0s autopkgtest [03:24:39]: starting date and time: 2024-11-14 03:24:39+0000
  0s autopkgtest [03:24:39]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [03:24:39]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._g_ukz1c/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-9.secgroup --name adt-plucky-ppc64el-uncalled-20241114-032439-juju-7f2275-prod-proposed-migration-environment-20-519ed0aa-9869-479e-b824-aac43b03338d --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -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/
112s autopkgtest [03:26:31]: testbed dpkg architecture: ppc64el
112s autopkgtest [03:26:31]: testbed apt version: 2.9.8
112s autopkgtest [03:26:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup
113s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
113s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.4 kB]
113s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
113s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [96.9 kB]
113s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [977 kB]
113s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [107 kB]
113s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [699 kB]
113s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8544 B]
114s Fetched 1985 kB in 1s (2148 kB/s)
114s Reading package lists...
117s Reading package lists...
117s Building dependency tree...
117s Reading state information...
117s Calculating upgrade...
117s The following NEW packages will be installed:
117s   python3.13-gdbm
117s The following packages will be upgraded:
117s   bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0
117s   libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3
117s   python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail
118s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
118s Need to get 4700 kB of archives.
118s After this operation, 215 kB of additional disk space will be used.
118s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB]
118s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB]
118s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB]
118s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB]
118s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB]
118s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB]
118s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB]
118s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB]
118s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B]
118s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB]
118s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB]
118s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB]
118s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB]
118s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B]
118s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB]
118s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B]
118s Fetched 4700 kB in 1s (6675 kB/s)
119s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
119s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ...
119s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
119s Setting up python3-minimal (3.12.7-1) ...
119s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
119s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ...
119s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
119s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ...
119s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ...
119s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ...
119s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ...
119s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ...
119s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
119s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ...
119s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
119s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ...
119s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
119s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ...
119s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
119s Selecting previously unselected package python3.13-gdbm.
119s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ...
119s Unpacking python3.13-gdbm (3.13.0-2) ...
119s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ...
119s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ...
119s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ...
119s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
119s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ...
119s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
119s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ...
119s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
119s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ...
119s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ...
119s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ...
119s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ...
119s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ...
119s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ...
119s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ...
119s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ...
119s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ...
120s Setting up libutempter0:ppc64el (1.2.1-4) ...
120s Setting up whiptail (0.52.24-2ubuntu4) ...
120s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ...
120s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ...
120s Setting up python3.13-gdbm (3.13.0-2) ...
120s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ...
120s Setting up bpftrace (0.21.2-2ubuntu2) ...
120s Setting up python3 (3.12.7-1) ...
120s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ...
120s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ...
120s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ...
120s Setting up python3-gdbm:ppc64el (3.12.7-1) ...
120s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ...
120s Processing triggers for man-db (2.12.1-3) ...
121s Processing triggers for libc-bin (2.40-1ubuntu3) ...
121s Reading package lists...
122s Building dependency tree...
122s Reading state information...
122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
122s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
122s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
122s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
122s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
123s Reading package lists...
123s Reading package lists...
124s Building dependency tree...
124s Reading state information...
124s Calculating upgrade...
124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
124s Reading package lists...
124s Building dependency tree...
124s Reading state information...
124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
127s autopkgtest [03:26:46]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024
127s autopkgtest [03:26:46]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled
129s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (dsc) [2117 B]
129s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (tar) [155 kB]
129s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (diff) [5072 B]
129s gpgv: Signature made Wed Aug 21 15:42:41 2024 UTC
129s gpgv:                using RSA key 33CB284313E90BD27DCB4523600316A6DC277476
129s gpgv: Can't check signature: No public key
129s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found
129s autopkgtest [03:26:48]: testing package uncalled version 2.3+ds-2
129s autopkgtest [03:26:48]: build not needed
130s autopkgtest [03:26:49]: test run-unit-test: preparing testbed
132s Reading package lists...
132s Building dependency tree...
132s Reading state information...
132s Starting pkgProblemResolver with broken count: 0
133s Starting 2 pkgProblemResolver with broken count: 0
133s Done
133s The following additional packages will be installed:
133s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 libsz2
133s   python3-numpy uncalled
133s Suggested packages:
133s   gcc gfortran python-numpy-doc python3-dev python3-pytest
133s The following NEW packages will be installed:
133s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3
133s   libsz2 python3-numpy uncalled
133s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded.
133s Need to get 10.1 MB/10.1 MB of archives.
133s After this operation, 42.2 MB of additional disk space will be used.
133s Get:1 /tmp/autopkgtest.ioExyF/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B]
133s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB]
133s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB]
133s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB]
133s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B]
133s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-4ubuntu3 [1387 kB]
133s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB]
139s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB]
139s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el uncalled ppc64el 2.3+ds-2 [634 kB]
139s Fetched 10.1 MB in 6s (1653 kB/s)
139s Selecting previously unselected package libaec0:ppc64el.
139s (Reading database ... 
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(Reading database ... 73775 files and directories currently installed.)
139s Preparing to unpack .../0-libaec0_1.1.3-1_ppc64el.deb ...
139s Unpacking libaec0:ppc64el (1.1.3-1) ...
139s Selecting previously unselected package libblas3:ppc64el.
139s Preparing to unpack .../1-libblas3_3.12.0-3build2_ppc64el.deb ...
139s Unpacking libblas3:ppc64el (3.12.0-3build2) ...
139s Selecting previously unselected package libgfortran5:ppc64el.
139s Preparing to unpack .../2-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ...
139s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
139s Selecting previously unselected package libsz2:ppc64el.
139s Preparing to unpack .../3-libsz2_1.1.3-1_ppc64el.deb ...
139s Unpacking libsz2:ppc64el (1.1.3-1) ...
139s Selecting previously unselected package libhdf5-103-1t64:ppc64el.
139s Preparing to unpack .../4-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_ppc64el.deb ...
139s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ...
139s Selecting previously unselected package liblapack3:ppc64el.
139s Preparing to unpack .../5-liblapack3_3.12.0-3build2_ppc64el.deb ...
139s Unpacking liblapack3:ppc64el (3.12.0-3build2) ...
139s Selecting previously unselected package python3-numpy.
139s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ...
139s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
140s Selecting previously unselected package uncalled.
140s Preparing to unpack .../7-uncalled_2.3+ds-2_ppc64el.deb ...
140s Unpacking uncalled (2.3+ds-2) ...
140s Selecting previously unselected package autopkgtest-satdep.
140s Preparing to unpack .../8-1-autopkgtest-satdep.deb ...
140s Unpacking autopkgtest-satdep (0) ...
140s Setting up libaec0:ppc64el (1.1.3-1) ...
140s Setting up libblas3:ppc64el (3.12.0-3build2) ...
140s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
140s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
140s Setting up libsz2:ppc64el (1.1.3-1) ...
140s Setting up liblapack3:ppc64el (3.12.0-3build2) ...
140s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
140s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
146s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ...
146s Setting up uncalled (2.3+ds-2) ...
146s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d'
146s   CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])")
147s Setting up autopkgtest-satdep (0) ...
147s Processing triggers for man-db (2.12.1-3) ...
147s Processing triggers for libc-bin (2.40-1ubuntu3) ...
149s (Reading database ... 74735 files and directories currently installed.)
149s Removing autopkgtest-satdep (0) ...
151s autopkgtest [03:27:08]: test run-unit-test: [-----------------------
151s 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:11.852423
151s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-'
151s   log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+")
151s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d'
151s   port_re = re.compile("grpc_port = (\d+)")
151s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s'
151s   device_re = re.compile("(device_id|instance) = ([^\s,]+)")
151s [bwa_index] Pack FASTA... 0.00 sec
151s [bwa_index] Construct BWT for the packed sequence...
151s [bwa_index] 0.00 seconds elapse.
151s [bwa_index] Update BWT... 0.00 sec
151s [bwa_index] Pack forward-only FASTA... 0.00 sec
151s [bwa_index] Construct SA from BWT and Occ... 0.00 sec
151s Initializing parameter search
151s Computing default parameters
151s Writing default parameters
151s Done
151s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-'
151s   log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+")
151s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d'
151s   port_re = re.compile("grpc_port = (\d+)")
151s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s'
151s   device_re = re.compile("(device_id|instance) = ([^\s,]+)")
151s Loading fast5s
151s Mapping
151s Finishing
151s autopkgtest [03:27:09]: test run-unit-test: -----------------------]
151s autopkgtest [03:27:10]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
151s run-unit-test        PASS
152s autopkgtest [03:27:11]: @@@@@@@@@@@@@@@@@@@@ summary
152s run-unit-test        PASS
157s nova [W] Using flock in prodstack6-ppc64el
157s Creating nova instance adt-plucky-ppc64el-uncalled-20241114-032439-juju-7f2275-prod-proposed-migration-environment-20-519ed0aa-9869-479e-b824-aac43b03338d from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...