0s autopkgtest [01:26:08]: starting date and time: 2024-04-19 01:26:08+0000 0s autopkgtest [01:26:08]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [01:26:08]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.chj3if70/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:gsl --apt-upgrade igor --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@bos02-arm64-23.secgroup --name adt-noble-arm64-igor-20240419-012607-juju-7f2275-prod-proposed-migration-environment-3-43944b13-89e1-4160-be99-a59d02cd8326 --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/ 251s autopkgtest [01:30:19]: testbed dpkg architecture: arm64 251s autopkgtest [01:30:19]: testbed apt version: 2.7.14build2 251s autopkgtest [01:30:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 252s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 253s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 254s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 254s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [53.4 kB] 254s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [338 kB] 256s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [129 kB] 257s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 257s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [92.9 kB] 259s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 259s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [464 kB] 262s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 262s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 269s Fetched 1221 kB in 10s (123 kB/s) 269s Reading package lists... 272s sh: 4: dhclient: not found 275s Reading package lists... 275s Building dependency tree... 275s Reading state information... 277s Calculating upgrade... 278s The following packages will be upgraded: 278s apport apport-core-dump-handler libkeyutils1 libnetplan1 libnuma1 libunwind8 278s make man-db netcat-openbsd netplan-generator netplan.io numactl 278s python3-apport python3-netplan python3-problem-report 279s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 279s Need to get 2062 kB of archives. 279s After this operation, 1024 B of additional disk space will be used. 279s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB] 279s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3-apport all 2.28.1-0ubuntu1 [92.1 kB] 279s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB] 279s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 apport all 2.28.1-0ubuntu1 [83.5 kB] 279s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3build1 [9654 B] 279s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 netplan-generator arm64 1.0-2ubuntu1 [58.9 kB] 280s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 python3-netplan arm64 1.0-2ubuntu1 [21.5 kB] 280s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 netplan.io arm64 1.0-2ubuntu1 [65.8 kB] 280s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libnetplan1 arm64 1.0-2ubuntu1 [119 kB] 280s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 netcat-openbsd arm64 1.226-1ubuntu2 [43.8 kB] 280s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1build1 [23.6 kB] 280s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 man-db arm64 2.12.0-4build2 [1232 kB] 282s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libunwind8 arm64 1.6.2-3build1 [53.5 kB] 282s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build2 [178 kB] 282s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 numactl arm64 2.0.18-1build1 [39.5 kB] 283s Preconfiguring packages ... 283s Fetched 2062 kB in 3s (593 kB/s) 283s (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 ... 77740 files and directories currently installed.) 283s Preparing to unpack .../00-python3-problem-report_2.28.1-0ubuntu1_all.deb ... 284s Unpacking python3-problem-report (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 284s Preparing to unpack .../01-python3-apport_2.28.1-0ubuntu1_all.deb ... 284s Unpacking python3-apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 284s Preparing to unpack .../02-apport-core-dump-handler_2.28.1-0ubuntu1_all.deb ... 284s Unpacking apport-core-dump-handler (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 284s Preparing to unpack .../03-apport_2.28.1-0ubuntu1_all.deb ... 285s Unpacking apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 285s Preparing to unpack .../04-libkeyutils1_1.6.3-3build1_arm64.deb ... 285s Unpacking libkeyutils1:arm64 (1.6.3-3build1) over (1.6.3-3) ... 285s Preparing to unpack .../05-netplan-generator_1.0-2ubuntu1_arm64.deb ... 285s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 285s Unpacking netplan-generator (1.0-2ubuntu1) over (1.0-2build1) ... 285s Preparing to unpack .../06-python3-netplan_1.0-2ubuntu1_arm64.deb ... 285s Unpacking python3-netplan (1.0-2ubuntu1) over (1.0-2build1) ... 285s Preparing to unpack .../07-netplan.io_1.0-2ubuntu1_arm64.deb ... 285s Unpacking netplan.io (1.0-2ubuntu1) over (1.0-2build1) ... 286s Preparing to unpack .../08-libnetplan1_1.0-2ubuntu1_arm64.deb ... 286s Unpacking libnetplan1:arm64 (1.0-2ubuntu1) over (1.0-2build1) ... 286s Preparing to unpack .../09-netcat-openbsd_1.226-1ubuntu2_arm64.deb ... 286s Unpacking netcat-openbsd (1.226-1ubuntu2) over (1.226-1ubuntu1) ... 286s Preparing to unpack .../10-libnuma1_2.0.18-1build1_arm64.deb ... 286s Unpacking libnuma1:arm64 (2.0.18-1build1) over (2.0.18-1) ... 286s Preparing to unpack .../11-man-db_2.12.0-4build2_arm64.deb ... 286s Unpacking man-db (2.12.0-4build2) over (2.12.0-4build1) ... 286s Preparing to unpack .../12-libunwind8_1.6.2-3build1_arm64.deb ... 286s Unpacking libunwind8:arm64 (1.6.2-3build1) over (1.6.2-3) ... 287s Preparing to unpack .../13-make_4.3-4.1build2_arm64.deb ... 287s Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... 287s Preparing to unpack .../14-numactl_2.0.18-1build1_arm64.deb ... 287s Unpacking numactl (2.0.18-1build1) over (2.0.18-1) ... 287s Setting up libkeyutils1:arm64 (1.6.3-3build1) ... 287s Setting up python3-problem-report (2.28.1-0ubuntu1) ... 288s Setting up netcat-openbsd (1.226-1ubuntu2) ... 288s Setting up libnetplan1:arm64 (1.0-2ubuntu1) ... 288s Setting up man-db (2.12.0-4build2) ... 288s Updating database of manual pages ... 294s man-db.service is a disabled or a static unit not running, not starting it. 295s Setting up libunwind8:arm64 (1.6.2-3build1) ... 295s Setting up python3-apport (2.28.1-0ubuntu1) ... 295s Setting up make (4.3-4.1build2) ... 295s Setting up libnuma1:arm64 (2.0.18-1build1) ... 296s Setting up python3-netplan (1.0-2ubuntu1) ... 296s Setting up netplan-generator (1.0-2ubuntu1) ... 296s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 296s Setting up numactl (2.0.18-1build1) ... 296s Setting up netplan.io (1.0-2ubuntu1) ... 296s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ... 300s Setting up apport (2.28.1-0ubuntu1) ... 300s Installing new version of config file /etc/apport/crashdb.conf ... 303s apport-autoreport.service is a disabled or a static unit not running, not starting it. 303s Processing triggers for dbus (1.14.10-4ubuntu4) ... 303s Processing triggers for libc-bin (2.39-0ubuntu8) ... 304s Reading package lists... 305s Building dependency tree... 305s Reading state information... 307s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 308s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 308s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 308s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 308s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 314s Reading package lists... 314s Reading package lists... 315s Building dependency tree... 315s Reading state information... 317s Calculating upgrade... 318s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 318s Reading package lists... 319s Building dependency tree... 320s Reading state information... 321s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 322s autopkgtest [01:31:30]: rebooting testbed after setup commands that affected boot 489s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 497s autopkgtest [01:34:25]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP PREEMPT_DYNAMIC Fri Apr 5 02:52:09 UTC 2024 502s autopkgtest [01:34:30]: @@@@@@@@@@@@@@@@@@@@ apt-source igor 506s Get:1 http://ftpmaster.internal/ubuntu noble/universe igor 1.4.0+dfsg-4 (dsc) [2046 B] 506s Get:2 http://ftpmaster.internal/ubuntu noble/universe igor 1.4.0+dfsg-4 (tar) [1001 kB] 506s Get:3 http://ftpmaster.internal/ubuntu noble/universe igor 1.4.0+dfsg-4 (diff) [5200 B] 506s gpgv: Signature made Sat Nov 5 19:49:36 2022 UTC 506s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 506s gpgv: issuer "tille@debian.org" 506s gpgv: Can't check signature: No public key 506s dpkg-source: warning: cannot verify inline signature for ./igor_1.4.0+dfsg-4.dsc: no acceptable signature found 507s autopkgtest [01:34:35]: testing package igor version 1.4.0+dfsg-4 507s autopkgtest [01:34:35]: build not needed 508s autopkgtest [01:34:36]: test run-unit-test: preparing testbed 510s Reading package lists... 510s Building dependency tree... 510s Reading state information... 511s Starting pkgProblemResolver with broken count: 0 512s Starting 2 pkgProblemResolver with broken count: 0 512s Done 513s The following additional packages will be installed: 513s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 513s g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 513s gcc-13-aarch64-linux-gnu gcc-13-base gcc-aarch64-linux-gnu igor libasan8 513s libatomic1 libblas3 libcc1-0 libgcc-13-dev libgomp1 libgsl27 libgslcblas0 513s libhwasan0 libisl23 libitm1 libjemalloc2 liblsan0 libmpc3 libstdc++-13-dev 513s libtsan2 libubsan1 513s Suggested packages: 513s cpp-doc gcc-13-locales cpp-13-doc gcc-13-doc gcc-multilib manpages-dev 513s autoconf automake libtool flex bison gdb gcc-doc gdb-aarch64-linux-gnu 513s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libstdc++-13-doc 514s The following NEW packages will be installed: 514s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 514s cpp-aarch64-linux-gnu g++ g++-13 g++-13-aarch64-linux-gnu 514s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu gcc-13-base 514s gcc-aarch64-linux-gnu igor libasan8 libatomic1 libblas3 libcc1-0 514s libgcc-13-dev libgomp1 libgsl27 libgslcblas0 libhwasan0 libisl23 libitm1 514s libjemalloc2 liblsan0 libmpc3 libstdc++-13-dev libtsan2 libubsan1 514s 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. 514s Need to get 60.0 MB/60.0 MB of archives. 514s After this operation, 209 MB of additional disk space will be used. 514s Get:1 /tmp/autopkgtest.dSRGWd/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 514s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-base arm64 13.2.0-23ubuntu4 [49.0 kB] 514s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3build1 [669 kB] 515s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1build1 [56.4 kB] 516s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [10.3 MB] 530s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-23ubuntu4 [1032 B] 530s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 530s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 530s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240412-0ubuntu1 [44.7 kB] 530s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240412-0ubuntu1 [144 kB] 530s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240412-0ubuntu1 [27.9 kB] 530s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240412-0ubuntu1 [11.4 kB] 530s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240412-0ubuntu1 [2921 kB] 532s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240412-0ubuntu1 [1286 kB] 533s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240412-0ubuntu1 [2692 kB] 535s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240412-0ubuntu1 [1155 kB] 535s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240412-0ubuntu1 [1604 kB] 536s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-23ubuntu4 [2470 kB] 538s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [20.1 MB] 576s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-23ubuntu4 [472 kB] 578s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 578s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 578s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-23ubuntu4 [2379 kB] 590s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [11.7 MB] 651s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-23ubuntu4 [14.5 kB] 651s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 651s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 651s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 651s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 651s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu2 [72.8 kB] 651s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu2 [918 kB] 652s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 libjemalloc2 arm64 5.3.0-2 [203 kB] 653s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 igor arm64 1.4.0+dfsg-4 [514 kB] 655s Fetched 60.0 MB in 2min 20s (429 kB/s) 655s Selecting previously unselected package gcc-13-base:arm64. 656s (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 ... 77739 files and directories currently installed.) 656s Preparing to unpack .../00-gcc-13-base_13.2.0-23ubuntu4_arm64.deb ... 656s Unpacking gcc-13-base:arm64 (13.2.0-23ubuntu4) ... 656s Selecting previously unselected package libisl23:arm64. 656s Preparing to unpack .../01-libisl23_0.26-3build1_arm64.deb ... 656s Unpacking libisl23:arm64 (0.26-3build1) ... 656s Selecting previously unselected package libmpc3:arm64. 656s Preparing to unpack .../02-libmpc3_1.3.1-1build1_arm64.deb ... 656s Unpacking libmpc3:arm64 (1.3.1-1build1) ... 656s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 656s Preparing to unpack .../03-cpp-13-aarch64-linux-gnu_13.2.0-23ubuntu4_arm64.deb ... 656s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... 657s Selecting previously unselected package cpp-13. 658s Preparing to unpack .../04-cpp-13_13.2.0-23ubuntu4_arm64.deb ... 658s Unpacking cpp-13 (13.2.0-23ubuntu4) ... 658s Selecting previously unselected package cpp-aarch64-linux-gnu. 658s Preparing to unpack .../05-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 658s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 658s Selecting previously unselected package cpp. 658s Preparing to unpack .../06-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 658s Unpacking cpp (4:13.2.0-7ubuntu1) ... 658s Selecting previously unselected package libcc1-0:arm64. 658s Preparing to unpack .../07-libcc1-0_14-20240412-0ubuntu1_arm64.deb ... 658s Unpacking libcc1-0:arm64 (14-20240412-0ubuntu1) ... 658s Selecting previously unselected package libgomp1:arm64. 658s Preparing to unpack .../08-libgomp1_14-20240412-0ubuntu1_arm64.deb ... 658s Unpacking libgomp1:arm64 (14-20240412-0ubuntu1) ... 658s Selecting previously unselected package libitm1:arm64. 658s Preparing to unpack .../09-libitm1_14-20240412-0ubuntu1_arm64.deb ... 658s Unpacking libitm1:arm64 (14-20240412-0ubuntu1) ... 658s Selecting previously unselected package libatomic1:arm64. 658s Preparing to unpack .../10-libatomic1_14-20240412-0ubuntu1_arm64.deb ... 658s Unpacking libatomic1:arm64 (14-20240412-0ubuntu1) ... 658s Selecting previously unselected package libasan8:arm64. 658s Preparing to unpack .../11-libasan8_14-20240412-0ubuntu1_arm64.deb ... 658s Unpacking libasan8:arm64 (14-20240412-0ubuntu1) ... 659s Selecting previously unselected package liblsan0:arm64. 659s Preparing to unpack .../12-liblsan0_14-20240412-0ubuntu1_arm64.deb ... 659s Unpacking liblsan0:arm64 (14-20240412-0ubuntu1) ... 659s Selecting previously unselected package libtsan2:arm64. 659s Preparing to unpack .../13-libtsan2_14-20240412-0ubuntu1_arm64.deb ... 659s Unpacking libtsan2:arm64 (14-20240412-0ubuntu1) ... 659s Selecting previously unselected package libubsan1:arm64. 659s Preparing to unpack .../14-libubsan1_14-20240412-0ubuntu1_arm64.deb ... 659s Unpacking libubsan1:arm64 (14-20240412-0ubuntu1) ... 660s Selecting previously unselected package libhwasan0:arm64. 660s Preparing to unpack .../15-libhwasan0_14-20240412-0ubuntu1_arm64.deb ... 660s Unpacking libhwasan0:arm64 (14-20240412-0ubuntu1) ... 660s Selecting previously unselected package libgcc-13-dev:arm64. 660s Preparing to unpack .../16-libgcc-13-dev_13.2.0-23ubuntu4_arm64.deb ... 660s Unpacking libgcc-13-dev:arm64 (13.2.0-23ubuntu4) ... 660s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 660s Preparing to unpack .../17-gcc-13-aarch64-linux-gnu_13.2.0-23ubuntu4_arm64.deb ... 660s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... 663s Selecting previously unselected package gcc-13. 663s Preparing to unpack .../18-gcc-13_13.2.0-23ubuntu4_arm64.deb ... 663s Unpacking gcc-13 (13.2.0-23ubuntu4) ... 663s Selecting previously unselected package gcc-aarch64-linux-gnu. 663s Preparing to unpack .../19-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 663s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 663s Selecting previously unselected package gcc. 663s Preparing to unpack .../20-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 663s Unpacking gcc (4:13.2.0-7ubuntu1) ... 663s Selecting previously unselected package libstdc++-13-dev:arm64. 663s Preparing to unpack .../21-libstdc++-13-dev_13.2.0-23ubuntu4_arm64.deb ... 663s Unpacking libstdc++-13-dev:arm64 (13.2.0-23ubuntu4) ... 665s Selecting previously unselected package g++-13-aarch64-linux-gnu. 665s Preparing to unpack .../22-g++-13-aarch64-linux-gnu_13.2.0-23ubuntu4_arm64.deb ... 665s Unpacking g++-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... 666s Selecting previously unselected package g++-13. 666s Preparing to unpack .../23-g++-13_13.2.0-23ubuntu4_arm64.deb ... 666s Unpacking g++-13 (13.2.0-23ubuntu4) ... 666s Selecting previously unselected package g++-aarch64-linux-gnu. 666s Preparing to unpack .../24-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 666s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 666s Selecting previously unselected package g++. 666s Preparing to unpack .../25-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 666s Unpacking g++ (4:13.2.0-7ubuntu1) ... 667s Selecting previously unselected package build-essential. 667s Preparing to unpack .../26-build-essential_12.10ubuntu1_arm64.deb ... 667s Unpacking build-essential (12.10ubuntu1) ... 667s Selecting previously unselected package libblas3:arm64. 667s Preparing to unpack .../27-libblas3_3.12.0-3build1_arm64.deb ... 667s Unpacking libblas3:arm64 (3.12.0-3build1) ... 667s Selecting previously unselected package libgslcblas0:arm64. 667s Preparing to unpack .../28-libgslcblas0_2.7.1+dfsg-6ubuntu2_arm64.deb ... 667s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 667s Selecting previously unselected package libgsl27:arm64. 667s Preparing to unpack .../29-libgsl27_2.7.1+dfsg-6ubuntu2_arm64.deb ... 667s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 667s Selecting previously unselected package libjemalloc2:arm64. 667s Preparing to unpack .../30-libjemalloc2_5.3.0-2_arm64.deb ... 667s Unpacking libjemalloc2:arm64 (5.3.0-2) ... 667s Selecting previously unselected package igor. 667s Preparing to unpack .../31-igor_1.4.0+dfsg-4_arm64.deb ... 667s Unpacking igor (1.4.0+dfsg-4) ... 667s Selecting previously unselected package autopkgtest-satdep. 667s Preparing to unpack .../32-1-autopkgtest-satdep.deb ... 667s Unpacking autopkgtest-satdep (0) ... 668s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 668s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 668s Setting up libjemalloc2:arm64 (5.3.0-2) ... 668s Setting up libgomp1:arm64 (14-20240412-0ubuntu1) ... 668s Setting up libblas3:arm64 (3.12.0-3build1) ... 668s 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 668s Setting up gcc-13-base:arm64 (13.2.0-23ubuntu4) ... 668s Setting up libmpc3:arm64 (1.3.1-1build1) ... 668s Setting up libatomic1:arm64 (14-20240412-0ubuntu1) ... 668s Setting up libubsan1:arm64 (14-20240412-0ubuntu1) ... 668s Setting up libhwasan0:arm64 (14-20240412-0ubuntu1) ... 668s Setting up libasan8:arm64 (14-20240412-0ubuntu1) ... 668s Setting up libtsan2:arm64 (14-20240412-0ubuntu1) ... 668s Setting up libisl23:arm64 (0.26-3build1) ... 668s Setting up libcc1-0:arm64 (14-20240412-0ubuntu1) ... 668s Setting up liblsan0:arm64 (14-20240412-0ubuntu1) ... 668s Setting up libitm1:arm64 (14-20240412-0ubuntu1) ... 668s Setting up cpp-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... 668s Setting up igor (1.4.0+dfsg-4) ... 668s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 668s Setting up libgcc-13-dev:arm64 (13.2.0-23ubuntu4) ... 668s Setting up libstdc++-13-dev:arm64 (13.2.0-23ubuntu4) ... 668s Setting up cpp-13 (13.2.0-23ubuntu4) ... 668s Setting up gcc-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... 668s Setting up gcc-13 (13.2.0-23ubuntu4) ... 668s Setting up cpp (4:13.2.0-7ubuntu1) ... 668s Setting up g++-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... 668s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 668s Setting up g++-13 (13.2.0-23ubuntu4) ... 668s Setting up gcc (4:13.2.0-7ubuntu1) ... 668s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 668s Setting up g++ (4:13.2.0-7ubuntu1) ... 668s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 668s Setting up build-essential (12.10ubuntu1) ... 668s Setting up autopkgtest-satdep (0) ... 668s Processing triggers for man-db (2.12.0-4build2) ... 670s Processing triggers for libc-bin (2.39-0ubuntu8) ... 678s (Reading database ... 79010 files and directories currently installed.) 678s Removing autopkgtest-satdep (0) ... 679s autopkgtest [01:37:27]: test run-unit-test: [----------------------- 680s genomicDs.fasta 680s genomicJs_all_curated.fasta 680s genomicVs_with_primers.fasta 680s murugan_naive1_noncoding_demo_seqs.txt 680s =================== BEGIN TEST genomicDs.fasta ============================== 680s Batch name set to: foo_ 680s FASTA extension detected for the input sequence file 680s Working directory set to: "/tmp/igor-test-output.OgQpjX/" 680s Batch name set to: foo_ 680s Species parameter set to: human 680s Chain parameter set to: beta 680s Working directory set to: "/tmp/igor-test-output.OgQpjX/" 680s Performing V alignments.... 680s V_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 680s Performing D alignments.... 680s D_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 680s Performing J alignments.... 680s J_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 680s Performing CDR3 sequence extraction .... 680s ==========================PASSED================================ 680s =================== BEGIN TEST genomicJs_all_curated.fasta ============================== 680s Batch name set to: foo_ 680s FASTA extension detected for the input sequence file 680s Working directory set to: "/tmp/igor-test-output.OgQpjX/" 680s Batch name set to: foo_ 680s Species parameter set to: human 680s Chain parameter set to: beta 680s Working directory set to: "/tmp/igor-test-output.OgQpjX/" 680s Performing V alignments.... 684s V_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 684s Performing D alignments.... 685s D_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 685s Performing J alignments.... 685s J_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 685s Performing CDR3 sequence extraction .... 685s ==========================PASSED================================ 685s =================== BEGIN TEST genomicVs_with_primers.fasta ============================== 685s Batch name set to: foo_ 685s FASTA extension detected for the input sequence file 685s Working directory set to: "/tmp/igor-test-output.OgQpjX/" 685s Batch name set to: foo_ 685s Species parameter set to: human 685s Chain parameter set to: beta 685s Working directory set to: "/tmp/igor-test-output.OgQpjX/" 685s Performing V alignments.... 851s V_gene alignments [|||||||||||||||||||||||||||| ] 56.17 % V_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 851s Performing D alignments.... 851s D_gene alignments [|||||||||||||||||||||||||||| ] 56.17 % D_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 851s Performing J alignments.... 856s J_gene alignments [|||||||||||||||||||||||||||| ] 56.17 % J_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 856s Performing CDR3 sequence extraction .... 856s ==========================PASSED================================ 856s =================== BEGIN TEST murugan_naive1_noncoding_demo_seqs.txt ============================== 856s Batch name set to: foo_ 856s TXT extension detected for the input sequence file 856s Working directory set to: "/tmp/igor-test-output.OgQpjX/" 857s Batch name set to: foo_ 857s Species parameter set to: human 857s Chain parameter set to: beta 857s Working directory set to: "/tmp/igor-test-output.OgQpjX/" 857s Performing V alignments.... 967s V_gene alignments [|||||||| ] 16.66 % V_gene alignments [|||||||||||||||| ] 33.33 % V_gene alignments [||||||||||||||||||||||||| ] 50.00 % V_gene alignments [||||||||||||||||||||||||||||||||| ] 66.66 % V_gene alignments [||||||||||||||||||||||||||||||||||||||||| ] 83.33 % V_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] 100.0 % V_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 967s Performing D alignments.... 967s D_gene alignments [|||||||| ] 16.66 % D_gene alignments [|||||||||||||||| ] 33.33 % D_gene alignments [||||||||||||||||||||||||| ] 50.00 % D_gene alignments [||||||||||||||||||||||||||||||||| ] 66.66 % D_gene alignments [||||||||||||||||||||||||||||||||||||||||| ] 83.33 % D_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] 100.0 % D_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 967s Performing J alignments.... 971s J_gene alignments [|||||||| ] 16.66 % J_gene alignments [|||||||||||||||| ] 33.33 % J_gene alignments [||||||||||||||||||||||||| ] 50.00 % J_gene alignments [||||||||||||||||||||||||||||||||| ] 66.66 % J_gene alignments [||||||||||||||||||||||||||||||||||||||||| ] 83.33 % J_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] 100.0 % J_gene alignments [||||||||||||||||||||||||||||||||||||||||||||||||||] Done. 971s Performing CDR3 sequence extraction .... 971s ==========================PASSED================================ 971s autopkgtest [01:42:19]: test run-unit-test: -----------------------] 972s autopkgtest [01:42:20]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 972s run-unit-test PASS 973s autopkgtest [01:42:21]: @@@@@@@@@@@@@@@@@@@@ summary 973s run-unit-test PASS 984s Creating nova instance adt-noble-arm64-igor-20240419-012607-juju-7f2275-prod-proposed-migration-environment-3-43944b13-89e1-4160-be99-a59d02cd8326 from image adt/ubuntu-noble-arm64-server-20240418.img (UUID 6f8e97a7-9a55-4e99-9797-31213b709dd4)...