0s autopkgtest [15:19:45]: starting date and time: 2024-03-23 15:19:45+0000
  0s autopkgtest [15:19:45]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [15:19:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.g_6rl57m/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade lumpy-sv --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-4.secgroup --name adt-noble-ppc64el-lumpy-sv-20240323-151945-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/
139s autopkgtest [15:22:04]: testbed dpkg architecture: ppc64el
139s autopkgtest [15:22:04]: testbed apt version: 2.7.12
139s autopkgtest [15:22:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup
140s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB]
140s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
140s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB]
140s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB]
140s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB]
140s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
140s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
140s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
140s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB]
141s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
141s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB]
141s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
144s Fetched 9623 kB in 2s (4035 kB/s)
144s Reading package lists...
147s Reading package lists...
147s Building dependency tree...
147s Reading state information...
147s Calculating upgrade...
147s The following packages will be REMOVED:
147s   libssl3
147s The following NEW packages will be installed:
147s   libssl3t64
147s The following packages have been kept back:
147s   curl
147s The following packages will be upgraded:
147s   openssl
147s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
147s Need to get 3151 kB of archives.
147s After this operation, 73.7 kB of additional disk space will be used.
147s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB]
148s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB]
148s Fetched 3151 kB in 1s (4445 kB/s)
148s (Reading database ... 
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(Reading database ... 70156 files and directories currently installed.)
148s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ...
148s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
148s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested:
148s  wget depends on libssl3 (>= 3.0.0).
148s  tnftp depends on libssl3 (>= 3.0.0).
148s  tcpdump depends on libssl3 (>= 3.0.0).
148s  systemd-resolved depends on libssl3 (>= 3.0.0).
148s  systemd depends on libssl3 (>= 3.0.0).
148s  sudo depends on libssl3 (>= 3.0.0).
148s  rsync depends on libssl3 (>= 3.0.0).
148s  python3-cryptography depends on libssl3 (>= 3.0.0).
148s  openssh-server depends on libssl3 (>= 3.0.10).
148s  openssh-client depends on libssl3 (>= 3.0.10).
148s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
148s  libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0).
148s  libssh-4:ppc64el depends on libssl3 (>= 3.0.0).
148s  libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0).
148s  libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0).
148s  libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0).
148s  libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0).
148s  libnvme1 depends on libssl3 (>= 3.0.0).
148s  libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0).
148s  libkmod2:ppc64el depends on libssl3 (>= 3.0.0).
148s  libfido2-1:ppc64el depends on libssl3 (>= 3.0.0).
148s  libcurl4:ppc64el depends on libssl3 (>= 3.0.0).
148s  libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0).
148s  kmod depends on libssl3 (>= 3.0.0).
148s  dhcpcd-base depends on libssl3 (>= 3.0.0).
148s  bind9-libs:ppc64el depends on libssl3 (>= 3.0.0).
148s 
148s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70156 files and directories currently installed.)
148s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ...
148s Selecting previously unselected package libssl3t64:ppc64el.
148s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 70145 files and directories currently installed.)
148s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ...
148s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
149s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
149s Setting up openssl (3.0.13-0ubuntu2) ...
149s Processing triggers for man-db (2.12.0-3) ...
149s Processing triggers for libc-bin (2.39-0ubuntu6) ...
149s Reading package lists...
149s Building dependency tree...
149s Reading state information...
150s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
150s sh: Attempting to set up Debian/Ubuntu apt sources automatically
150s sh: Distribution appears to be Ubuntu
151s Reading package lists...
151s Building dependency tree...
151s Reading state information...
151s eatmydata is already the newest version (131-1).
151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
151s Reading package lists...
151s Building dependency tree...
151s Reading state information...
152s dbus is already the newest version (1.14.10-4ubuntu1).
152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
152s Reading package lists...
152s Building dependency tree...
152s Reading state information...
152s rng-tools-debian is already the newest version (2.4).
152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
152s Reading package lists...
152s Building dependency tree...
152s Reading state information...
152s The following packages will be REMOVED:
152s   cloud-init* python3-configobj* python3-debconf*
152s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
152s After this operation, 3256 kB disk space will be freed.
152s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70158 files and directories currently installed.)
152s Removing cloud-init (24.1.2-0ubuntu1) ...
153s Removing python3-configobj (5.0.8-3) ...
153s Removing python3-debconf (1.5.86) ...
153s Processing triggers for man-db (2.12.0-3) ...
153s (Reading database ... 
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(Reading database ... 80%
(Reading database ... 85%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 69769 files and directories currently installed.)
153s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
154s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
154s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
154s invoke-rc.d: policy-rc.d denied execution of try-restart.
154s Reading package lists...
154s Building dependency tree...
154s Reading state information...
154s linux-generic is already the newest version (6.8.0-11.11+1).
154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
155s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
155s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
155s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
157s Reading package lists...
157s Reading package lists...
157s Building dependency tree...
157s Reading state information...
158s Calculating upgrade...
158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
158s Reading package lists...
158s Building dependency tree...
158s Reading state information...
158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
158s autopkgtest [15:22:23]: rebooting testbed after setup commands that affected boot
322s autopkgtest [15:25:07]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024
325s autopkgtest [15:25:10]: @@@@@@@@@@@@@@@@@@@@ apt-source lumpy-sv
328s Get:1 http://ftpmaster.internal/ubuntu noble/universe lumpy-sv 0.3.1+dfsg-7build1 (dsc) [2384 B]
328s Get:2 http://ftpmaster.internal/ubuntu noble/universe lumpy-sv 0.3.1+dfsg-7build1 (tar) [112 kB]
328s Get:3 http://ftpmaster.internal/ubuntu noble/universe lumpy-sv 0.3.1+dfsg-7build1 (diff) [39.2 MB]
329s gpgv: Signature made Sat Nov 19 21:49:32 2022 UTC
329s gpgv:                using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D
329s gpgv:                issuer "steve.langasek@ubuntu.com"
329s gpgv: Can't check signature: No public key
329s dpkg-source: warning: cannot verify inline signature for ./lumpy-sv_0.3.1+dfsg-7build1.dsc: no acceptable signature found
333s autopkgtest [15:25:18]: testing package lumpy-sv version 0.3.1+dfsg-7build1
454s autopkgtest [15:27:19]: build not needed
624s autopkgtest [15:30:09]: test run-unit-test: preparing testbed
625s Reading package lists...
625s Building dependency tree...
625s Reading state information...
625s Starting pkgProblemResolver with broken count: 0
625s Starting 2 pkgProblemResolver with broken count: 0
625s Done
625s The following additional packages will be installed:
625s   bamkit libbamtools2.5.2 libblas3 libdeflate0 libgfortran5 libgzstream0
625s   libhts3 libhtscodecs2 liblapack3 lumpy-sv lumpy-sv-examples python3-numpy
625s   python3-pysam samblaster samtools
625s Suggested packages:
625s   gcc gfortran python3-dev python3-pytest cwltool
625s Recommended packages:
625s   sambamba
625s The following NEW packages will be installed:
625s   autopkgtest-satdep bamkit libbamtools2.5.2 libblas3 libdeflate0 libgfortran5
625s   libgzstream0 libhts3 libhtscodecs2 liblapack3 lumpy-sv lumpy-sv-examples
625s   python3-numpy python3-pysam samblaster samtools
625s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded.
625s Need to get 70.5 MB/70.5 MB of archives.
625s After this operation, 152 MB of additional disk space will be used.
625s Get:1 /tmp/autopkgtest.OdiRhF/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B]
626s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB]
626s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB]
626s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB]
626s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB]
626s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el bamkit all 0.0.1+git20170413.ccd079d-3 [14.9 kB]
626s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libbamtools2.5.2 ppc64el 2.5.2+dfsg-4 [161 kB]
626s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB]
626s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB]
626s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgzstream0 ppc64el 1.5+git20171107.9a20658-1 [7734 B]
626s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB]
626s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el samblaster ppc64el 0.1.26-4 [27.4 kB]
626s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB]
626s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB]
627s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el lumpy-sv ppc64el 0.3.1+dfsg-7build1 [146 kB]
627s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el lumpy-sv-examples all 0.3.1+dfsg-7build1 [54.6 MB]
628s Fetched 70.5 MB in 2s (28.3 MB/s)
628s Selecting previously unselected package libdeflate0:ppc64el.
628s (Reading database ... 
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(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 ... 69714 files and directories currently installed.)
628s Preparing to unpack .../00-libdeflate0_1.19-1_ppc64el.deb ...
628s Unpacking libdeflate0:ppc64el (1.19-1) ...
628s Selecting previously unselected package libhtscodecs2:ppc64el.
628s Preparing to unpack .../01-libhtscodecs2_1.6.0-1_ppc64el.deb ...
628s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ...
628s Selecting previously unselected package libhts3:ppc64el.
628s Preparing to unpack .../02-libhts3_1.18+ds-1_ppc64el.deb ...
628s Unpacking libhts3:ppc64el (1.18+ds-1) ...
628s Selecting previously unselected package python3-pysam.
628s Preparing to unpack .../03-python3-pysam_0.22.0+ds-1_ppc64el.deb ...
628s Unpacking python3-pysam (0.22.0+ds-1) ...
629s Selecting previously unselected package bamkit.
629s Preparing to unpack .../04-bamkit_0.0.1+git20170413.ccd079d-3_all.deb ...
629s Unpacking bamkit (0.0.1+git20170413.ccd079d-3) ...
629s Selecting previously unselected package libbamtools2.5.2:ppc64el.
629s Preparing to unpack .../05-libbamtools2.5.2_2.5.2+dfsg-4_ppc64el.deb ...
629s Unpacking libbamtools2.5.2:ppc64el (2.5.2+dfsg-4) ...
629s Selecting previously unselected package libblas3:ppc64el.
629s Preparing to unpack .../06-libblas3_3.12.0-3_ppc64el.deb ...
629s Unpacking libblas3:ppc64el (3.12.0-3) ...
629s Selecting previously unselected package libgfortran5:ppc64el.
629s Preparing to unpack .../07-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ...
629s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ...
629s Selecting previously unselected package libgzstream0:ppc64el.
629s Preparing to unpack .../08-libgzstream0_1.5+git20171107.9a20658-1_ppc64el.deb ...
629s Unpacking libgzstream0:ppc64el (1.5+git20171107.9a20658-1) ...
629s Selecting previously unselected package liblapack3:ppc64el.
629s Preparing to unpack .../09-liblapack3_3.12.0-3_ppc64el.deb ...
629s Unpacking liblapack3:ppc64el (3.12.0-3) ...
629s Selecting previously unselected package samblaster.
629s Preparing to unpack .../10-samblaster_0.1.26-4_ppc64el.deb ...
629s Unpacking samblaster (0.1.26-4) ...
629s Selecting previously unselected package samtools.
629s Preparing to unpack .../11-samtools_1.19.2-1_ppc64el.deb ...
629s Unpacking samtools (1.19.2-1) ...
629s Selecting previously unselected package python3-numpy.
629s Preparing to unpack .../12-python3-numpy_1%3a1.24.2-2_ppc64el.deb ...
629s Unpacking python3-numpy (1:1.24.2-2) ...
629s Selecting previously unselected package lumpy-sv.
629s Preparing to unpack .../13-lumpy-sv_0.3.1+dfsg-7build1_ppc64el.deb ...
629s Unpacking lumpy-sv (0.3.1+dfsg-7build1) ...
629s Selecting previously unselected package lumpy-sv-examples.
629s Preparing to unpack .../14-lumpy-sv-examples_0.3.1+dfsg-7build1_all.deb ...
629s Unpacking lumpy-sv-examples (0.3.1+dfsg-7build1) ...
630s Selecting previously unselected package autopkgtest-satdep.
630s Preparing to unpack .../15-1-autopkgtest-satdep.deb ...
630s Unpacking autopkgtest-satdep (0) ...
630s Setting up libhtscodecs2:ppc64el (1.6.0-1) ...
630s Setting up samblaster (0.1.26-4) ...
630s Setting up libdeflate0:ppc64el (1.19-1) ...
630s Setting up lumpy-sv-examples (0.3.1+dfsg-7build1) ...
630s Setting up libblas3:ppc64el (3.12.0-3) ...
630s 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
630s Setting up libbamtools2.5.2:ppc64el (2.5.2+dfsg-4) ...
630s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ...
630s Setting up libgzstream0:ppc64el (1.5+git20171107.9a20658-1) ...
630s Setting up liblapack3:ppc64el (3.12.0-3) ...
630s 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
630s Setting up libhts3:ppc64el (1.18+ds-1) ...
630s Setting up python3-pysam (0.22.0+ds-1) ...
630s Setting up bamkit (0.0.1+git20170413.ccd079d-3) ...
630s Setting up samtools (1.19.2-1) ...
630s Setting up python3-numpy (1:1.24.2-2) ...
632s Setting up lumpy-sv (0.3.1+dfsg-7build1) ...
632s Setting up autopkgtest-satdep (0) ...
632s Processing triggers for man-db (2.12.0-3) ...
633s Processing triggers for libc-bin (2.39-0ubuntu6) ...
636s (Reading database ... 71339 files and directories currently installed.)
636s Removing autopkgtest-satdep (0) ...
636s autopkgtest [15:30:21]: test run-unit-test: [-----------------------
636s + cp -a /usr/share/doc/lumpy-sv/examples/data /usr/share/doc/lumpy-sv/examples/lumpy_tests /usr/share/doc/lumpy-sv/examples/test /tmp/autopkgtest.OdiRhF/autopkgtest_tmp
636s + cd /tmp/autopkgtest.OdiRhF/autopkgtest_tmp
636s + gunzip -r data lumpy_tests test
636s + cd test
636s + sed -i -e 's:\.\./scripts:/usr/share/lumpy-sv/scripts:' -e 's:\.\./bin/lumpy:/usr/bin/lumpy:' bp_pe.sh bp_pe_pl.sh bp_pesr.sh bp_pesr_pl.sh bp_sr.sh functional-test.sh test.sh test_pl.sh
636s + ./test.sh
636s Testing lumpy paired-end
637s Removed 12 outliers with isize >= 850
637s 549	0
637s chr10	1000000
642s Install bedtools to compare result to known deletions
642s Testing lumpy split-read
642s chr10	1000000
642s Install bedtools to compare result to known deletions
642s Testing lumpy paired-end and split-read
642s Removed 12 outliers with isize >= 850
642s 549	0
642s chr10	1000000
648s Install bedtools to compare result to known deletions
648s autopkgtest [15:30:33]: test run-unit-test: -----------------------]
648s run-unit-test        PASS
648s autopkgtest [15:30:33]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
649s autopkgtest [15:30:34]: @@@@@@@@@@@@@@@@@@@@ summary
649s run-unit-test        PASS
660s Creating nova instance adt-noble-ppc64el-lumpy-sv-20240323-151945-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...