0s autopkgtest [17:13:57]: starting date and time: 2024-03-16 17:13:57+0000 0s autopkgtest [17:13:57]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:13:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ywu0oy54/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade nanopolish --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build2 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-25.secgroup --name adt-noble-arm64-nanopolish-20240316-171357-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/ 89s autopkgtest [17:15:26]: testbed dpkg architecture: arm64 89s autopkgtest [17:15:26]: testbed apt version: 2.7.12 89s autopkgtest [17:15:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 90s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 90s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 90s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 90s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 90s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 90s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 90s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 90s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 90s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 90s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 91s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 91s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 91s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 93s Fetched 9063 kB in 2s (5003 kB/s) 93s Reading package lists... 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s Calculating upgrade... 99s The following packages will be REMOVED: 99s libssl3 99s The following NEW packages will be installed: 99s libssl3t64 99s The following packages have been kept back: 99s curl 99s The following packages will be upgraded: 99s openssl ubuntu-minimal ubuntu-standard 99s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 99s Need to get 2775 kB of archives. 99s After this operation, 72.7 kB of additional disk space will be used. 99s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 99s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 99s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 99s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 100s Fetched 2775 kB in 1s (3729 kB/s) 100s (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 ... 74758 files and directories currently installed.) 100s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 100s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 101s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 101s wget depends on libssl3 (>= 3.0.0). 101s u-boot-tools depends on libssl3 (>= 3.0.0). 101s tnftp depends on libssl3 (>= 3.0.0). 101s tcpdump depends on libssl3 (>= 3.0.0). 101s systemd-resolved depends on libssl3 (>= 3.0.0). 101s systemd depends on libssl3 (>= 3.0.0). 101s sudo depends on libssl3 (>= 3.0.0). 101s sbsigntool depends on libssl3 (>= 3.0.0). 101s rsync depends on libssl3 (>= 3.0.0). 101s python3-cryptography depends on libssl3 (>= 3.0.0). 101s openssh-server depends on libssl3 (>= 3.0.10). 101s openssh-client depends on libssl3 (>= 3.0.10). 101s mtd-utils depends on libssl3 (>= 3.0.0). 101s mokutil depends on libssl3 (>= 3.0.0). 101s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 101s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 101s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 101s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 101s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 101s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 101s libnvme1 depends on libssl3 (>= 3.0.0). 101s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 101s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 101s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 101s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 101s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 101s kmod depends on libssl3 (>= 3.0.0). 101s dhcpcd-base depends on libssl3 (>= 3.0.0). 101s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 101s 101s (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 ... 74758 files and directories currently installed.) 101s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 101s Selecting previously unselected package libssl3t64:arm64. 101s (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 ... 74747 files and directories currently installed.) 101s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 101s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 101s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ... 101s Unpacking ubuntu-minimal (1.536) over (1.535) ... 101s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ... 101s Unpacking ubuntu-standard (1.536) over (1.535) ... 101s Setting up ubuntu-minimal (1.536) ... 101s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 101s Setting up ubuntu-standard (1.536) ... 101s Setting up openssl (3.0.13-0ubuntu1) ... 101s Processing triggers for man-db (2.12.0-3) ... 101s Processing triggers for libc-bin (2.39-0ubuntu2) ... 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 103s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade... 106s The following packages have been kept back: 106s curl 106s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 110s autopkgtest [17:15:47]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 110s autopkgtest [17:15:47]: @@@@@@@@@@@@@@@@@@@@ apt-source nanopolish 113s Get:1 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (dsc) [2256 B] 113s Get:2 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (tar) [4074 kB] 113s Get:3 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (diff) [9120 B] 113s gpgv: Signature made Wed Jan 25 21:10:28 2023 UTC 113s gpgv: using RSA key 7E6D9F62AD7303887A3C1DD04916D7AB1D7A3804 113s gpgv: Can't check signature: No public key 113s dpkg-source: warning: cannot verify inline signature for ./nanopolish_0.14.0-1ubuntu1.dsc: no acceptable signature found 114s autopkgtest [17:15:51]: testing package nanopolish version 0.14.0-1ubuntu1 114s autopkgtest [17:15:51]: build not needed 115s autopkgtest [17:15:52]: test run-unit-test: preparing testbed 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 117s The following additional packages will be installed: 117s libaec0 libdeflate0 libgomp1 libhdf5-103-1 libhts3 libhtscodecs2 libslow5-0 117s libstreamvbyte0 libsz2 nanopolish 117s Recommended packages: 117s python3-biopython python3-pysam 117s The following NEW packages will be installed: 117s autopkgtest-satdep libaec0 libdeflate0 libgomp1 libhdf5-103-1 libhts3 117s libhtscodecs2 libslow5-0 libstreamvbyte0 libsz2 nanopolish 117s 0 upgraded, 11 newly installed, 0 to remove and 1 not upgraded. 117s Need to get 4315 kB/4316 kB of archives. 117s After this operation, 15.9 MB of additional disk space will be used. 117s Get:1 /tmp/autopkgtest.gmAZmx/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 117s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 118s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 118s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 118s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 118s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 118s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 118s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhts3 arm64 1.19+ds-1 [429 kB] 118s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libslow5-0 arm64 0.7.0+dfsg-2ubuntu4 [61.3 kB] 118s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libstreamvbyte0 arm64 0.4.1-4ubuntu1 [6260 B] 118s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 nanopolish arm64 0.14.0-1ubuntu1 [2337 kB] 119s Fetched 4315 kB in 1s (5321 kB/s) 119s Selecting previously unselected package libaec0:arm64. 119s (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 ... 74760 files and directories currently installed.) 119s Preparing to unpack .../00-libaec0_1.1.2-1_arm64.deb ... 119s Unpacking libaec0:arm64 (1.1.2-1) ... 119s Selecting previously unselected package libdeflate0:arm64. 119s Preparing to unpack .../01-libdeflate0_1.19-1_arm64.deb ... 119s Unpacking libdeflate0:arm64 (1.19-1) ... 119s Selecting previously unselected package libgomp1:arm64. 119s Preparing to unpack .../02-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 119s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 119s Selecting previously unselected package libsz2:arm64. 119s Preparing to unpack .../03-libsz2_1.1.2-1_arm64.deb ... 119s Unpacking libsz2:arm64 (1.1.2-1) ... 119s Selecting previously unselected package libhdf5-103-1:arm64. 119s Preparing to unpack .../04-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 119s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 119s Selecting previously unselected package libhtscodecs2:arm64. 119s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_arm64.deb ... 119s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 119s Selecting previously unselected package libhts3:arm64. 119s Preparing to unpack .../06-libhts3_1.19+ds-1_arm64.deb ... 119s Unpacking libhts3:arm64 (1.19+ds-1) ... 119s Selecting previously unselected package libslow5-0:arm64. 119s Preparing to unpack .../07-libslow5-0_0.7.0+dfsg-2ubuntu4_arm64.deb ... 119s Unpacking libslow5-0:arm64 (0.7.0+dfsg-2ubuntu4) ... 119s Selecting previously unselected package libstreamvbyte0:arm64. 119s Preparing to unpack .../08-libstreamvbyte0_0.4.1-4ubuntu1_arm64.deb ... 119s Unpacking libstreamvbyte0:arm64 (0.4.1-4ubuntu1) ... 119s Selecting previously unselected package nanopolish. 119s Preparing to unpack .../09-nanopolish_0.14.0-1ubuntu1_arm64.deb ... 119s Unpacking nanopolish (0.14.0-1ubuntu1) ... 119s Selecting previously unselected package autopkgtest-satdep. 119s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 119s Unpacking autopkgtest-satdep (0) ... 119s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 119s Setting up libstreamvbyte0:arm64 (0.4.1-4ubuntu1) ... 119s Setting up libdeflate0:arm64 (1.19-1) ... 119s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 119s Setting up libaec0:arm64 (1.1.2-1) ... 119s Setting up libslow5-0:arm64 (0.7.0+dfsg-2ubuntu4) ... 119s Setting up libsz2:arm64 (1.1.2-1) ... 119s Setting up libhts3:arm64 (1.19+ds-1) ... 119s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 119s Setting up nanopolish (0.14.0-1ubuntu1) ... 119s Setting up autopkgtest-satdep (0) ... 119s Processing triggers for man-db (2.12.0-3) ... 120s Processing triggers for libc-bin (2.39-0ubuntu2) ... 123s (Reading database ... 74851 files and directories currently installed.) 123s Removing autopkgtest-satdep (0) ... 123s autopkgtest [17:16:00]: test run-unit-test: [----------------------- 124s =============================================================================== 124s All tests passed (636 assertions in 6 test cases) 124s 124s autopkgtest [17:16:01]: test run-unit-test: -----------------------] 125s run-unit-test PASS 125s autopkgtest [17:16:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 125s autopkgtest [17:16:02]: @@@@@@@@@@@@@@@@@@@@ summary 125s run-unit-test PASS 144s Creating nova instance adt-noble-arm64-nanopolish-20240316-171357-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...