9s autopkgtest [10:07:47]: starting date and time: 2024-11-13 10:07:47+0000 24s autopkgtest [10:08:03]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 24s autopkgtest [10:08:03]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.39r_put4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade uncalled --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-31.secgroup --name adt-plucky-arm64-uncalled-20241113-100725-juju-7f2275-prod-proposed-migration-environment-20-c2ec0b70-11d0-42cc-8392-773cc4148fbf --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 241s autopkgtest [10:11:40]: testbed dpkg architecture: arm64 241s autopkgtest [10:11:40]: testbed apt version: 2.9.8 241s autopkgtest [10:11:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 242s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 242s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 242s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 242s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 242s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 243s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 243s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 243s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 243s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 243s Fetched 1794 kB in 1s (2055 kB/s) 243s Reading package lists... 246s Reading package lists... 246s Building dependency tree... 246s Reading state information... 247s Calculating upgrade... 248s The following NEW packages will be installed: 248s python3.13-gdbm 248s The following packages will be upgraded: 248s libpython3-stdlib python3 python3-gdbm python3-minimal 248s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 248s Need to get 101 kB of archives. 248s After this operation, 141 kB of additional disk space will be used. 248s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 248s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 248s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 248s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 248s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 248s Fetched 101 kB in 0s (275 kB/s) 249s (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 ... 79924 files and directories currently installed.) 249s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 249s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 249s Setting up python3-minimal (3.12.7-1) ... 249s (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 ... 79924 files and directories currently installed.) 249s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 250s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 250s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 250s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 250s Selecting previously unselected package python3.13-gdbm. 250s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 250s Unpacking python3.13-gdbm (3.13.0-2) ... 250s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 250s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 250s Setting up python3.13-gdbm (3.13.0-2) ... 250s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 250s Setting up python3 (3.12.7-1) ... 250s Setting up python3-gdbm:arm64 (3.12.7-1) ... 250s Processing triggers for man-db (2.12.1-3) ... 251s Reading package lists... 252s Building dependency tree... 252s Reading state information... 253s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 253s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 253s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 253s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 253s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 256s Reading package lists... 256s Reading package lists... 256s Building dependency tree... 256s Reading state information... 256s Calculating upgrade... 256s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 257s Reading package lists... 257s Building dependency tree... 257s Reading state information... 258s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 261s autopkgtest [10:12:00]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 261s autopkgtest [10:12:00]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled 263s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (dsc) [2117 B] 263s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (tar) [155 kB] 263s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (diff) [5072 B] 263s gpgv: Signature made Wed Aug 21 15:42:41 2024 UTC 263s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 263s gpgv: Can't check signature: No public key 263s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found 263s autopkgtest [10:12:02]: testing package uncalled version 2.3+ds-2 264s autopkgtest [10:12:03]: build not needed 264s autopkgtest [10:12:03]: test run-unit-test: preparing testbed 265s Reading package lists... 266s Building dependency tree... 266s Reading state information... 267s Starting pkgProblemResolver with broken count: 0 267s Starting 2 pkgProblemResolver with broken count: 0 267s Done 268s The following additional packages will be installed: 268s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 libsz2 268s python3-numpy uncalled 268s Suggested packages: 268s gcc gfortran python-numpy-doc python3-dev python3-pytest 268s The following NEW packages will be installed: 268s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 268s libsz2 python3-numpy uncalled 268s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 268s Need to get 8345 kB/8346 kB of archives. 268s After this operation, 33.6 MB of additional disk space will be used. 268s Get:1 /tmp/autopkgtest.9y15DJ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 268s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 268s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 268s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 268s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 268s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 269s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 269s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 269s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 uncalled arm64 2.3+ds-2 [574 kB] 269s Fetched 8345 kB in 1s (9569 kB/s) 269s Selecting previously unselected package libaec0:arm64. 269s (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 ... 79931 files and directories currently installed.) 269s Preparing to unpack .../0-libaec0_1.1.3-1_arm64.deb ... 269s Unpacking libaec0:arm64 (1.1.3-1) ... 269s Selecting previously unselected package libblas3:arm64. 269s Preparing to unpack .../1-libblas3_3.12.0-3build2_arm64.deb ... 269s Unpacking libblas3:arm64 (3.12.0-3build2) ... 269s Selecting previously unselected package libgfortran5:arm64. 269s Preparing to unpack .../2-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 269s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 269s Selecting previously unselected package libsz2:arm64. 269s Preparing to unpack .../3-libsz2_1.1.3-1_arm64.deb ... 269s Unpacking libsz2:arm64 (1.1.3-1) ... 269s Selecting previously unselected package libhdf5-103-1t64:arm64. 269s Preparing to unpack .../4-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 269s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 270s Selecting previously unselected package liblapack3:arm64. 270s Preparing to unpack .../5-liblapack3_3.12.0-3build2_arm64.deb ... 270s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 270s Selecting previously unselected package python3-numpy. 270s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 270s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 270s Selecting previously unselected package uncalled. 270s Preparing to unpack .../7-uncalled_2.3+ds-2_arm64.deb ... 270s Unpacking uncalled (2.3+ds-2) ... 270s Selecting previously unselected package autopkgtest-satdep. 270s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 270s Unpacking autopkgtest-satdep (0) ... 270s Setting up libaec0:arm64 (1.1.3-1) ... 270s Setting up libblas3:arm64 (3.12.0-3build2) ... 270s 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 270s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 270s Setting up libsz2:arm64 (1.1.3-1) ... 270s Setting up liblapack3:arm64 (3.12.0-3build2) ... 270s 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 270s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 272s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 272s Setting up uncalled (2.3+ds-2) ... 272s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' 272s CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") 273s Setting up autopkgtest-satdep (0) ... 273s Processing triggers for man-db (2.12.1-3) ... 273s Processing triggers for libc-bin (2.40-1ubuntu3) ... 276s (Reading database ... 80891 files and directories currently installed.) 276s Removing autopkgtest-satdep (0) ... 277s autopkgtest [10:12:16]: test run-unit-test: [----------------------- 277s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 277s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 277s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 277s port_re = re.compile("grpc_port = (\d+)") 277s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 277s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 278s [bwa_index] Pack FASTA... 0.00 sec 278s [bwa_index] Construct BWT for the packed sequence... 278s [bwa_index] 0.00 seconds elapse. 278s [bwa_index] Update BWT... 0.00 sec 278s [bwa_index] Pack forward-only FASTA... 0.00 sec 278s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 278s Initializing parameter search 278s Computing default parameters 278s Writing default parameters 278s Done 278s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 278s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 278s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 278s port_re = re.compile("grpc_port = (\d+)") 278s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 278s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 278s Loading fast5s 278s Mapping 278s Finishing 278s f41a60f7-de4a-4b17-9f54-387e52d60b65 106 73 106 - Escherichia_coli_chromosome:2400000-2410000 10000 6938 6976 38 39 255 ch:i:486 st:i:257117 mt:f:8.946902 278s autopkgtest [10:12:17]: test run-unit-test: -----------------------] 279s run-unit-test PASS 279s autopkgtest [10:12:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 279s autopkgtest [10:12:18]: @@@@@@@@@@@@@@@@@@@@ summary 279s run-unit-test PASS 291s nova [W] Skipping flock in bos03-arm64 291s Creating nova instance adt-plucky-arm64-uncalled-20241113-100725-juju-7f2275-prod-proposed-migration-environment-20-c2ec0b70-11d0-42cc-8392-773cc4148fbf from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...