0s autopkgtest [16:55:11]: starting date and time: 2024-03-24 16:55:11+0000
  0s autopkgtest [16:55:11]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [16:55:11]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b42rx4e4/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@bos03-arm64-8.secgroup --name adt-noble-arm64-lumpy-sv-20240324-165511-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/
 72s autopkgtest [16:56:23]: testbed dpkg architecture: arm64
 72s autopkgtest [16:56:23]: testbed apt version: 2.7.12
 72s autopkgtest [16:56:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 73s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 73s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 73s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB]
 74s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB]
 74s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB]
 74s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB]
 74s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 74s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB]
 74s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 74s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB]
 74s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 74s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB]
 74s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
 75s Fetched 9850 kB in 2s (5532 kB/s)
 76s Reading package lists...
 78s Reading package lists...
 79s Building dependency tree...
 79s Reading state information...
 79s Calculating upgrade...
 80s The following packages will be REMOVED:
 80s   libssl3
 80s The following NEW packages will be installed:
 80s   libssl3t64
 80s The following packages have been kept back:
 80s   curl
 80s The following packages will be upgraded:
 80s   openssl
 80s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
 80s Need to get 2777 kB of archives.
 80s After this operation, 139 kB of additional disk space will be used.
 80s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB]
 80s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB]
 81s Fetched 2777 kB in 1s (3977 kB/s)
 81s (Reading database ... 
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(Reading database ... 74819 files and directories currently installed.)
 81s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ...
 81s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
 81s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
 81s  wget depends on libssl3 (>= 3.0.0).
 81s  u-boot-tools depends on libssl3 (>= 3.0.0).
 81s  tnftp depends on libssl3 (>= 3.0.0).
 81s  tcpdump depends on libssl3 (>= 3.0.0).
 81s  systemd-resolved depends on libssl3 (>= 3.0.0).
 81s  systemd depends on libssl3 (>= 3.0.0).
 81s  sudo depends on libssl3 (>= 3.0.0).
 81s  sbsigntool depends on libssl3 (>= 3.0.0).
 81s  rsync depends on libssl3 (>= 3.0.0).
 81s  python3-cryptography depends on libssl3 (>= 3.0.0).
 81s  openssh-server depends on libssl3 (>= 3.0.10).
 81s  openssh-client depends on libssl3 (>= 3.0.10).
 81s  mtd-utils depends on libssl3 (>= 3.0.0).
 81s  mokutil depends on libssl3 (>= 3.0.0).
 81s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
 81s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
 81s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
 81s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
 81s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
 81s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
 81s  libnvme1 depends on libssl3 (>= 3.0.0).
 81s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
 81s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
 81s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
 81s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
 81s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
 81s  kmod depends on libssl3 (>= 3.0.0).
 81s  dhcpcd-base depends on libssl3 (>= 3.0.0).
 81s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
 81s 
 81s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 74819 files and directories currently installed.)
 81s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
 81s Selecting previously unselected package libssl3t64:arm64.
 81s (Reading database ... 
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(Reading database ... 74808 files and directories currently installed.)
 81s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ...
 81s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ...
 82s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ...
 82s Setting up openssl (3.0.13-0ubuntu2) ...
 82s Processing triggers for man-db (2.12.0-3) ...
 82s Processing triggers for libc-bin (2.39-0ubuntu6) ...
 83s Reading package lists...
 83s Building dependency tree...
 83s Reading state information...
 84s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
 84s sh: Attempting to set up Debian/Ubuntu apt sources automatically
 84s sh: Distribution appears to be Ubuntu
 85s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 86s eatmydata is already the newest version (131-1).
 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 86s Reading package lists...
 86s Building dependency tree...
 86s Reading state information...
 87s dbus is already the newest version (1.14.10-4ubuntu1).
 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 87s Reading package lists...
 87s Building dependency tree...
 87s Reading state information...
 88s rng-tools-debian is already the newest version (2.4).
 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 88s Reading package lists...
 88s Building dependency tree...
 88s Reading state information...
 89s The following packages will be REMOVED:
 89s   cloud-init* python3-configobj* python3-debconf*
 89s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
 89s After this operation, 3256 kB disk space will be freed.
 89s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 74821 files and directories currently installed.)
 89s Removing cloud-init (24.1.2-0ubuntu1) ...
 90s Removing python3-configobj (5.0.8-3) ...
 90s Removing python3-debconf (1.5.86) ...
 90s Processing triggers for man-db (2.12.0-3) ...
 90s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74432 files and directories currently installed.)
 90s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
 91s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
 91s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
 91s invoke-rc.d: policy-rc.d denied execution of try-restart.
 91s Reading package lists...
 92s Building dependency tree...
 92s Reading state information...
 92s linux-generic is already the newest version (6.8.0-11.11+1).
 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 93s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
 93s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
 93s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
 95s Reading package lists...
 95s Reading package lists...
 95s Building dependency tree...
 95s Reading state information...
 95s Calculating upgrade...
 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 96s Reading package lists...
 96s Building dependency tree...
 96s Reading state information...
 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 97s autopkgtest [16:56:48]: rebooting testbed after setup commands that affected boot
129s autopkgtest [16:57:20]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
133s autopkgtest [16:57:24]: @@@@@@@@@@@@@@@@@@@@ apt-source lumpy-sv
137s Get:1 http://ftpmaster.internal/ubuntu noble/universe lumpy-sv 0.3.1+dfsg-7build1 (dsc) [2384 B]
137s Get:2 http://ftpmaster.internal/ubuntu noble/universe lumpy-sv 0.3.1+dfsg-7build1 (tar) [112 kB]
137s Get:3 http://ftpmaster.internal/ubuntu noble/universe lumpy-sv 0.3.1+dfsg-7build1 (diff) [39.2 MB]
137s gpgv: Signature made Sat Nov 19 21:49:32 2022 UTC
137s gpgv:                using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D
137s gpgv:                issuer "steve.langasek@ubuntu.com"
137s gpgv: Can't check signature: No public key
137s dpkg-source: warning: cannot verify inline signature for ./lumpy-sv_0.3.1+dfsg-7build1.dsc: no acceptable signature found
141s autopkgtest [16:57:32]: testing package lumpy-sv version 0.3.1+dfsg-7build1
152s autopkgtest [16:57:43]: build not needed
163s autopkgtest [16:57:54]: test run-unit-test: preparing testbed
167s Reading package lists...
167s Building dependency tree...
167s Reading state information...
168s Starting pkgProblemResolver with broken count: 0
168s Starting 2 pkgProblemResolver with broken count: 0
168s Done
168s The following additional packages will be installed:
168s   bamkit libbamtools2.5.2 libblas3 libdeflate0 libgfortran5 libgzstream0
168s   libhts3 libhtscodecs2 liblapack3 libpython3.11-minimal libpython3.11-stdlib
168s   lumpy-sv lumpy-sv-examples python3-numpy python3-pysam python3.11
168s   python3.11-minimal samblaster samtools
168s Suggested packages:
168s   gcc gfortran python3-dev python3-pytest python3.11-venv python3.11-doc
168s   binfmt-support cwltool
168s Recommended packages:
168s   sambamba
168s The following NEW packages will be installed:
168s   autopkgtest-satdep bamkit libbamtools2.5.2 libblas3 libdeflate0 libgfortran5
168s   libgzstream0 libhts3 libhtscodecs2 liblapack3 libpython3.11-minimal
168s   libpython3.11-stdlib lumpy-sv lumpy-sv-examples python3-numpy python3-pysam
168s   python3.11 python3.11-minimal samblaster samtools
168s 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
168s Need to get 73.2 MB/73.2 MB of archives.
168s After this operation, 158 MB of additional disk space will be used.
168s Get:1 /tmp/autopkgtest.fVUvlR/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B]
169s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB]
169s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB]
169s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB]
169s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB]
169s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
169s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
169s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB]
169s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB]
169s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 bamkit all 0.0.1+git20170413.ccd079d-3 [14.9 kB]
169s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB]
169s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
169s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
169s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libgzstream0 arm64 1.5+git20171107.9a20658-1 [7406 B]
169s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
169s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 samblaster arm64 0.1.26-4 [23.7 kB]
169s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB]
169s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
169s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 lumpy-sv arm64 0.3.1+dfsg-7build1 [133 kB]
169s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 lumpy-sv-examples all 0.3.1+dfsg-7build1 [54.6 MB]
171s Fetched 73.2 MB in 2s (32.6 MB/s)
171s Selecting previously unselected package libpython3.11-minimal:arm64.
171s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 74377 files and directories currently installed.)
171s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ...
171s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ...
171s Selecting previously unselected package python3.11-minimal.
171s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ...
171s Unpacking python3.11-minimal (3.11.8-1) ...
172s Selecting previously unselected package libpython3.11-stdlib:arm64.
172s Preparing to unpack .../02-libpython3.11-stdlib_3.11.8-1_arm64.deb ...
172s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ...
172s Selecting previously unselected package python3.11.
172s Preparing to unpack .../03-python3.11_3.11.8-1_arm64.deb ...
172s Unpacking python3.11 (3.11.8-1) ...
172s Selecting previously unselected package libdeflate0:arm64.
172s Preparing to unpack .../04-libdeflate0_1.19-1_arm64.deb ...
172s Unpacking libdeflate0:arm64 (1.19-1) ...
172s Selecting previously unselected package libhtscodecs2:arm64.
172s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_arm64.deb ...
172s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
172s Selecting previously unselected package libhts3:arm64.
172s Preparing to unpack .../06-libhts3_1.18+ds-1_arm64.deb ...
172s Unpacking libhts3:arm64 (1.18+ds-1) ...
172s Selecting previously unselected package python3-pysam.
172s Preparing to unpack .../07-python3-pysam_0.22.0+ds-1_arm64.deb ...
172s Unpacking python3-pysam (0.22.0+ds-1) ...
172s Selecting previously unselected package bamkit.
172s Preparing to unpack .../08-bamkit_0.0.1+git20170413.ccd079d-3_all.deb ...
172s Unpacking bamkit (0.0.1+git20170413.ccd079d-3) ...
172s Selecting previously unselected package libbamtools2.5.2:arm64.
172s Preparing to unpack .../09-libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb ...
172s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ...
172s Selecting previously unselected package libblas3:arm64.
172s Preparing to unpack .../10-libblas3_3.12.0-3_arm64.deb ...
172s Unpacking libblas3:arm64 (3.12.0-3) ...
172s Selecting previously unselected package libgfortran5:arm64.
172s Preparing to unpack .../11-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
172s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
172s Selecting previously unselected package libgzstream0:arm64.
172s Preparing to unpack .../12-libgzstream0_1.5+git20171107.9a20658-1_arm64.deb ...
172s Unpacking libgzstream0:arm64 (1.5+git20171107.9a20658-1) ...
172s Selecting previously unselected package liblapack3:arm64.
172s Preparing to unpack .../13-liblapack3_3.12.0-3_arm64.deb ...
172s Unpacking liblapack3:arm64 (3.12.0-3) ...
172s Selecting previously unselected package samblaster.
172s Preparing to unpack .../14-samblaster_0.1.26-4_arm64.deb ...
172s Unpacking samblaster (0.1.26-4) ...
172s Selecting previously unselected package samtools.
172s Preparing to unpack .../15-samtools_1.19.2-1_arm64.deb ...
172s Unpacking samtools (1.19.2-1) ...
172s Selecting previously unselected package python3-numpy.
172s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_arm64.deb ...
172s Unpacking python3-numpy (1:1.24.2-2) ...
173s Selecting previously unselected package lumpy-sv.
173s Preparing to unpack .../17-lumpy-sv_0.3.1+dfsg-7build1_arm64.deb ...
173s Unpacking lumpy-sv (0.3.1+dfsg-7build1) ...
173s Selecting previously unselected package lumpy-sv-examples.
173s Preparing to unpack .../18-lumpy-sv-examples_0.3.1+dfsg-7build1_all.deb ...
173s Unpacking lumpy-sv-examples (0.3.1+dfsg-7build1) ...
173s Selecting previously unselected package autopkgtest-satdep.
173s Preparing to unpack .../19-1-autopkgtest-satdep.deb ...
173s Unpacking autopkgtest-satdep (0) ...
173s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
173s Setting up samblaster (0.1.26-4) ...
173s Setting up libdeflate0:arm64 (1.19-1) ...
173s Setting up lumpy-sv-examples (0.3.1+dfsg-7build1) ...
173s Setting up libblas3:arm64 (3.12.0-3) ...
173s 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
173s Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ...
173s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
173s Setting up libgzstream0:arm64 (1.5+git20171107.9a20658-1) ...
173s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ...
173s Setting up python3.11-minimal (3.11.8-1) ...
174s Setting up liblapack3:arm64 (3.12.0-3) ...
174s 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
174s Setting up libhts3:arm64 (1.18+ds-1) ...
174s Setting up python3-pysam (0.22.0+ds-1) ...
174s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ...
174s Setting up bamkit (0.0.1+git20170413.ccd079d-3) ...
174s Setting up samtools (1.19.2-1) ...
174s Setting up python3.11 (3.11.8-1) ...
175s Setting up python3-numpy (1:1.24.2-2) ...
176s Setting up lumpy-sv (0.3.1+dfsg-7build1) ...
177s Setting up autopkgtest-satdep (0) ...
177s Processing triggers for systemd (255.2-3ubuntu2) ...
177s Processing triggers for man-db (2.12.0-3) ...
177s Processing triggers for libc-bin (2.39-0ubuntu6) ...
181s (Reading database ... 76698 files and directories currently installed.)
181s Removing autopkgtest-satdep (0) ...
181s autopkgtest [16:58:12]: test run-unit-test: [-----------------------
182s + 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.fVUvlR/autopkgtest_tmp
182s + cd /tmp/autopkgtest.fVUvlR/autopkgtest_tmp
182s + gunzip -r data lumpy_tests test
182s + cd test
182s + 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
182s + ./test.sh
182s Testing lumpy paired-end
182s Removed 12 outliers with isize >= 850
182s 549	0
182s chr10	1000000
185s Install bedtools to compare result to known deletions
185s Testing lumpy split-read
185s chr10	1000000
185s Install bedtools to compare result to known deletions
185s Testing lumpy paired-end and split-read
185s Removed 12 outliers with isize >= 850
185s 549	0
185s chr10	1000000
189s Install bedtools to compare result to known deletions
189s autopkgtest [16:58:20]: test run-unit-test: -----------------------]
190s run-unit-test        PASS
190s autopkgtest [16:58:21]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
190s autopkgtest [16:58:21]: @@@@@@@@@@@@@@@@@@@@ summary
190s run-unit-test        PASS
195s Creating nova instance adt-noble-arm64-lumpy-sv-20240324-165511-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)...