00-libctf0_2.42.90.20240720-2ubuntu1_ppc64el.deb ... 87s Unpacking libctf0:ppc64el (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 87s Preparing to unpack .../01-libctf-nobfd0_2.42.90.20240720-2ubuntu1_ppc64el.deb ... 87s Unpacking libctf-nobfd0:ppc64el (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 87s Preparing to unpack .../02-binutils-powerpc64le-linux-gnu_2.42.90.20240720-2ubuntu1_ppc64el.deb ... 87s Unpacking binutils-powerpc64le-linux-gnu (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 88s Preparing to unpack .../03-libbinutils_2.42.90.20240720-2ubuntu1_ppc64el.deb ... 88s Unpacking libbinutils:ppc64el (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 88s Preparing to unpack .../04-binutils_2.42.90.20240720-2ubuntu1_ppc64el.deb ... 88s Unpacking binutils (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 88s Preparing to unpack .../05-binutils-common_2.42.90.20240720-2ubuntu1_ppc64el.deb ... 88s Unpacking binutils-common:ppc64el (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 88s Preparing to unpack .../06-libsframe1_2.42.90.20240720-2ubuntu1_ppc64el.deb ... 88s Unpacking libsframe1:ppc64el (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 88s Preparing to unpack .../07-libclang-cpp18_1%3a18.1.8-4ubuntu1_ppc64el.deb ... 88s Unpacking libclang-cpp18 (1:18.1.8-4ubuntu1) over (1:18.1.8-1) ... 88s Preparing to unpack .../08-libllvm18_1%3a18.1.8-4ubuntu1_ppc64el.deb ... 88s Unpacking libllvm18:ppc64el (1:18.1.8-4ubuntu1) over (1:18.1.8-1) ... 89s Preparing to unpack .../09-libclang1-18_1%3a18.1.8-4ubuntu1_ppc64el.deb ... 89s Unpacking libclang1-18 (1:18.1.8-4ubuntu1) over (1:18.1.8-1) ... 89s Preparing to unpack .../10-bpftrace_0.21.2-1ubuntu1_ppc64el.deb ... 89s Unpacking bpftrace (0.21.2-1ubuntu1) over (0.21.0-1ubuntu6) ... 89s Setting up binutils-common:ppc64el (2.42.90.20240720-2ubuntu1) ... 89s Setting up libctf-nobfd0:ppc64el (2.42.90.20240720-2ubuntu1) ... 89s Setting up libsframe1:ppc64el (2.42.90.20240720-2ubuntu1) ... 89s Setting up libbinutils:ppc64el (2.42.90.20240720-2ubuntu1) ... 89s Setting up libllvm18:ppc64el (1:18.1.8-4ubuntu1) ... 89s Setting up libctf0:ppc64el (2.42.90.20240720-2ubuntu1) ... 89s Setting up libclang1-18 (1:18.1.8-4ubuntu1) ... 89s Setting up bpftrace (0.21.2-1ubuntu1) ... 89s Setting up binutils-powerpc64le-linux-gnu (2.42.90.20240720-2ubuntu1) ... 89s Setting up libclang-cpp18 (1:18.1.8-4ubuntu1) ... 89s Setting up binutils (2.42.90.20240720-2ubuntu1) ... 89s Processing triggers for libc-bin (2.39-0ubuntu9) ... 89s Processing triggers for man-db (2.12.1-2) ... 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 93s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 93s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 93s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 94s Reading package lists... 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s autopkgtest [02:23:08]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 97s autopkgtest [02:23:08]: @@@@@@@@@@@@@@@@@@@@ apt-source kleborate 110s Get:1 http://ftpmaster.internal/ubuntu oracular/universe kleborate 2.4.1-3build1 (dsc) [2290 B] 110s Get:2 http://ftpmaster.internal/ubuntu oracular/universe kleborate 2.4.1-3build1 (tar) [91.6 MB] 110s Get:3 http://ftpmaster.internal/ubuntu oracular/universe kleborate 2.4.1-3build1 (diff) [5997 kB] 111s gpgv: Signature made Mon Apr 1 06:04:16 2024 UTC 111s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 111s gpgv: Can't check signature: No public key 111s dpkg-source: warning: cannot verify inline signature for ./kleborate_2.4.1-3build1.dsc: no acceptable signature found 113s autopkgtest [02:23:24]: testing package kleborate version 2.4.1-3build1 114s autopkgtest [02:23:25]: build not needed 120s autopkgtest [02:23:31]: test run-unit-test: preparing testbed 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 121s The following additional packages will be installed: 121s fonts-urw-base35 kaptive kaptive-data kleborate kleborate-examples libblas3 121s libcairo2 libcapnp-1.0.1 libfontenc1 libgfortran5 libgsl27 libgslcblas0 121s liblapack3 liblcms2-2 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 121s libmurmurhash2 libopenjp2-7 libpixman-1-0 libwebpdemux2 libwebpmux3 121s libxcb-render0 libxcb-shm0 libxrender1 mash ncbi-blast+ ncbi-data 121s python3-biopython python3-cairo python3-freetype python3-numpy python3-pil 121s python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib x11-common 121s xfonts-encodings xfonts-utils xml-core 121s Suggested packages: 121s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre kaptive-example 121s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblcms2-utils 121s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 121s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 121s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 121s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 121s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 121s rl-renderpm sgml-base-doc debhelper 121s Recommended packages: 121s python-biopython-doc python3-olefile fonts-dejavu-extra 121s The following NEW packages will be installed: 121s autopkgtest-satdep fonts-urw-base35 kaptive kaptive-data kleborate 121s kleborate-examples libblas3 libcairo2 libcapnp-1.0.1 libfontenc1 121s libgfortran5 libgsl27 libgslcblas0 liblapack3 liblcms2-2 libmbedcrypto7t64 121s libmbedtls14t64 libmbedx509-1t64 libmurmurhash2 libopenjp2-7 libpixman-1-0 121s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mash 121s ncbi-blast+ ncbi-data python3-biopython python3-cairo python3-freetype 121s python3-numpy python3-pil python3-reportlab python3-rlpycairo sgml-base 121s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 121s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. 121s Need to get 68.7 MB/68.8 MB of archives. 121s After this operation, 284 MB of additional disk space will be used. 121s Get:1 /tmp/autopkgtest.wEy7Rc/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 122s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el sgml-base all 1.31 [11.4 kB] 122s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 122s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 122s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 122s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el xfonts-utils ppc64el 1:7.7+6build3 [113 kB] 122s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 122s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 122s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14.1.0-5ubuntu1 [571 kB] 122s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 123s Get:11 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-10 [4408 kB] 123s Get:12 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblcms2-2 ppc64el 2.14-2build1 [233 kB] 123s Get:13 http://ftpmaster.internal/ubuntu oracular/main ppc64el libopenjp2-7 ppc64el 2.5.0-2build3 [239 kB] 123s Get:14 http://ftpmaster.internal/ubuntu oracular/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 123s Get:15 http://ftpmaster.internal/ubuntu oracular/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 123s Get:16 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-pil ppc64el 10.4.0-1 [495 kB] 123s Get:17 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpixman-1-0 ppc64el 0.42.2-1build1 [336 kB] 123s Get:18 http://ftpmaster.internal/ubuntu oracular/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 123s Get:19 http://ftpmaster.internal/ubuntu oracular/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 123s Get:20 http://ftpmaster.internal/ubuntu oracular/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 123s Get:21 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcairo2 ppc64el 1.18.0-3build1 [751 kB] 123s Get:22 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-cairo ppc64el 1.26.1-1 [129 kB] 123s Get:23 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-freetype all 2.4.0-2 [81.3 kB] 123s Get:24 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 123s Get:25 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-reportlab all 4.2.2-1 [1130 kB] 123s Get:26 http://ftpmaster.internal/ubuntu oracular/main ppc64el xml-core all 0.19 [20.3 kB] 123s Get:27 http://ftpmaster.internal/ubuntu oracular/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 123s Get:28 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-biopython ppc64el 1.83+dfsg1-3 [1696 kB] 123s Get:29 http://ftpmaster.internal/ubuntu oracular/universe ppc64el ncbi-data all 6.1.20170106+dfsg2-3 [3966 kB] 123s Get:30 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libmbedcrypto7t64 ppc64el 2.28.8-1 [267 kB] 123s Get:31 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libmbedx509-1t64 ppc64el 2.28.8-1 [51.7 kB] 123s Get:32 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libmbedtls14t64 ppc64el 2.28.8-1 [90.6 kB] 123s Get:33 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el ncbi-blast+ ppc64el 2.16.0+ds-3 [16.1 MB] 123s Get:34 http://ftpmaster.internal/ubuntu oracular/universe ppc64el kaptive all 2.0.8-1 [28.1 kB] 123s Get:35 http://ftpmaster.internal/ubuntu oracular/universe ppc64el kaptive-data all 2.0.8-1 [5432 kB] 123s Get:36 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libcapnp-1.0.1 ppc64el 1.0.1-4 [1561 kB] 124s Get:37 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu2 [86.6 kB] 124s Get:38 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu2 [1090 kB] 124s Get:39 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libmurmurhash2 ppc64el 1.6-1 [6626 B] 124s Get:40 http://ftpmaster.internal/ubuntu oracular/universe ppc64el mash ppc64el 2.3+dfsg-6 [159 kB] 124s Get:41 http://ftpmaster.internal/ubuntu oracular/universe ppc64el kleborate ppc64el 2.4.1-3build1 [8742 kB] 124s Get:42 http://ftpmaster.internal/ubuntu oracular/universe ppc64el kleborate-examples all 2.4.1-3build1 [5990 kB] 125s Fetched 68.7 MB in 3s (24.0 MB/s) 125s Selecting previously unselected package sgml-base. 125s (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 ... 72809 files and directories currently installed.) 125s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 125s Unpacking sgml-base (1.31) ... 125s Selecting previously unselected package libfontenc1:ppc64el. 125s Preparing to unpack .../01-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 125s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 125s Selecting previously unselected package x11-common. 125s Preparing to unpack .../02-x11-common_1%3a7.7+23ubuntu3_all.deb ... 125s Unpacking x11-common (1:7.7+23ubuntu3) ... 125s Selecting previously unselected package xfonts-encodings. 125s Preparing to unpack .../03-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 125s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 125s Selecting previously unselected package xfonts-utils. 125s Preparing to unpack .../04-xfonts-utils_1%3a7.7+6build3_ppc64el.deb ... 125s Unpacking xfonts-utils (1:7.7+6build3) ... 125s Selecting previously unselected package fonts-urw-base35. 125s Preparing to unpack .../05-fonts-urw-base35_20200910-8_all.deb ... 125s Unpacking fonts-urw-base35 (20200910-8) ... 125s Selecting previously unselected package libblas3:ppc64el. 125s Preparing to unpack .../06-libblas3_3.12.0-3build1_ppc64el.deb ... 125s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 125s Selecting previously unselected package libgfortran5:ppc64el. 125s Preparing to unpack .../07-libgfortran5_14.1.0-5ubuntu1_ppc64el.deb ... 125s Unpacking libgfortran5:ppc64el (14.1.0-5ubuntu1) ... 125s Selecting previously unselected package liblapack3:ppc64el. 125s Preparing to unpack .../08-liblapack3_3.12.0-3build1_ppc64el.deb ... 125s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 125s Selecting previously unselected package python3-numpy. 125s Preparing to unpack .../09-python3-numpy_1%3a1.26.4+ds-10_ppc64el.deb ... 125s Unpacking python3-numpy (1:1.26.4+ds-10) ... 125s Selecting previously unselected package liblcms2-2:ppc64el. 125s Preparing to unpack .../10-liblcms2-2_2.14-2build1_ppc64el.deb ... 125s Unpacking liblcms2-2:ppc64el (2.14-2build1) ... 125s Selecting previously unselected package libopenjp2-7:ppc64el. 125s Preparing to unpack .../11-libopenjp2-7_2.5.0-2build3_ppc64el.deb ... 125s Unpacking libopenjp2-7:ppc64el (2.5.0-2build3) ... 125s Selecting previously unselected package libwebpdemux2:ppc64el. 125s Preparing to unpack .../12-libwebpdemux2_1.4.0-0.1_ppc64el.deb ... 125s Unpacking libwebpdemux2:ppc64el (1.4.0-0.1) ... 125s Selecting previously unselected package libwebpmux3:ppc64el. 125s Preparing to unpack .../13-libwebpmux3_1.4.0-0.1_ppc64el.deb ... 125s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ... 125s Selecting previously unselected package python3-pil:ppc64el. 125s Preparing to unpack .../14-python3-pil_10.4.0-1_ppc64el.deb ... 125s Unpacking python3-pil:ppc64el (10.4.0-1) ... 125s Selecting previously unselected package libpixman-1-0:ppc64el. 125s Preparing to unpack .../15-libpixman-1-0_0.42.2-1build1_ppc64el.deb ... 125s Unpacking libpixman-1-0:ppc64el (0.42.2-1build1) ... 125s Selecting previously unselected package libxcb-render0:ppc64el. 125s Preparing to unpack .../16-libxcb-render0_1.17.0-2_ppc64el.deb ... 125s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 125s Selecting previously unselected package libxcb-shm0:ppc64el. 125s Preparing to unpack .../17-libxcb-shm0_1.17.0-2_ppc64el.deb ... 125s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 125s Selecting previously unselected package libxrender1:ppc64el. 125s Preparing to unpack .../18-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 125s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 126s Selecting previously unselected package libcairo2:ppc64el. 126s Preparing to unpack .../19-libcairo2_1.18.0-3build1_ppc64el.deb ... 126s Unpacking libcairo2:ppc64el (1.18.0-3build1) ... 126s Selecting previously unselected package python3-cairo. 126s Preparing to unpack .../20-python3-cairo_1.26.1-1_ppc64el.deb ... 126s Unpacking python3-cairo (1.26.1-1) ... 126s Selecting previously unselected package python3-freetype. 126s Preparing to unpack .../21-python3-freetype_2.4.0-2_all.deb ... 126s Unpacking python3-freetype (2.4.0-2) ... 126s Selecting previously unselected package python3-rlpycairo. 126s Preparing to unpack .../22-python3-rlpycairo_0.3.0-3_all.deb ... 126s Unpacking python3-rlpycairo (0.3.0-3) ... 126s Selecting previously unselected package python3-reportlab. 126s Preparing to unpack .../23-python3-reportlab_4.2.2-1_all.deb ... 126s Unpacking python3-reportlab (4.2.2-1) ... 126s Selecting previously unselected package xml-core. 126s Preparing to unpack .../24-xml-core_0.19_all.deb ... 126s Unpacking xml-core (0.19) ... 126s Selecting previously unselected package w3c-sgml-lib. 126s Preparing to unpack .../25-w3c-sgml-lib_1.3-3_all.deb ... 126s Unpacking w3c-sgml-lib (1.3-3) ... 126s Selecting previously unselected package python3-biopython. 126s Preparing to unpack .../26-python3-biopython_1.83+dfsg1-3_ppc64el.deb ... 126s Unpacking python3-biopython (1.83+dfsg1-3) ... 126s Selecting previously unselected package ncbi-data. 126s Preparing to unpack .../27-ncbi-data_6.1.20170106+dfsg2-3_all.deb ... 126s Unpacking ncbi-data (6.1.20170106+dfsg2-3) ... 126s Selecting previously unselected package libmbedcrypto7t64:ppc64el. 126s Preparing to unpack .../28-libmbedcrypto7t64_2.28.8-1_ppc64el.deb ... 126s Unpacking libmbedcrypto7t64:ppc64el (2.28.8-1) ... 126s Selecting previously unselected package libmbedx509-1t64:ppc64el. 126s Preparing to unpack .../29-libmbedx509-1t64_2.28.8-1_ppc64el.deb ... 126s Unpacking libmbedx509-1t64:ppc64el (2.28.8-1) ... 126s Selecting previously unselected package libmbedtls14t64:ppc64el. 126s Preparing to unpack .../30-libmbedtls14t64_2.28.8-1_ppc64el.deb ... 126s Unpacking libmbedtls14t64:ppc64el (2.28.8-1) ... 126s Selecting previously unselected package ncbi-blast+. 126s Preparing to unpack .../31-ncbi-blast+_2.16.0+ds-3_ppc64el.deb ... 126s Unpacking ncbi-blast+ (2.16.0+ds-3) ... 126s Selecting previously unselected package kaptive. 126s Preparing to unpack .../32-kaptive_2.0.8-1_all.deb ... 126s Unpacking kaptive (2.0.8-1) ... 126s Selecting previously unselected package kaptive-data. 126s Preparing to unpack .../33-kaptive-data_2.0.8-1_all.deb ... 126s Unpacking kaptive-data (2.0.8-1) ... 127s Selecting previously unselected package libcapnp-1.0.1:ppc64el. 127s Preparing to unpack .../34-libcapnp-1.0.1_1.0.1-4_ppc64el.deb ... 127s Unpacking libcapnp-1.0.1:ppc64el (1.0.1-4) ... 127s Selecting previously unselected package libgslcblas0:ppc64el. 127s Preparing to unpack .../35-libgslcblas0_2.7.1+dfsg-6ubuntu2_ppc64el.deb ... 127s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu2) ... 127s Selecting previously unselected package libgsl27:ppc64el. 127s Preparing to unpack .../36-libgsl27_2.7.1+dfsg-6ubuntu2_ppc64el.deb ... 127s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu2) ... 127s Selecting previously unselected package libmurmurhash2:ppc64el. 127s Preparing to unpack .../37-libmurmurhash2_1.6-1_ppc64el.deb ... 127s Unpacking libmurmurhash2:ppc64el (1.6-1) ... 127s Selecting previously unselected package mash. 127s Preparing to unpack .../38-mash_2.3+dfsg-6_ppc64el.deb ... 127s Unpacking mash (2.3+dfsg-6) ... 127s Selecting previously unselected package kleborate. 127s Preparing to unpack .../39-kleborate_2.4.1-3build1_ppc64el.deb ... 127s Unpacking kleborate (2.4.1-3build1) ... 127s Selecting previously unselected package kleborate-examples. 127s Preparing to unpack .../40-kleborate-examples_2.4.1-3build1_all.deb ... 127s Unpacking kleborate-examples (2.4.1-3build1) ... 127s Selecting previously unselected package autopkgtest-satdep. 127s Preparing to unpack .../41-1-autopkgtest-satdep.deb ... 127s Unpacking autopkgtest-satdep (0) ... 127s Setting up liblcms2-2:ppc64el (2.14-2build1) ... 127s Setting up ncbi-data (6.1.20170106+dfsg2-3) ... 127s Setting up libpixman-1-0:ppc64el (0.42.2-1build1) ... 127s Setting up libmbedcrypto7t64:ppc64el (2.28.8-1) ... 127s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ... 127s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu2) ... 127s Setting up libmurmurhash2:ppc64el (1.6-1) ... 127s Setting up libcapnp-1.0.1:ppc64el (1.0.1-4) ... 127s Setting up libxcb-render0:ppc64el (1.17.0-2) ... 127s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ... 127s Setting up x11-common (1:7.7+23ubuntu3) ... 128s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu2) ... 128s Setting up libxcb-shm0:ppc64el (1.17.0-2) ... 128s Setting up python3-freetype (2.4.0-2) ... 128s Setting up libcairo2:ppc64el (1.18.0-3build1) ... 128s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ... 128s Setting up libblas3:ppc64el (3.12.0-3build1) ... 128s 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 128s Setting up kleborate-examples (2.4.1-3build1) ... 128s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 128s Setting up mash (2.3+dfsg-6) ... 128s Setting up kaptive-data (2.0.8-1) ... 128s Setting up libgfortran5:ppc64el (14.1.0-5ubuntu1) ... 128s Setting up libopenjp2-7:ppc64el (2.5.0-2build3) ... 128s Setting up sgml-base (1.31) ... 128s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ... 128s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 128s 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 128s Setting up libmbedx509-1t64:ppc64el (2.28.8-1) ... 128s Setting up python3-cairo (1.26.1-1) ... 128s Setting up xfonts-utils (1:7.7+6build3) ... 128s Setting up python3-pil:ppc64el (10.4.0-1) ... 128s Setting up python3-rlpycairo (0.3.0-3) ... 128s Setting up python3-numpy (1:1.26.4+ds-10) ... 131s Setting up libmbedtls14t64:ppc64el (2.28.8-1) ... 131s Setting up xml-core (0.19) ... 131s Setting up fonts-urw-base35 (20200910-8) ... 131s Setting up ncbi-blast+ (2.16.0+ds-3) ... 131s Setting up python3-reportlab (4.2.2-1) ... 132s Processing triggers for libc-bin (2.39-0ubuntu9) ... 132s Processing triggers for man-db (2.12.1-2) ... 133s Processing triggers for sgml-base (1.31) ... 133s Setting up w3c-sgml-lib (1.3-3) ... 160s Setting up python3-biopython (1.83+dfsg1-3) ... 162s Setting up kaptive (2.0.8-1) ... 162s Setting up kleborate (2.4.1-3build1) ... 163s Setting up autopkgtest-satdep (0) ... 165s (Reading database ... 76292 files and directories currently installed.) 165s Removing autopkgtest-satdep (0) ... 166s autopkgtest [02:24:17]: test run-unit-test: [----------------------- 167s /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. 167s warnings.warn( 273s strain species ST virulence_score Yersiniabactin YbST Colibactin CbST Aerobactin AbST Salmochelin SmST RmpADC RmST rmpA2 wzi K_locus 273s Klebs_HS11286 Klebsiella pneumoniae ST11 1 ybt 9; ICEKp3 15 - 0 - 0 - 0 - 0 - wzi74 KL103 273s Klebs_Kp1084 Klebsiella pneumoniae ST23 2 ybt 1; ICEKp10 47 clb 2 37 - 0 - 0 - 0 - wzi172 KL1 273s MGH78578 Klebsiella pneumoniae ST38 0 - 0 - 0 - 0 - 0 - 0 - wzi50 KL15 (KL17,KL51,KL52) 273s 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 273s /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. 273s warnings.warn( 439s 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 439s 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% 439s Klebs_Kp1084 Klebsiella pneumoniae ST23 2 0 ybt 1; ICEKp10 47 clb 2 37 - 0 - 0 - 0 - wzi172 KL1 - - - - - - - - - - - - - - - - - SHV-11^ 35Q - - - - - 439s 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% - 439s 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 - - - - - 439s /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. 439s warnings.warn( 941s 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 941s 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% 941s 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 - - - - - 941s 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% - 941s 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 - - - - - 942s autopkgtest [02:37:13]: test run-unit-test: -----------------------] 942s autopkgtest [02:37:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 942s run-unit-test PASS 943s autopkgtest [02:37:14]: @@@@@@@@@@@@@@@@@@@@ summary 943s run-unit-test PASS 954s nova [W] Using flock in prodstack6-ppc64el 954s Creating nova instance adt-oracular-ppc64el-kleborate-20240727-022131-juju-7f2275-prod-proposed-migration-environment-2-bb36eda3-2c9e-4a09-b732-1e3934647278 from image adt/ubuntu-oracular-ppc64el-server-20240726.img (UUID cf08a693-81bf-423c-a684-4129eea7b1f2)...