0s autopkgtest [01:44:07]: starting date and time: 2024-04-19 01:44:07+0000 0s autopkgtest [01:44:07]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [01:44:07]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1q6wia8o/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:gsl --apt-upgrade fastani --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=gsl/2.7.1+dfsg-6ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-1.secgroup --name adt-noble-arm64-fastani-20240419-012555-juju-7f2275-prod-proposed-migration-environment-3-eae0b313-6387-4f5f-99fa-a0dadee9875f --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 106s autopkgtest [01:45:53]: testbed dpkg architecture: arm64 106s autopkgtest [01:45:53]: testbed apt version: 2.7.14build2 106s autopkgtest [01:45:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 107s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 107s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 107s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [53.4 kB] 107s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [338 kB] 107s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 107s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [129 kB] 108s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 108s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [92.9 kB] 108s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 108s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [464 kB] 108s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 108s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 110s Fetched 1221 kB in 1s (910 kB/s) 111s Reading package lists... 120s Reading package lists...Setting LLMNR support level "yes" for "2", but the global support level is "no". 122s 123s Building dependency tree... 123s Reading state information... 124s Calculating upgrade... 125s The following packages will be upgraded: 125s apport apport-core-dump-handler libkeyutils1 libnetplan1 libnuma1 libunwind8 125s make man-db netcat-openbsd netplan-generator netplan.io numactl 125s python3-apport python3-netplan python3-problem-report 125s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 2062 kB of archives. 125s After this operation, 1024 B of additional disk space will be used. 125s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB] 125s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3-apport all 2.28.1-0ubuntu1 [92.1 kB] 125s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB] 125s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 apport all 2.28.1-0ubuntu1 [83.5 kB] 125s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3build1 [9654 B] 125s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 netplan-generator arm64 1.0-2ubuntu1 [58.9 kB] 125s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 python3-netplan arm64 1.0-2ubuntu1 [21.5 kB] 125s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 netplan.io arm64 1.0-2ubuntu1 [65.8 kB] 125s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libnetplan1 arm64 1.0-2ubuntu1 [119 kB] 125s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 netcat-openbsd arm64 1.226-1ubuntu2 [43.8 kB] 125s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1build1 [23.6 kB] 126s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 man-db arm64 2.12.0-4build2 [1232 kB] 126s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libunwind8 arm64 1.6.2-3build1 [53.5 kB] 126s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build2 [178 kB] 126s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 numactl arm64 2.0.18-1build1 [39.5 kB] 127s Preconfiguring packages ... 127s Fetched 2062 kB in 1s (2790 kB/s) 128s (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 ... 112118 files and directories currently installed.) 128s Preparing to unpack .../00-python3-problem-report_2.28.1-0ubuntu1_all.deb ... 128s Unpacking python3-problem-report (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 128s Preparing to unpack .../01-python3-apport_2.28.1-0ubuntu1_all.deb ... 128s Unpacking python3-apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 128s Preparing to unpack .../02-apport-core-dump-handler_2.28.1-0ubuntu1_all.deb ... 128s Unpacking apport-core-dump-handler (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 128s Preparing to unpack .../03-apport_2.28.1-0ubuntu1_all.deb ... 128s Unpacking apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 129s Preparing to unpack .../04-libkeyutils1_1.6.3-3build1_arm64.deb ... 129s Unpacking libkeyutils1:arm64 (1.6.3-3build1) over (1.6.3-3) ... 129s Preparing to unpack .../05-netplan-generator_1.0-2ubuntu1_arm64.deb ... 129s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 129s Unpacking netplan-generator (1.0-2ubuntu1) over (1.0-2build1) ... 129s Preparing to unpack .../06-python3-netplan_1.0-2ubuntu1_arm64.deb ... 129s Unpacking python3-netplan (1.0-2ubuntu1) over (1.0-2build1) ... 130s Preparing to unpack .../07-netplan.io_1.0-2ubuntu1_arm64.deb ... 130s Unpacking netplan.io (1.0-2ubuntu1) over (1.0-2build1) ... 130s Preparing to unpack .../08-libnetplan1_1.0-2ubuntu1_arm64.deb ... 130s Unpacking libnetplan1:arm64 (1.0-2ubuntu1) over (1.0-2build1) ... 130s Preparing to unpack .../09-netcat-openbsd_1.226-1ubuntu2_arm64.deb ... 130s Unpacking netcat-openbsd (1.226-1ubuntu2) over (1.226-1ubuntu1) ... 130s Preparing to unpack .../10-libnuma1_2.0.18-1build1_arm64.deb ... 130s Unpacking libnuma1:arm64 (2.0.18-1build1) over (2.0.18-1) ... 130s Preparing to unpack .../11-man-db_2.12.0-4build2_arm64.deb ... 130s Unpacking man-db (2.12.0-4build2) over (2.12.0-4build1) ... 130s Preparing to unpack .../12-libunwind8_1.6.2-3build1_arm64.deb ... 130s Unpacking libunwind8:arm64 (1.6.2-3build1) over (1.6.2-3) ... 130s Preparing to unpack .../13-make_4.3-4.1build2_arm64.deb ... 130s Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... 130s Preparing to unpack .../14-numactl_2.0.18-1build1_arm64.deb ... 130s Unpacking numactl (2.0.18-1build1) over (2.0.18-1) ... 130s Setting up libkeyutils1:arm64 (1.6.3-3build1) ... 130s Setting up python3-problem-report (2.28.1-0ubuntu1) ... 131s Setting up netcat-openbsd (1.226-1ubuntu2) ... 131s Setting up libnetplan1:arm64 (1.0-2ubuntu1) ... 131s Setting up man-db (2.12.0-4build2) ... 131s Updating database of manual pages ... 133s man-db.service is a disabled or a static unit not running, not starting it. 133s Setting up libunwind8:arm64 (1.6.2-3build1) ... 133s Setting up python3-apport (2.28.1-0ubuntu1) ... 133s Setting up make (4.3-4.1build2) ... 133s Setting up libnuma1:arm64 (2.0.18-1build1) ... 133s Setting up python3-netplan (1.0-2ubuntu1) ... 133s Setting up netplan-generator (1.0-2ubuntu1) ... 133s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 133s Setting up numactl (2.0.18-1build1) ... 133s Setting up netplan.io (1.0-2ubuntu1) ... 133s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ... 134s Setting up apport (2.28.1-0ubuntu1) ... 134s Installing new version of config file /etc/apport/crashdb.conf ... 135s apport-autoreport.service is a disabled or a static unit not running, not starting it. 135s Processing triggers for dbus (1.14.10-4ubuntu4) ... 135s Processing triggers for libc-bin (2.39-0ubuntu8) ... 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 138s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 138s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 138s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 140s Reading package lists... 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Calculating upgrade... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s autopkgtest [01:46:30]: rebooting testbed after setup commands that affected boot 186s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 211s autopkgtest [01:47:38]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP PREEMPT_DYNAMIC Fri Apr 5 02:52:09 UTC 2024 215s autopkgtest [01:47:42]: @@@@@@@@@@@@@@@@@@@@ apt-source fastani 218s Get:1 http://ftpmaster.internal/ubuntu noble/universe fastani 1.33-3 (dsc) [1376 B] 218s Get:2 http://ftpmaster.internal/ubuntu noble/universe fastani 1.33-3 (tar) [2979 kB] 218s Get:3 http://ftpmaster.internal/ubuntu noble/universe fastani 1.33-3 (diff) [6712 B] 218s gpgv: Signature made Tue Sep 12 16:57:28 2023 UTC 218s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 218s gpgv: Can't check signature: No public key 218s dpkg-source: warning: cannot verify inline signature for ./fastani_1.33-3.dsc: no acceptable signature found 219s autopkgtest [01:47:46]: testing package fastani version 1.33-3 219s autopkgtest [01:47:46]: build not needed 226s autopkgtest [01:47:53]: test run-unit-test: preparing testbed 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s Starting pkgProblemResolver with broken count: 0 228s Starting 2 pkgProblemResolver with broken count: 0 228s Done 229s The following additional packages will be installed: 229s fastani fontconfig libblas3 libcairo2 libdatrie1 libgfortran5 libgomp1 229s libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libice6 liblapack3 229s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 229s libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data libthai0 libtk8.6 229s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler 229s r-base-core r-cran-ade4 r-cran-genoplotr r-cran-lattice r-cran-littler 229s r-cran-mass r-cran-pixmap r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 229s r-cran-sp unzip x11-common xdg-utils zip 229s Suggested packages: 229s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 229s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-adegraphics 229s r-cran-adephylo r-cran-ape r-cran-deldir r-cran-spdep r-cran-waveslim 229s r-cran-progress r-cran-foreach r-cran-doparallel r-cran-iterators 229s r-cran-getopt r-cran-inline 229s Recommended packages: 229s r-recommended r-base-dev r-doc-html r-cran-rcolorbrewer r-cran-gstat 229s r-cran-deldir r-cran-knitr r-cran-rmarkdown r-cran-sf r-cran-terra 229s r-cran-raster libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl 229s x11-utils x11-xserver-utils 230s The following NEW packages will be installed: 230s autopkgtest-satdep fastani fontconfig libblas3 libcairo2 libdatrie1 230s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 230s libice6 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 230s libpaper-utils libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data 230s libthai0 libtk8.6 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 230s libxt6t64 littler r-base-core r-cran-ade4 r-cran-genoplotr r-cran-lattice 230s r-cran-littler r-cran-mass r-cran-pixmap r-cran-pkgkitten r-cran-rcpp 230s r-cran-rcpparmadillo r-cran-sp unzip x11-common xdg-utils zip 230s 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. 230s Need to get 48.7 MB/48.7 MB of archives. 230s After this operation, 102 MB of additional disk space will be used. 230s Get:1 /tmp/autopkgtest.KZXTly/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 230s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240412-0ubuntu1 [144 kB] 230s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu2 [72.8 kB] 230s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu2 [918 kB] 230s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 fastani arm64 1.33-3 [104 kB] 230s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB] 230s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 230s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1build1 [204 kB] 230s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 230s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 230s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 230s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-3build1 [555 kB] 230s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 230s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240412-0ubuntu1 [444 kB] 231s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2build1 [70.8 kB] 231s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2build2 [463 kB] 231s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 231s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build3 [41.1 kB] 231s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 231s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 231s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 231s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.52.1+ds-1build1 [228 kB] 231s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.52.1+ds-1build1 [42.0 kB] 231s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.52.1+ds-1build1 [27.4 kB] 231s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29build1 [13.4 kB] 231s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29build1 [8490 B] 231s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build3 [15.6 kB] 231s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1build1 [978 kB] 231s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 231s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 231s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.14-1build1 [767 kB] 231s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 231s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13build1 [171 kB] 231s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu4 [171 kB] 231s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 231s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.3-2build2 [26.8 MB] 231s Get:37 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 231s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 231s Get:39 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 231s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pixmap all 0.4-12-1 [201 kB] 231s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 231s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sp arm64 1:2.1-2+dfsg-1 [1448 kB] 231s Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 231s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 232s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpparmadillo arm64 0.12.8.1.0-1build1 [859 kB] 232s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ade4 arm64 1.7-22-1 [5324 kB] 232s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-genoplotr all 0.8.11+dfsg-2 [875 kB] 232s Preconfiguring packages ... 232s Fetched 48.7 MB in 2s (23.2 MB/s) 233s Selecting previously unselected package libgomp1:arm64. 233s (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 ... 112117 files and directories currently installed.) 233s Preparing to unpack .../00-libgomp1_14-20240412-0ubuntu1_arm64.deb ... 233s Unpacking libgomp1:arm64 (14-20240412-0ubuntu1) ... 233s Selecting previously unselected package libgslcblas0:arm64. 233s Preparing to unpack .../01-libgslcblas0_2.7.1+dfsg-6ubuntu2_arm64.deb ... 233s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 233s Selecting previously unselected package libgsl27:arm64. 233s Preparing to unpack .../02-libgsl27_2.7.1+dfsg-6ubuntu2_arm64.deb ... 233s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 233s Selecting previously unselected package fastani. 233s Preparing to unpack .../03-fastani_1.33-3_arm64.deb ... 233s Unpacking fastani (1.33-3) ... 233s Selecting previously unselected package fontconfig. 233s Preparing to unpack .../04-fontconfig_2.15.0-1.1ubuntu2_arm64.deb ... 233s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 233s Selecting previously unselected package libblas3:arm64. 233s Preparing to unpack .../05-libblas3_3.12.0-3build1_arm64.deb ... 233s Unpacking libblas3:arm64 (3.12.0-3build1) ... 233s Selecting previously unselected package libpixman-1-0:arm64. 233s Preparing to unpack .../06-libpixman-1-0_0.42.2-1build1_arm64.deb ... 233s Unpacking libpixman-1-0:arm64 (0.42.2-1build1) ... 233s Selecting previously unselected package libxcb-render0:arm64. 234s Preparing to unpack .../07-libxcb-render0_1.15-1_arm64.deb ... 234s Unpacking libxcb-render0:arm64 (1.15-1) ... 234s Selecting previously unselected package libxcb-shm0:arm64. 234s Preparing to unpack .../08-libxcb-shm0_1.15-1_arm64.deb ... 234s Unpacking libxcb-shm0:arm64 (1.15-1) ... 234s Selecting previously unselected package libxrender1:arm64. 234s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 234s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 234s Selecting previously unselected package libcairo2:arm64. 234s Preparing to unpack .../10-libcairo2_1.18.0-3build1_arm64.deb ... 234s Unpacking libcairo2:arm64 (1.18.0-3build1) ... 234s Selecting previously unselected package libdatrie1:arm64. 234s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_arm64.deb ... 234s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 234s Selecting previously unselected package libgfortran5:arm64. 234s Preparing to unpack .../12-libgfortran5_14-20240412-0ubuntu1_arm64.deb ... 234s Unpacking libgfortran5:arm64 (14-20240412-0ubuntu1) ... 234s Selecting previously unselected package libgraphite2-3:arm64. 234s Preparing to unpack .../13-libgraphite2-3_1.3.14-2build1_arm64.deb ... 234s Unpacking libgraphite2-3:arm64 (1.3.14-2build1) ... 234s Selecting previously unselected package libharfbuzz0b:arm64. 234s Preparing to unpack .../14-libharfbuzz0b_8.3.0-2build2_arm64.deb ... 234s Unpacking libharfbuzz0b:arm64 (8.3.0-2build2) ... 234s Selecting previously unselected package x11-common. 234s Preparing to unpack .../15-x11-common_1%3a7.7+23ubuntu3_all.deb ... 234s Unpacking x11-common (1:7.7+23ubuntu3) ... 234s Selecting previously unselected package libice6:arm64. 234s Preparing to unpack .../16-libice6_2%3a1.0.10-1build3_arm64.deb ... 234s Unpacking libice6:arm64 (2:1.0.10-1build3) ... 234s Selecting previously unselected package liblapack3:arm64. 234s Preparing to unpack .../17-liblapack3_3.12.0-3build1_arm64.deb ... 234s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 234s Selecting previously unselected package libthai-data. 234s Preparing to unpack .../18-libthai-data_0.1.29-2build1_all.deb ... 234s Unpacking libthai-data (0.1.29-2build1) ... 234s Selecting previously unselected package libthai0:arm64. 234s Preparing to unpack .../19-libthai0_0.1.29-2build1_arm64.deb ... 234s Unpacking libthai0:arm64 (0.1.29-2build1) ... 234s Selecting previously unselected package libpango-1.0-0:arm64. 234s Preparing to unpack .../20-libpango-1.0-0_1.52.1+ds-1build1_arm64.deb ... 234s Unpacking libpango-1.0-0:arm64 (1.52.1+ds-1build1) ... 234s Selecting previously unselected package libpangoft2-1.0-0:arm64. 234s Preparing to unpack .../21-libpangoft2-1.0-0_1.52.1+ds-1build1_arm64.deb ... 234s Unpacking libpangoft2-1.0-0:arm64 (1.52.1+ds-1build1) ... 234s Selecting previously unselected package libpangocairo-1.0-0:arm64. 235s Preparing to unpack .../22-libpangocairo-1.0-0_1.52.1+ds-1build1_arm64.deb ... 235s Unpacking libpangocairo-1.0-0:arm64 (1.52.1+ds-1build1) ... 235s Selecting previously unselected package libpaper1:arm64. 235s Preparing to unpack .../23-libpaper1_1.1.29build1_arm64.deb ... 235s Unpacking libpaper1:arm64 (1.1.29build1) ... 235s Selecting previously unselected package libpaper-utils. 235s Preparing to unpack .../24-libpaper-utils_1.1.29build1_arm64.deb ... 235s Unpacking libpaper-utils (1.1.29build1) ... 235s Selecting previously unselected package libsm6:arm64. 235s Preparing to unpack .../25-libsm6_2%3a1.2.3-1build3_arm64.deb ... 235s Unpacking libsm6:arm64 (2:1.2.3-1build3) ... 235s Selecting previously unselected package libtcl8.6:arm64. 235s Preparing to unpack .../26-libtcl8.6_8.6.14+dfsg-1build1_arm64.deb ... 235s Unpacking libtcl8.6:arm64 (8.6.14+dfsg-1build1) ... 235s Selecting previously unselected package libxft2:arm64. 235s Preparing to unpack .../27-libxft2_2.3.6-1build1_arm64.deb ... 235s Unpacking libxft2:arm64 (2.3.6-1build1) ... 235s Selecting previously unselected package libxss1:arm64. 235s Preparing to unpack .../28-libxss1_1%3a1.2.3-1build3_arm64.deb 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237s Preparing to unpack .../40-r-cran-sp_1%3a2.1-2+dfsg-1_arm64.deb ... 237s Unpacking r-cran-sp (1:2.1-2+dfsg-1) ... 237s Selecting previously unselected package r-cran-pkgkitten. 237s Preparing to unpack .../41-r-cran-pkgkitten_0.2.3-1_all.deb ... 237s Unpacking r-cran-pkgkitten (0.2.3-1) ... 237s Selecting previously unselected package r-cran-rcpp. 237s Preparing to unpack .../42-r-cran-rcpp_1.0.12-1_arm64.deb ... 237s Unpacking r-cran-rcpp (1.0.12-1) ... 237s Selecting previously unselected package r-cran-rcpparmadillo. 238s Preparing to unpack .../43-r-cran-rcpparmadillo_0.12.8.1.0-1build1_arm64.deb ... 238s Unpacking r-cran-rcpparmadillo (0.12.8.1.0-1build1) ... 238s Selecting previously unselected package r-cran-ade4. 238s Preparing to unpack .../44-r-cran-ade4_1.7-22-1_arm64.deb ... 238s Unpacking r-cran-ade4 (1.7-22-1) ... 238s Selecting previously unselected package r-cran-genoplotr. 238s Preparing to unpack .../45-r-cran-genoplotr_0.8.11+dfsg-2_all.deb ... 238s Unpacking r-cran-genoplotr (0.8.11+dfsg-2) ... 238s Selecting previously unselected package autopkgtest-satdep. 238s Preparing to unpack .../46-1-autopkgtest-satdep.deb ... 238s Unpacking autopkgtest-satdep (0) ... 238s Setting up libgraphite2-3:arm64 (1.3.14-2build1) ... 238s Setting up libpixman-1-0:arm64 (0.42.2-1build1) ... 238s Setting up libpaper1:arm64 (1.1.29build1) ... 238s 238s Creating config file /etc/papersize with new version 239s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 241s Regenerating fonts cache... done. 241s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 241s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 241s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 241s Setting up libxcb-render0:arm64 (1.15-1) ... 241s Setting up unzip (6.0-28ubuntu4) ... 241s Setting up x11-common (1:7.7+23ubuntu3) ... 242s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 242s Setting up libxcb-shm0:arm64 (1.15-1) ... 242s Setting up libpaper-utils (1.1.29build1) ... 242s Setting up libgomp1:arm64 (14-20240412-0ubuntu1) ... 242s Setting up libcairo2:arm64 (1.18.0-3build1) ... 242s Setting up zip (3.0-13build1) ... 242s Setting up libblas3:arm64 (3.12.0-3build1) ... 242s 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 242s Setting up fastani (1.33-3) ... 242s Setting up libtcl8.6:arm64 (8.6.14+dfsg-1build1) ... 242s Setting up libgfortran5:arm64 (14-20240412-0ubuntu1) ... 242s Setting up libharfbuzz0b:arm64 (8.3.0-2build2) ... 242s Setting up libthai-data (0.1.29-2build1) ... 242s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 242s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 242s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 242s Setting up libice6:arm64 (2:1.0.10-1build3) ... 242s Setting up liblapack3:arm64 (3.12.0-3build1) ... 242s 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 242s Setting up libxft2:arm64 (2.3.6-1build1) ... 242s Setting up libtk8.6:arm64 (8.6.14-1build1) ... 242s Setting up libthai0:arm64 (0.1.29-2build1) ... 242s Setting up libsm6:arm64 (2:1.2.3-1build3) ... 242s Setting up libpango-1.0-0:arm64 (1.52.1+ds-1build1) ... 242s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 242s Setting up libpangoft2-1.0-0:arm64 (1.52.1+ds-1build1) ... 242s Setting up libpangocairo-1.0-0:arm64 (1.52.1+ds-1build1) ... 242s Setting up r-base-core (4.3.3-2build2) ... 242s 242s Creating config file /etc/R/Renviron with new version 242s Setting up r-cran-lattice (0.22-5-1) ... 242s Setting up r-cran-pixmap (0.4-12-1) ... 242s Setting up r-cran-pkgkitten (0.2.3-1) ... 242s Setting up r-cran-littler (0.3.19-1) ... 242s Setting up r-cran-rcpp (1.0.12-1) ... 242s Setting up littler (0.3.19-1) ... 242s Setting up r-cran-mass (7.3-60.0.1-1) ... 242s Setting up r-cran-sp (1:2.1-2+dfsg-1) ... 242s Setting up r-cran-rcpparmadillo (0.12.8.1.0-1build1) ... 242s Setting up r-cran-ade4 (1.7-22-1) ... 242s Setting up r-cran-genoplotr (0.8.11+dfsg-2) ... 242s Setting up autopkgtest-satdep (0) ... 242s Processing triggers for man-db (2.12.0-4build2) ... 244s Processing triggers for install-info (7.1-3build2) ... 244s Processing triggers for libc-bin (2.39-0ubuntu8) ... 249s (Reading database ... 116098 files and directories currently installed.) 249s Removing autopkgtest-satdep (0) ... 250s autopkgtest [01:48:17]: test run-unit-test: [----------------------- 250s Test functionality 250s >>>>>>>>>>>>>>>>>> 250s Reference = [Escherichia_coli_str_K12_MG1655.fna] 250s Query = [Shigella_flexneri_2a_01.fna] 250s Kmer size = 16 250s Fragment length = 3000 250s Threads = 1 250s ANI output file = fastani.out 250s >>>>>>>>>>>>>>>>>> 250s INFO [thread 0], skch::main, Count of threads executing parallel_for : 1 250s INFO [thread 0], skch::Sketch::build, window size for minimizer sampling = 24 251s INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 371301 251s INFO [thread 0], skch::Sketch::index, unique minimizers = 361568 251s INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 357382) ... (59, 1) 251s INFO [thread 0], skch::Sketch::computeFreqHist, consider all minimizers during lookup. 251s INFO [thread 0], skch::main, Time spent sketching the reference : 0.463659 sec 252s INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 1.24624 sec 252s INFO [thread 0], skch::main, Time spent post mapping : 0.0018446 sec 252s INFO [thread 0], skch::main, ready to exit the loop 252s INFO, skch::main, parallel_for execution finished 252s Shigella_flexneri_2a_01.fna Escherichia_coli_str_K12_MG1655.fna 97.7507 1303 1608 253s Loading required package: ade4 253s Loading required package: grid 254s null device 254s 1 254s PASS 255s autopkgtest [01:48:22]: test run-unit-test: -----------------------] 255s run-unit-test PASS 255s autopkgtest [01:48:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 256s autopkgtest [01:48:23]: @@@@@@@@@@@@@@@@@@@@ summary 256s run-unit-test PASS 267s Creating nova instance adt-noble-arm64-fastani-20240419-012555-juju-7f2275-prod-proposed-migration-environment-3-eae0b313-6387-4f5f-99fa-a0dadee9875f from image adt/ubuntu-noble-arm64-server-20240418.img (UUID c141647a-22ea-481a-97c5-a98894f31daa)...