0s autopkgtest [12:12:32]: starting date and time: 2024-11-15 12:12:32+0000
  0s autopkgtest [12:12:32]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [12:12:32]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.oq15cvtn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade uncalled --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-17.secgroup --name adt-plucky-amd64-uncalled-20241115-121232-juju-7f2275-prod-proposed-migration-environment-15-386cf2a5-df18-4889-a395-0f2c86e02f87 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/
 48s autopkgtest [12:13:20]: testbed dpkg architecture: amd64
 48s autopkgtest [12:13:20]: testbed apt version: 2.9.8
 48s autopkgtest [12:13:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 49s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 49s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.5 kB]
 49s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1052 kB]
 49s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB]
 49s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 49s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [109 kB]
 49s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB]
 49s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
 49s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [831 kB]
 49s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [295 kB]
 49s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B]
 49s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B]
 49s Fetched 2696 kB in 1s (3195 kB/s)
 50s Reading package lists...
 52s Reading package lists...
 52s Building dependency tree...
 52s Reading state information...
 52s Calculating upgrade...
 52s The following packages will be upgraded:
 52s   firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0
 52s   libexpat1 lxd-installer man-db pastebinit python3-markupsafe python3-systemd
 52s   xfsprogs
 53s 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 53s Need to get 13.6 MB of archives.
 53s After this operation, 493 kB of additional disk space will be used.
 53s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB]
 54s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB]
 54s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB]
 54s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB]
 54s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB]
 54s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB]
 54s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB]
 54s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB]
 54s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B]
 54s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB]
 54s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build3 [13.0 kB]
 54s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB]
 54s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB]
 54s Preconfiguring packages ...
 54s Fetched 13.6 MB in 1s (9688 kB/s)
 54s (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.)
 54s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ...
 54s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ...
 55s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ...
 55s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ...
 55s Setting up libcap-ng0:amd64 (0.8.5-3build1) ...
 55s (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.)
 55s Preparing to unpack .../00-libexpat1_2.6.4-1_amd64.deb ...
 55s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ...
 55s Preparing to unpack .../01-man-db_2.13.0-1_amd64.deb ...
 55s Unpacking man-db (2.13.0-1) over (2.12.1-3) ...
 55s Preparing to unpack .../02-grub2-common_2.12-5ubuntu7_amd64.deb ...
 55s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 55s Preparing to unpack .../03-grub-pc_2.12-5ubuntu7_amd64.deb ...
 55s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 55s Preparing to unpack .../04-grub-pc-bin_2.12-5ubuntu7_amd64.deb ...
 55s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 55s Preparing to unpack .../05-grub-common_2.12-5ubuntu7_amd64.deb ...
 55s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 55s Preparing to unpack .../06-lxd-installer_9_all.deb ...
 55s Unpacking lxd-installer (9) over (8) ...
 56s Preparing to unpack .../07-pastebinit_1.7.1-1_all.deb ...
 56s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
 56s Preparing to unpack .../08-python3-markupsafe_2.1.5-1build3_amd64.deb ...
 56s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ...
 56s Preparing to unpack .../09-python3-systemd_235-1build5_amd64.deb ...
 56s Unpacking python3-systemd (235-1build5) over (235-1build4) ...
 56s Preparing to unpack .../10-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ...
 56s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ...
 56s Setting up libexpat1:amd64 (2.6.4-1) ...
 56s Setting up firmware-sof-signed (2024.06-1ubuntu2) ...
 56s Setting up pastebinit (1.7.1-1) ...
 56s Setting up man-db (2.13.0-1) ...
 56s Updating database of manual pages ...
 58s man-db.service is a disabled or a static unit not running, not starting it.
 58s Setting up python3-markupsafe (2.1.5-1build3) ...
 59s Setting up grub-common (2.12-5ubuntu7) ...
 59s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
 59s Setting up xfsprogs (6.8.0-2.2ubuntu2) ...
 59s update-initramfs: deferring update (trigger activated)
 60s Setting up lxd-installer (9) ...
 60s Setting up python3-systemd (235-1build5) ...
 60s Setting up grub2-common (2.12-5ubuntu7) ...
 60s Setting up grub-pc-bin (2.12-5ubuntu7) ...
 60s Setting up grub-pc (2.12-5ubuntu7) ...
 61s Installing for i386-pc platform.
 61s Installation finished. No error reported.
 61s Sourcing file `/etc/default/grub'
 61s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
 61s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
 61s Generating grub configuration file ...
 61s Found linux image: /boot/vmlinuz-6.11.0-8-generic
 61s Found initrd image: /boot/initrd.img-6.11.0-8-generic
 61s Warning: os-prober will not be executed to detect other bootable partitions.
 61s Systems on them will not be added to the GRUB boot configuration.
 61s Check GRUB_DISABLE_OS_PROBER documentation entry.
 61s Adding boot menu entry for UEFI Firmware Settings ...
 62s done
 62s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 62s Processing triggers for install-info (7.1.1-1) ...
 62s Processing triggers for initramfs-tools (0.142ubuntu34) ...
 62s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic
 62s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
 70s Reading package lists...
 70s Building dependency tree...
 70s Reading state information...
 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 71s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 71s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 71s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 71s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 72s Reading package lists...
 72s Reading package lists...
 72s Building dependency tree...
 72s Reading state information...
 72s Calculating upgrade...
 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 72s Reading package lists...
 73s Building dependency tree...
 73s Reading state information...
 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 73s autopkgtest [12:13:45]: rebooting testbed after setup commands that affected boot
 77s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
 93s autopkgtest [12:14:05]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 95s autopkgtest [12:14:07]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled
 98s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (dsc) [2117 B]
 98s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (tar) [155 kB]
 98s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (diff) [5072 B]
 98s gpgv: Signature made Wed Aug 21 15:42:41 2024 UTC
 98s gpgv:                using RSA key 33CB284313E90BD27DCB4523600316A6DC277476
 98s gpgv: Can't check signature: No public key
 98s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found
 98s autopkgtest [12:14:10]: testing package uncalled version 2.3+ds-2
 98s autopkgtest [12:14:10]: build not needed
 99s autopkgtest [12:14:11]: test run-unit-test: preparing testbed
100s Reading package lists...
101s Building dependency tree...
101s Reading state information...
101s Starting pkgProblemResolver with broken count: 0
101s Starting 2 pkgProblemResolver with broken count: 0
101s Done
101s The following additional packages will be installed:
101s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 libsz2
101s   python3-numpy uncalled
101s Suggested packages:
101s   gcc gfortran python-numpy-doc python3-dev python3-pytest
101s The following NEW packages will be installed:
101s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3
101s   libsz2 python3-numpy uncalled
101s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded.
101s Need to get 11.1 MB/11.1 MB of archives.
101s After this operation, 56.2 MB of additional disk space will be used.
101s Get:1 /tmp/autopkgtest.kN6n9v/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [708 B]
101s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB]
102s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
102s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
103s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B]
103s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB]
104s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
104s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB]
105s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 uncalled amd64 2.3+ds-2 [632 kB]
106s Fetched 11.1 MB in 4s (2568 kB/s)
106s Selecting previously unselected package libaec0:amd64.
106s (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 ... 75576 files and directories currently installed.)
106s Preparing to unpack .../0-libaec0_1.1.3-1_amd64.deb ...
106s Unpacking libaec0:amd64 (1.1.3-1) ...
106s Selecting previously unselected package libblas3:amd64.
106s Preparing to unpack .../1-libblas3_3.12.0-3build2_amd64.deb ...
106s Unpacking libblas3:amd64 (3.12.0-3build2) ...
106s Selecting previously unselected package libgfortran5:amd64.
106s Preparing to unpack .../2-libgfortran5_14.2.0-8ubuntu1_amd64.deb ...
106s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ...
106s Selecting previously unselected package libsz2:amd64.
106s Preparing to unpack .../3-libsz2_1.1.3-1_amd64.deb ...
106s Unpacking libsz2:amd64 (1.1.3-1) ...
106s Selecting previously unselected package libhdf5-103-1t64:amd64.
106s Preparing to unpack .../4-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ...
106s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ...
106s Selecting previously unselected package liblapack3:amd64.
106s Preparing to unpack .../5-liblapack3_3.12.0-3build2_amd64.deb ...
106s Unpacking liblapack3:amd64 (3.12.0-3build2) ...
106s Selecting previously unselected package python3-numpy.
106s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ...
106s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ...
107s Selecting previously unselected package uncalled.
107s Preparing to unpack .../7-uncalled_2.3+ds-2_amd64.deb ...
107s Unpacking uncalled (2.3+ds-2) ...
107s Selecting previously unselected package autopkgtest-satdep.
107s Preparing to unpack .../8-1-autopkgtest-satdep.deb ...
107s Unpacking autopkgtest-satdep (0) ...
107s Setting up libaec0:amd64 (1.1.3-1) ...
107s Setting up libblas3:amd64 (3.12.0-3build2) ...
107s 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
107s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ...
107s Setting up libsz2:amd64 (1.1.3-1) ...
107s Setting up liblapack3:amd64 (3.12.0-3build2) ...
107s 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
107s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ...
108s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ...
108s Setting up uncalled (2.3+ds-2) ...
108s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d'
108s   CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])")
108s Setting up autopkgtest-satdep (0) ...
108s Processing triggers for man-db (2.13.0-1) ...
109s Processing triggers for libc-bin (2.40-1ubuntu3) ...
111s (Reading database ... 76556 files and directories currently installed.)
111s Removing autopkgtest-satdep (0) ...
112s autopkgtest [12:14:24]: test run-unit-test: [-----------------------
112s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-'
112s   log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+")
112s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d'
112s   port_re = re.compile("grpc_port = (\d+)")
112s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s'
112s   device_re = re.compile("(device_id|instance) = ([^\s,]+)")
112s [bwa_index] Pack FASTA... 0.00 sec
112s [bwa_index] Construct BWT for the packed sequence...
112s [bwa_index] 0.00 seconds elapse.
112s [bwa_index] Update BWT... 0.00 sec
112s [bwa_index] Pack forward-only FASTA... 0.00 sec
112s [bwa_index] Construct SA from BWT and Occ... 0.00 sec
112s Initializing parameter search
112s Computing default parameters
112s Writing default parameters
112s Done
112s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-'
112s   log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+")
112s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d'
112s   port_re = re.compile("grpc_port = (\d+)")
112s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s'
112s   device_re = re.compile("(device_id|instance) = ([^\s,]+)")
113s Loading fast5s
113s Mapping
113s Finishing
113s 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:10.952803
113s autopkgtest [12:14:25]: test run-unit-test: -----------------------]
113s run-unit-test        PASS
113s autopkgtest [12:14:25]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
114s autopkgtest [12:14:26]: @@@@@@@@@@@@@@@@@@@@ summary
114s run-unit-test        PASS
126s nova [W] Skipping flock for amd64
126s Creating nova instance adt-plucky-amd64-uncalled-20241115-121232-juju-7f2275-prod-proposed-migration-environment-15-386cf2a5-df18-4889-a395-0f2c86e02f87 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...