0s autopkgtest [02:21:28]: starting date and time: 2024-07-27 02:21:28+0000 0s autopkgtest [02:21:28]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [02:21:28]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.37p7d74h/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-5.secgroup --name adt-oracular-arm64-kleborate-20240727-022128-juju-7f2275-prod-proposed-migration-environment-3-fda14b2c-8fe8-48dd-a739-90337e2251a9 --image adt/ubuntu-oracular-arm64-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/ 362s autopkgtest [02:27:30]: testbed dpkg architecture: arm64 362s autopkgtest [02:27:30]: testbed apt version: 2.9.6 362s autopkgtest [02:27:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 365s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 365s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4288 B] 366s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 366s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [51.2 kB] 366s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [401 kB] 366s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [92.5 kB] 366s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2116 B] 366s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB] 366s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B] 366s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [360 kB] 367s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [8752 B] 367s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [8744 B] 367s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B] 374s Fetched 1108 kB in 3s (386 kB/s) 374s Reading package lists... 382s Reading package lists... 382s Building dependency tree... 382s Reading state information... 383s Calculating upgrade... 383s The following packages will be upgraded: 383s binutils binutils-aarch64-linux-gnu binutils-common bpftrace libbinutils 383s libclang-cpp18 libclang1-18 libctf-nobfd0 libctf0 libgprofng0 libllvm18 383s libsframe1 383s 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 383s Need to get 63.8 MB of archives. 383s After this operation, 73.7 kB of additional disk space will be used. 383s Get:1 http://ftpmaster.internal/ubuntu oracular/main arm64 libgprofng0 arm64 2.42.90.20240720-2ubuntu1 [789 kB] 384s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 libctf0 arm64 2.42.90.20240720-2ubuntu1 [96.7 kB] 384s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libctf-nobfd0 arm64 2.42.90.20240720-2ubuntu1 [101 kB] 384s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 binutils-aarch64-linux-gnu arm64 2.42.90.20240720-2ubuntu1 [3335 kB] 385s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 libbinutils arm64 2.42.90.20240720-2ubuntu1 [774 kB] 385s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 binutils arm64 2.42.90.20240720-2ubuntu1 [18.1 kB] 385s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 binutils-common arm64 2.42.90.20240720-2ubuntu1 [243 kB] 385s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 libsframe1 arm64 2.42.90.20240720-2ubuntu1 [14.1 kB] 385s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 libclang-cpp18 arm64 1:18.1.8-4ubuntu1 [13.1 MB] 387s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 libllvm18 arm64 1:18.1.8-4ubuntu1 [26.2 MB] 388s Get:11 http://ftpmaster.internal/ubuntu oracular/main arm64 libclang1-18 arm64 1:18.1.8-4ubuntu1 [7506 kB] 388s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 bpftrace arm64 0.21.2-1ubuntu1 [11.7 MB] 390s Fetched 63.8 MB in 5s (11.8 MB/s) 390s (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 ... 78607 files and directories currently installed.) 390s Preparing to unpack .../00-libgprofng0_2.42.90.20240720-2ubuntu1_arm64.deb ... 390s Unpacking libgprofng0:arm64 (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 390s Preparing to unpack .../01-libctf0_2.42.90.20240720-2ubuntu1_arm64.deb ... 390s Unpacking libctf0:arm64 (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 391s Preparing to unpack .../02-libctf-nobfd0_2.42.90.20240720-2ubuntu1_arm64.deb ... 391s Unpacking libctf-nobfd0:arm64 (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 392s Preparing to unpack .../03-binutils-aarch64-linux-gnu_2.42.90.20240720-2ubuntu1_arm64.deb ... 392s Unpacking binutils-aarch64-linux-gnu (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 393s Preparing to unpack .../04-libbinutils_2.42.90.20240720-2ubuntu1_arm64.deb ... 393s Unpacking libbinutils:arm64 (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 393s Preparing to unpack .../05-binutils_2.42.90.20240720-2ubuntu1_arm64.deb ... 393s Unpacking binutils (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 394s Preparing to unpack .../06-binutils-common_2.42.90.20240720-2ubuntu1_arm64.deb ... 394s Unpacking binutils-common:arm64 (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 394s Preparing to unpack .../07-libsframe1_2.42.90.20240720-2ubuntu1_arm64.deb ... 394s Unpacking libsframe1:arm64 (2.42.90.20240720-2ubuntu1) over (2.42.50.20240710-1ubuntu1) ... 395s Preparing to unpack .../08-libclang-cpp18_1%3a18.1.8-4ubuntu1_arm64.deb ... 395s Unpacking libclang-cpp18 (1:18.1.8-4ubuntu1) over (1:18.1.8-1) ... 397s Preparing to unpack .../09-libllvm18_1%3a18.1.8-4ubuntu1_arm64.deb ... 397s Unpacking libllvm18:arm64 (1:18.1.8-4ubuntu1) over (1:18.1.8-1) ... 398s Preparing to unpack .../10-libclang1-18_1%3a18.1.8-4ubuntu1_arm64.deb ... 398s Unpacking libclang1-18 (1:18.1.8-4ubuntu1) over (1:18.1.8-1) ... 398s Preparing to unpack .../11-bpftrace_0.21.2-1ubuntu1_arm64.deb ... 398s Unpacking bpftrace (0.21.2-1ubuntu1) over (0.21.0-1ubuntu6) ... 400s Setting up binutils-common:arm64 (2.42.90.20240720-2ubuntu1) ... 400s Setting up libctf-nobfd0:arm64 (2.42.90.20240720-2ubuntu1) ... 400s Setting up libsframe1:arm64 (2.42.90.20240720-2ubuntu1) ... 400s Setting up libbinutils:arm64 (2.42.90.20240720-2ubuntu1) ... 400s Setting up libllvm18:arm64 (1:18.1.8-4ubuntu1) ... 400s Setting up libctf0:arm64 (2.42.90.20240720-2ubuntu1) ... 400s Setting up libclang1-18 (1:18.1.8-4ubuntu1) ... 400s Setting up bpftrace (0.21.2-1ubuntu1) ... 400s Setting up libgprofng0:arm64 (2.42.90.20240720-2ubuntu1) ... 400s Setting up libclang-cpp18 (1:18.1.8-4ubuntu1) ... 400s Setting up binutils-aarch64-linux-gnu (2.42.90.20240720-2ubuntu1) ... 400s Setting up binutils (2.42.90.20240720-2ubuntu1) ... 400s Processing triggers for libc-bin (2.39-0ubuntu9) ... 400s Processing triggers for man-db (2.12.1-2) ... 403s Reading package lists... 403s Building dependency tree... 403s Reading state information... 404s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 406s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 406s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 406s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 406s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 410s Reading package lists... 411s Reading package lists... 411s Building dependency tree... 411s Reading state information... 411s Calculating upgrade... 412s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 412s Reading package lists... 413s Building dependency tree... 413s Reading state information... 413s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 443s autopkgtest [02:28:51]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 445s autopkgtest [02:28:53]: @@@@@@@@@@@@@@@@@@@@ apt-source kleborate 469s Get:1 http://ftpmaster.internal/ubuntu oracular/universe kleborate 2.4.1-3build1 (dsc) [2290 B] 469s Get:2 http://ftpmaster.internal/ubuntu oracular/universe kleborate 2.4.1-3build1 (tar) [91.6 MB] 469s Get:3 http://ftpmaster.internal/ubuntu oracular/universe kleborate 2.4.1-3build1 (diff) [5997 kB] 472s gpgv: Signature made Mon Apr 1 06:04:16 2024 UTC 472s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 472s gpgv: Can't check signature: No public key 472s dpkg-source: warning: cannot verify inline signature for ./kleborate_2.4.1-3build1.dsc: no acceptable signature found 480s autopkgtest [02:29:28]: testing package kleborate version 2.4.1-3build1 482s autopkgtest [02:29:30]: build not needed 489s autopkgtest [02:29:37]: test run-unit-test: preparing testbed 493s Reading package lists... 493s Building dependency tree... 493s Reading state information... 494s Starting pkgProblemResolver with broken count: 0 494s Starting 2 pkgProblemResolver with broken count: 0 494s Done 495s The following additional packages will be installed: 495s fonts-urw-base35 kaptive kaptive-data kleborate kleborate-examples libblas3 495s libcairo2 libcapnp-1.0.1 libfontenc1 libgfortran5 libgsl27 libgslcblas0 495s liblapack3 liblcms2-2 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 495s libmurmurhash2 libopenjp2-7 libpixman-1-0 libwebpdemux2 libwebpmux3 495s libxcb-render0 libxcb-shm0 libxrender1 mash ncbi-blast+ ncbi-data 495s python3-biopython python3-cairo python3-freetype python3-numpy python3-pil 495s python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib x11-common 495s xfonts-encodings xfonts-utils xml-core 495s Suggested packages: 495s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre kaptive-example 495s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html liblcms2-utils 495s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 495s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 495s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 495s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 495s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 495s rl-renderpm sgml-base-doc debhelper 495s Recommended packages: 495s python-biopython-doc python3-olefile fonts-dejavu-extra 495s The following NEW packages will be installed: 495s autopkgtest-satdep fonts-urw-base35 kaptive kaptive-data kleborate 495s kleborate-examples libblas3 libcairo2 libcapnp-1.0.1 libfontenc1 495s libgfortran5 libgsl27 libgslcblas0 liblapack3 liblcms2-2 libmbedcrypto7t64 495s libmbedtls14t64 libmbedx509-1t64 libmurmurhash2 libopenjp2-7 libpixman-1-0 495s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mash 495s ncbi-blast+ ncbi-data python3-biopython python3-cairo python3-freetype 495s python3-numpy python3-pil python3-reportlab python3-rlpycairo sgml-base 495s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 495s 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. 495s Need to get 64.7 MB/64.7 MB of archives. 495s After this operation, 263 MB of additional disk space will be used. 495s Get:1 /tmp/autopkgtest.to7P5Y/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 495s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 sgml-base all 1.31 [11.4 kB] 495s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 495s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 495s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 495s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 xfonts-utils arm64 1:7.7+6build3 [93.1 kB] 495s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 496s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 496s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14.1.0-5ubuntu1 [438 kB] 496s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 496s Get:11 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-numpy arm64 1:1.26.4+ds-10 [3565 kB] 496s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 liblcms2-2 arm64 2.14-2build1 [161 kB] 496s Get:13 http://ftpmaster.internal/ubuntu oracular/main arm64 libopenjp2-7 arm64 2.5.0-2build3 [171 kB] 496s Get:14 http://ftpmaster.internal/ubuntu oracular/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 496s Get:15 http://ftpmaster.internal/ubuntu oracular/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 496s Get:16 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-pil arm64 10.4.0-1 [450 kB] 496s Get:17 http://ftpmaster.internal/ubuntu oracular/main arm64 libpixman-1-0 arm64 0.42.2-1build1 [204 kB] 496s Get:18 http://ftpmaster.internal/ubuntu oracular/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 496s Get:19 http://ftpmaster.internal/ubuntu oracular/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 496s Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 496s Get:21 http://ftpmaster.internal/ubuntu oracular/main arm64 libcairo2 arm64 1.18.0-3build1 [555 kB] 496s Get:22 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-cairo arm64 1.26.1-1 [121 kB] 496s Get:23 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-freetype all 2.4.0-2 [81.3 kB] 496s Get:24 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 496s Get:25 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-reportlab all 4.2.2-1 [1130 kB] 496s Get:26 http://ftpmaster.internal/ubuntu oracular/main arm64 xml-core all 0.19 [20.3 kB] 496s Get:27 http://ftpmaster.internal/ubuntu oracular/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 496s Get:28 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-biopython arm64 1.83+dfsg1-3 [1646 kB] 496s Get:29 http://ftpmaster.internal/ubuntu oracular/universe arm64 ncbi-data all 6.1.20170106+dfsg2-3 [3966 kB] 496s Get:30 http://ftpmaster.internal/ubuntu oracular/universe arm64 libmbedcrypto7t64 arm64 2.28.8-1 [209 kB] 496s Get:31 http://ftpmaster.internal/ubuntu oracular/universe arm64 libmbedx509-1t64 arm64 2.28.8-1 [47.2 kB] 496s Get:32 http://ftpmaster.internal/ubuntu oracular/universe arm64 libmbedtls14t64 arm64 2.28.8-1 [82.2 kB] 496s Get:33 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 ncbi-blast+ arm64 2.16.0+ds-3 [14.7 MB] 497s Get:34 http://ftpmaster.internal/ubuntu oracular/universe arm64 kaptive all 2.0.8-1 [28.1 kB] 497s Get:35 http://ftpmaster.internal/ubuntu oracular/universe arm64 kaptive-data all 2.0.8-1 [5432 kB] 497s Get:36 http://ftpmaster.internal/ubuntu oracular/universe arm64 libcapnp-1.0.1 arm64 1.0.1-4 [1332 kB] 497s Get:37 http://ftpmaster.internal/ubuntu oracular/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu2 [72.8 kB] 497s Get:38 http://ftpmaster.internal/ubuntu oracular/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu2 [918 kB] 497s Get:39 http://ftpmaster.internal/ubuntu oracular/universe arm64 libmurmurhash2 arm64 1.6-1 [6098 B] 497s Get:40 http://ftpmaster.internal/ubuntu oracular/universe arm64 mash arm64 2.3+dfsg-6 [145 kB] 497s Get:41 http://ftpmaster.internal/ubuntu oracular/universe arm64 kleborate arm64 2.4.1-3build1 [8742 kB] 497s Get:42 http://ftpmaster.internal/ubuntu oracular/universe arm64 kleborate-examples all 2.4.1-3build1 [5990 kB] 498s Fetched 64.7 MB in 2s (27.8 MB/s) 498s Selecting previously unselected package sgml-base. 498s (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 ... 78608 files and directories currently installed.) 498s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 498s Unpacking sgml-base (1.31) ... 498s Selecting previously unselected package libfontenc1:arm64. 498s Preparing to unpack .../01-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 498s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 498s Selecting previously unselected package x11-common. 498s Preparing to unpack .../02-x11-common_1%3a7.7+23ubuntu3_all.deb ... 498s Unpacking x11-common (1:7.7+23ubuntu3) ... 498s Selecting previously unselected package xfonts-encodings. 498s Preparing to unpack .../03-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 498s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 498s Selecting previously unselected package xfonts-utils. 499s Preparing to unpack .../04-xfonts-utils_1%3a7.7+6build3_arm64.deb ... 499s Unpacking xfonts-utils (1:7.7+6build3) ... 499s Selecting previously unselected package fonts-urw-base35. 499s Preparing to unpack .../05-fonts-urw-base35_20200910-8_all.deb ... 500s Unpacking fonts-urw-base35 (20200910-8) ... 500s Selecting previously unselected package libblas3:arm64. 501s Preparing to unpack .../06-libblas3_3.12.0-3build1_arm64.deb ... 501s Unpacking libblas3:arm64 (3.12.0-3build1) ... 501s Selecting previously unselected package libgfortran5:arm64. 501s Preparing to unpack .../07-libgfortran5_14.1.0-5ubuntu1_arm64.deb ... 501s Unpacking libgfortran5:arm64 (14.1.0-5ubuntu1) ... 502s Selecting previously unselected package liblapack3:arm64. 503s Preparing to unpack .../08-liblapack3_3.12.0-3build1_arm64.deb ... 503s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 503s Selecting previously unselected package python3-numpy. 504s Preparing to unpack .../09-python3-numpy_1%3a1.26.4+ds-10_arm64.deb ... 504s Unpacking python3-numpy (1:1.26.4+ds-10) ... 504s Selecting previously unselected package liblcms2-2:arm64. 504s Preparing to unpack .../10-liblcms2-2_2.14-2build1_arm64.deb ... 504s Unpacking liblcms2-2:arm64 (2.14-2build1) ... 504s Selecting previously unselected package libopenjp2-7:arm64. 504s Preparing to unpack .../11-libopenjp2-7_2.5.0-2build3_arm64.deb ... 504s Unpacking libopenjp2-7:arm64 (2.5.0-2build3) ... 504s Selecting previously unselected package libwebpdemux2:arm64. 504s Preparing to unpack .../12-libwebpdemux2_1.4.0-0.1_arm64.deb ... 504s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 504s Selecting previously unselected package libwebpmux3:arm64. 504s Preparing to unpack .../13-libwebpmux3_1.4.0-0.1_arm64.deb ... 504s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 504s Selecting previously unselected package python3-pil:arm64. 504s Preparing to unpack .../14-python3-pil_10.4.0-1_arm64.deb ... 504s Unpacking python3-pil:arm64 (10.4.0-1) ... 504s Selecting previously unselected package libpixman-1-0:arm64. 505s Preparing to unpack .../15-libpixman-1-0_0.42.2-1build1_arm64.deb ... 505s Unpacking libpixman-1-0:arm64 (0.42.2-1build1) ... 505s Selecting previously unselected package libxcb-render0:arm64. 505s Preparing to unpack .../16-libxcb-render0_1.17.0-2_arm64.deb ... 505s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 505s Selecting previously unselected package libxcb-shm0:arm64. 505s Preparing to unpack .../17-libxcb-shm0_1.17.0-2_arm64.deb ... 505s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 505s Selecting previously unselected package libxrender1:arm64. 505s Preparing to unpack .../18-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 505s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 505s Selecting previously unselected package libcairo2:arm64. 505s Preparing to unpack .../19-libcairo2_1.18.0-3build1_arm64.deb ... 505s Unpacking libcairo2:arm64 (1.18.0-3build1) ... 505s Selecting previously unselected package python3-cairo. 505s Preparing to unpack .../20-python3-cairo_1.26.1-1_arm64.deb ... 505s Unpacking python3-cairo (1.26.1-1) ... 505s Selecting previously unselected package python3-freetype. 505s Preparing to unpack .../21-python3-freetype_2.4.0-2_all.deb ... 505s Unpacking python3-freetype (2.4.0-2) ... 505s Selecting previously unselected package python3-rlpycairo. 505s Preparing to unpack .../22-python3-rlpycairo_0.3.0-3_all.deb ... 505s Unpacking python3-rlpycairo (0.3.0-3) ... 505s Selecting previously unselected package python3-reportlab. 505s Preparing to unpack .../23-python3-reportlab_4.2.2-1_all.deb ... 505s Unpacking python3-reportlab (4.2.2-1) ... 505s Selecting previously unselected package xml-core. 505s Preparing to unpack .../24-xml-core_0.19_all.deb ... 505s Unpacking xml-core (0.19) ... 506s Selecting previously unselected package w3c-sgml-lib. 506s Preparing to unpack .../25-w3c-sgml-lib_1.3-3_all.deb ... 506s Unpacking w3c-sgml-lib (1.3-3) ... 506s Selecting previously unselected package python3-biopython. 506s Preparing to unpack .../26-python3-biopython_1.83+dfsg1-3_arm64.deb ... 506s Unpacking python3-biopython (1.83+dfsg1-3) ... 506s Selecting previously unselected package ncbi-data. 506s Preparing to unpack .../27-ncbi-data_6.1.20170106+dfsg2-3_all.deb ... 506s Unpacking ncbi-data (6.1.20170106+dfsg2-3) ... 506s Selecting previously unselected package libmbedcrypto7t64:arm64. 506s Preparing to unpack .../28-libmbedcrypto7t64_2.28.8-1_arm64.deb ... 506s Unpacking libmbedcrypto7t64:arm64 (2.28.8-1) ... 506s Selecting previously unselected package libmbedx509-1t64:arm64. 507s Preparing to unpack .../29-libmbedx509-1t64_2.28.8-1_arm64.deb ... 507s Unpacking libmbedx509-1t64:arm64 (2.28.8-1) ... 507s Selecting previously unselected package libmbedtls14t64:arm64. 507s Preparing to unpack .../30-libmbedtls14t64_2.28.8-1_arm64.deb ... 507s Unpacking libmbedtls14t64:arm64 (2.28.8-1) ... 507s Selecting previously unselected package ncbi-blast+. 507s Preparing to unpack .../31-ncbi-blast+_2.16.0+ds-3_arm64.deb ... 507s Unpacking ncbi-blast+ (2.16.0+ds-3) ... 507s Selecting previously unselected package kaptive. 507s Preparing to unpack .../32-kaptive_2.0.8-1_all.deb ... 507s Unpacking kaptive (2.0.8-1) ... 507s Selecting previously unselected package kaptive-data. 507s Preparing to unpack .../33-kaptive-data_2.0.8-1_all.deb ... 507s Unpacking kaptive-data (2.0.8-1) ... 507s Selecting previously unselected package libcapnp-1.0.1:arm64. 507s Preparing to unpack .../34-libcapnp-1.0.1_1.0.1-4_arm64.deb ... 507s Unpacking libcapnp-1.0.1:arm64 (1.0.1-4) ... 507s Selecting previously unselected package libgslcblas0:arm64. 508s Preparing to unpack .../35-libgslcblas0_2.7.1+dfsg-6ubuntu2_arm64.deb ... 508s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 508s Selecting previously unselected package libgsl27:arm64. 508s Preparing to unpack .../36-libgsl27_2.7.1+dfsg-6ubuntu2_arm64.deb ... 508s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 508s Selecting previously unselected package libmurmurhash2:arm64. 508s Preparing to unpack .../37-libmurmurhash2_1.6-1_arm64.deb ... 508s Unpacking libmurmurhash2:arm64 (1.6-1) ... 508s Selecting previously unselected package mash. 508s Preparing to unpack .../38-mash_2.3+dfsg-6_arm64.deb ... 508s Unpacking mash (2.3+dfsg-6) ... 508s Selecting previously unselected package kleborate. 508s Preparing to unpack .../39-kleborate_2.4.1-3build1_arm64.deb ... 508s Unpacking kleborate (2.4.1-3build1) ... 508s Selecting previously unselected package kleborate-examples. 508s Preparing to unpack .../40-kleborate-examples_2.4.1-3build1_all.deb ... 508s Unpacking kleborate-examples (2.4.1-3build1) ... 509s Selecting previously unselected package autopkgtest-satdep. 509s Preparing to unpack .../41-1-autopkgtest-satdep.deb ... 509s Unpacking autopkgtest-satdep (0) ... 509s Setting up liblcms2-2:arm64 (2.14-2build1) ... 509s Setting up ncbi-data (6.1.20170106+dfsg2-3) ... 509s Setting up libpixman-1-0:arm64 (0.42.2-1build1) ... 509s Setting up libmbedcrypto7t64:arm64 (2.28.8-1) ... 509s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 509s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 510s Setting up libmurmurhash2:arm64 (1.6-1) ... 510s Setting up libcapnp-1.0.1:arm64 (1.0.1-4) ... 510s Setting up libxcb-render0:arm64 (1.17.0-2) ... 510s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 510s Setting up x11-common (1:7.7+23ubuntu3) ... 518s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 518s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 518s Setting up python3-freetype (2.4.0-2) ... 519s Setting up libcairo2:arm64 (1.18.0-3build1) ... 519s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 519s Setting up libblas3:arm64 (3.12.0-3build1) ... 519s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 520s Setting up kleborate-examples (2.4.1-3build1) ... 520s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 520s Setting up mash (2.3+dfsg-6) ... 520s Setting up kaptive-data (2.0.8-1) ... 520s Setting up libgfortran5:arm64 (14.1.0-5ubuntu1) ... 520s Setting up libopenjp2-7:arm64 (2.5.0-2build3) ... 520s Setting up sgml-base (1.31) ... 520s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 520s Setting up liblapack3:arm64 (3.12.0-3build1) ... 520s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 520s Setting up libmbedx509-1t64:arm64 (2.28.8-1) ... 520s Setting up python3-cairo (1.26.1-1) ... 521s Setting up xfonts-utils (1:7.7+6build3) ... 521s Setting up python3-pil:arm64 (10.4.0-1) ... 521s Setting up python3-rlpycairo (0.3.0-3) ... 522s Setting up python3-numpy (1:1.26.4+ds-10) ... 524s Setting up libmbedtls14t64:arm64 (2.28.8-1) ... 524s Setting up xml-core (0.19) ... 524s Setting up fonts-urw-base35 (20200910-8) ... 525s Setting up ncbi-blast+ (2.16.0+ds-3) ... 525s Setting up python3-reportlab (4.2.2-1) ... 526s Processing triggers for libc-bin (2.39-0ubuntu9) ... 526s Processing triggers for man-db (2.12.1-2) ... 527s Processing triggers for sgml-base (1.31) ... 527s Setting up w3c-sgml-lib (1.3-3) ... 567s Setting up python3-biopython (1.83+dfsg1-3) ... 568s Setting up kaptive (2.0.8-1) ... 569s Setting up kleborate (2.4.1-3build1) ... 577s Setting up autopkgtest-satdep (0) ... 588s (Reading database ... 82091 files and directories currently installed.) 588s Removing autopkgtest-satdep (0) ... 592s autopkgtest [02:31:20]: test run-unit-test: [----------------------- 598s /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. 598s warnings.warn( 805s strain species ST virulence_score Yersiniabactin YbST Colibactin CbST Aerobactin AbST Salmochelin SmST RmpADC RmST rmpA2 wzi K_locus 805s Klebs_HS11286 Klebsiella pneumoniae ST11 1 ybt 9; ICEKp3 15 - 0 - 0 - 0 - 0 - wzi74 KL103 805s Klebs_Kp1084 Klebsiella pneumoniae ST23 2 ybt 1; ICEKp10 47 clb 2 37 - 0 - 0 - 0 - wzi172 KL1 805s MGH78578 Klebsiella pneumoniae ST38 0 - 0 - 0 - 0 - 0 - 0 - wzi50 KL15 (KL17,KL51,KL52) 805s 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 806s /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. 806s warnings.warn( 1155s 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 1155s 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% 1155s Klebs_Kp1084 Klebsiella pneumoniae ST23 2 0 ybt 1; ICEKp10 47 clb 2 37 - 0 - 0 - 0 - wzi172 KL1 - - - - - - - - - - - - - - - - - SHV-11^ 35Q - - - - - 1155s 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% - 1155s 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 - - - - - 1155s /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. 1155s warnings.warn( 1572s 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 1572s 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% 1572s 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 - - - - - 1572s 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% - 1572s 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 - - - - - 1572s autopkgtest [02:47:40]: test run-unit-test: -----------------------] 1573s autopkgtest [02:47:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1573s run-unit-test PASS 1573s autopkgtest [02:47:41]: @@@@@@@@@@@@@@@@@@@@ summary 1573s run-unit-test PASS 1585s nova [W] Skipping flock in bos03-arm64 1585s Creating nova instance adt-oracular-arm64-kleborate-20240727-022128-juju-7f2275-prod-proposed-migration-environment-3-fda14b2c-8fe8-48dd-a739-90337e2251a9 from image adt/ubuntu-oracular-arm64-server-20240726.img (UUID 33caccb7-bc3b-4ecc-9e17-59d67995dc9e)...