0s autopkgtest [02:42:55]: starting date and time: 2024-11-15 02:42:55+0000 0s autopkgtest [02:42:55]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [02:42:55]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zgsq2fx0/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-30.secgroup --name adt-plucky-amd64-uncalled-20241115-024255-juju-7f2275-prod-proposed-migration-environment-20-d9da0d59-497c-40b8-8602-dfb33d24f4c6 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 42s autopkgtest [02:43:37]: testbed dpkg architecture: amd64 42s autopkgtest [02:43:37]: testbed apt version: 2.9.8 42s autopkgtest [02:43:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 43s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 43s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 44s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1030 kB] 44s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 44s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 44s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [101 kB] 44s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [166 kB] 44s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 44s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [293 kB] 44s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [800 kB] 44s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 44s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9128 B] 44s Fetched 2631 kB in 1s (3061 kB/s) 44s Reading package lists... 46s Reading package lists... 46s Building dependency tree... 46s Reading state information... 47s Calculating upgrade... 47s The following NEW packages will be installed: 47s python3.13-gdbm 47s The following packages will be upgraded: 47s firmware-sof-signed libcap-ng0 libexpat1 libpython3-stdlib lxd-installer 47s man-db pastebinit python3 python3-gdbm python3-minimal python3-systemd 47s xfsprogs 47s 12 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 47s Need to get 9638 kB of archives. 47s After this operation, 542 kB of additional disk space will be used. 47s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 47s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 47s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 47s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 48s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 48s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 48s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 48s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 48s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 48s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 48s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 48s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 48s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 48s Preconfiguring packages ... 48s Fetched 9638 kB in 1s (11.5 MB/s) 48s (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 ... 75542 files and directories currently installed.) 48s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 48s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 48s Setting up python3-minimal (3.12.7-1) ... 48s (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 ... 75542 files and directories currently installed.) 48s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 49s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 49s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 49s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 49s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 49s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 49s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 49s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 49s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 49s (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 ... 75568 files and directories currently installed.) 49s Preparing to unpack .../0-libexpat1_2.6.4-1_amd64.deb ... 49s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 49s Preparing to unpack .../1-man-db_2.13.0-1_amd64.deb ... 49s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 49s Selecting previously unselected package python3.13-gdbm. 49s Preparing to unpack .../2-python3.13-gdbm_3.13.0-2_amd64.deb ... 49s Unpacking python3.13-gdbm (3.13.0-2) ... 49s Preparing to unpack .../3-python3-gdbm_3.12.7-1_amd64.deb ... 49s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 49s Preparing to unpack .../4-lxd-installer_9_all.deb ... 49s Unpacking lxd-installer (9) over (8) ... 49s Preparing to unpack .../5-pastebinit_1.7.1-1_all.deb ... 49s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 49s Preparing to unpack .../6-python3-systemd_235-1build5_amd64.deb ... 49s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 49s Preparing to unpack .../7-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 49s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 49s Setting up libexpat1:amd64 (2.6.4-1) ... 49s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 49s Setting up man-db (2.13.0-1) ... 49s Updating database of manual pages ... 51s man-db.service is a disabled or a static unit not running, not starting it. 51s Setting up lxd-installer (9) ... 51s Setting up python3.13-gdbm (3.13.0-2) ... 51s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 51s Setting up python3 (3.12.7-1) ... 52s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 52s update-initramfs: deferring update (trigger activated) 52s Setting up python3-systemd (235-1build5) ... 52s Setting up python3-gdbm:amd64 (3.12.7-1) ... 52s Setting up pastebinit (1.7.1-1) ... 52s Processing triggers for libc-bin (2.40-1ubuntu3) ... 52s Processing triggers for initramfs-tools (0.142ubuntu34) ... 52s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 52s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 61s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 61s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 61s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 62s Reading package lists... 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 63s Calculating upgrade... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s autopkgtest [02:43:58]: rebooting testbed after setup commands that affected boot 81s autopkgtest [02:44:16]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 84s autopkgtest [02:44:19]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled 85s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (dsc) [2117 B] 85s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (tar) [155 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (diff) [5072 B] 85s gpgv: Signature made Wed Aug 21 15:42:41 2024 UTC 85s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 85s gpgv: Can't check signature: No public key 85s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found 85s autopkgtest [02:44:20]: testing package uncalled version 2.3+ds-2 86s autopkgtest [02:44:21]: build not needed 86s autopkgtest [02:44:21]: test run-unit-test: preparing testbed 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s Starting pkgProblemResolver with broken count: 0 95s Starting 2 pkgProblemResolver with broken count: 0 95s Done 96s The following additional packages will be installed: 96s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 libsz2 96s python3-numpy uncalled 96s Suggested packages: 96s gcc gfortran python-numpy-doc python3-dev python3-pytest 96s The following NEW packages will be installed: 96s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 96s libsz2 python3-numpy uncalled 96s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 10.2 MB/10.2 MB of archives. 96s After this operation, 41.3 MB of additional disk space will be used. 96s Get:1 /tmp/autopkgtest.3C3l2q/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [704 B] 96s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 96s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 96s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 96s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 96s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 96s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 96s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 uncalled amd64 2.3+ds-2 [632 kB] 97s Fetched 10.2 MB in 1s (11.7 MB/s) 97s Selecting previously unselected package libaec0:amd64. 97s (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 ... 75581 files and directories currently installed.) 97s Preparing to unpack .../0-libaec0_1.1.3-1_amd64.deb ... 97s Unpacking libaec0:amd64 (1.1.3-1) ... 97s Selecting previously unselected package libblas3:amd64. 97s Preparing to unpack .../1-libblas3_3.12.0-3build2_amd64.deb ... 97s Unpacking libblas3:amd64 (3.12.0-3build2) ... 97s Selecting previously unselected package libgfortran5:amd64. 97s Preparing to unpack .../2-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 97s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 97s Selecting previously unselected package libsz2:amd64. 97s Preparing to unpack .../3-libsz2_1.1.3-1_amd64.deb ... 97s Unpacking libsz2:amd64 (1.1.3-1) ... 97s Selecting previously unselected package libhdf5-103-1t64:amd64. 97s Preparing to unpack .../4-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 97s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 97s Selecting previously unselected package liblapack3:amd64. 97s Preparing to unpack .../5-liblapack3_3.12.0-3build2_amd64.deb ... 97s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 97s Selecting previously unselected package python3-numpy. 97s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 97s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 97s Selecting previously unselected package uncalled. 97s Preparing to unpack .../7-uncalled_2.3+ds-2_amd64.deb ... 97s Unpacking uncalled (2.3+ds-2) ... 97s Selecting previously unselected package autopkgtest-satdep. 97s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 97s Unpacking autopkgtest-satdep (0) ... 97s Setting up libaec0:amd64 (1.1.3-1) ... 97s Setting up libblas3:amd64 (3.12.0-3build2) ... 98s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 98s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 98s Setting up libsz2:amd64 (1.1.3-1) ... 98s Setting up liblapack3:amd64 (3.12.0-3build2) ... 98s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 98s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 99s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 99s Setting up uncalled (2.3+ds-2) ... 99s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' 99s CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") 99s Setting up autopkgtest-satdep (0) ... 99s Processing triggers for man-db (2.13.0-1) ... 100s Processing triggers for libc-bin (2.40-1ubuntu3) ... 102s (Reading database ... 76541 files and directories currently installed.) 102s Removing autopkgtest-satdep (0) ... 102s autopkgtest [02:44:37]: test run-unit-test: [----------------------- 102s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 102s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 102s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 102s port_re = re.compile("grpc_port = (\d+)") 102s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 102s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 103s [bwa_index] Pack FASTA... 0.00 sec 103s [bwa_index] Construct BWT for the packed sequence... 103s [bwa_index] 0.00 seconds elapse. 103s [bwa_index] Update BWT... 0.00 sec 103s [bwa_index] Pack forward-only FASTA... 0.00 sec 103s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 103s Initializing parameter search 103s Computing default parameters 103s Writing default parameters 103s Done 103s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 103s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 103s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 103s port_re = re.compile("grpc_port = (\d+)") 103s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 103s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 103s Loading fast5s 103s Mapping 103s Finishing 103s 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:7.486459 103s autopkgtest [02:44:38]: test run-unit-test: -----------------------] 104s run-unit-test PASS 104s autopkgtest [02:44:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 104s autopkgtest [02:44:39]: @@@@@@@@@@@@@@@@@@@@ summary 104s run-unit-test PASS 117s nova [W] Skipping flock for amd64 117s Creating nova instance adt-plucky-amd64-uncalled-20241115-024255-juju-7f2275-prod-proposed-migration-environment-20-d9da0d59-497c-40b8-8602-dfb33d24f4c6 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...