0s autopkgtest [17:02:10]: starting date and time: 2024-03-16 17:02:10+0000 0s autopkgtest [17:02:10]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:02:10]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.owm9nmzn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:hdf5,src:curl,src:libpsl,src:mpich,src:openmpi,src:openssl,src:orthanc-python,src:pmix --apt-upgrade nanopolish --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=hdf5/1.10.10+repack-3.1ubuntu3 curl/8.5.0-2ubuntu7 libpsl/0.21.2-1.1 mpich/4.2.0-5build1 openmpi/4.1.6-6ubuntu1 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-2.secgroup --name adt-noble-arm64-nanopolish-20240316-170209-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/ 86s autopkgtest [17:03:36]: testbed dpkg architecture: arm64 86s autopkgtest [17:03:36]: testbed apt version: 2.7.12 86s autopkgtest [17:03:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 86s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 87s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 87s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 87s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 87s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 87s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 87s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 87s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 87s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 87s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 87s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 87s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 87s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 89s Fetched 9063 kB in 2s (5608 kB/s) 89s Reading package lists... 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 93s Calculating upgrade... 93s The following packages will be REMOVED: 93s libssl3 93s The following NEW packages will be installed: 93s libssl3t64 93s The following packages have been kept back: 93s curl 93s The following packages will be upgraded: 93s openssl ubuntu-minimal ubuntu-standard 94s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 94s Need to get 2775 kB of archives. 94s After this operation, 72.7 kB of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 94s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 94s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 94s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 95s Fetched 2775 kB in 1s (3606 kB/s) 95s (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.) 95s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 95s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 95s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 95s wget depends on libssl3 (>= 3.0.0). 95s u-boot-tools depends on libssl3 (>= 3.0.0). 95s tnftp depends on libssl3 (>= 3.0.0). 95s tcpdump depends on libssl3 (>= 3.0.0). 95s systemd-resolved depends on libssl3 (>= 3.0.0). 95s systemd depends on libssl3 (>= 3.0.0). 95s sudo depends on libssl3 (>= 3.0.0). 95s sbsigntool depends on libssl3 (>= 3.0.0). 95s rsync depends on libssl3 (>= 3.0.0). 95s python3-cryptography depends on libssl3 (>= 3.0.0). 95s openssh-server depends on libssl3 (>= 3.0.10). 95s openssh-client depends on libssl3 (>= 3.0.10). 95s mtd-utils depends on libssl3 (>= 3.0.0). 95s mokutil depends on libssl3 (>= 3.0.0). 95s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 95s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 95s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 95s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 95s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 95s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 95s libnvme1 depends on libssl3 (>= 3.0.0). 95s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 95s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 95s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 95s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 95s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 95s kmod depends on libssl3 (>= 3.0.0). 95s dhcpcd-base depends on libssl3 (>= 3.0.0). 95s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 95s 95s (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.) 95s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 95s Selecting previously unselected package libssl3t64:arm64. 96s (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.) 96s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 96s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 96s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ... 96s Unpacking ubuntu-minimal (1.536) over (1.535) ... 96s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ... 96s Unpacking ubuntu-standard (1.536) over (1.535) ... 96s Setting up ubuntu-minimal (1.536) ... 96s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 96s Setting up ubuntu-standard (1.536) ... 96s Setting up openssl (3.0.13-0ubuntu1) ... 96s Processing triggers for man-db (2.12.0-3) ... 97s Processing triggers for libc-bin (2.39-0ubuntu2) ... 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 98s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 98s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 99s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 99s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 100s Reading package lists... 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s Calculating upgrade... 101s The following packages have been kept back: 101s curl 101s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 104s autopkgtest [17:03:54]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 105s autopkgtest [17:03:55]: @@@@@@@@@@@@@@@@@@@@ apt-source nanopolish 107s Get:1 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (dsc) [2256 B] 107s Get:2 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (tar) [4074 kB] 107s Get:3 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (diff) [9120 B] 107s gpgv: Signature made Wed Jan 25 21:10:28 2023 UTC 107s gpgv: using RSA key 7E6D9F62AD7303887A3C1DD04916D7AB1D7A3804 107s gpgv: Can't check signature: No public key 107s dpkg-source: warning: cannot verify inline signature for ./nanopolish_0.14.0-1ubuntu1.dsc: no acceptable signature found 107s autopkgtest [17:03:57]: testing package nanopolish version 0.14.0-1ubuntu1 107s autopkgtest [17:03:57]: build not needed 108s autopkgtest [17:03:58]: test run-unit-test: preparing testbed 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 113s The following additional packages will be installed: 113s libaec0 libdeflate0 libgomp1 libhdf5-103-1 libhts3 libhtscodecs2 libslow5-0 113s libstreamvbyte0 libsz2 nanopolish 113s Recommended packages: 113s python3-biopython python3-pysam 113s The following NEW packages will be installed: 113s autopkgtest-satdep libaec0 libdeflate0 libgomp1 libhdf5-103-1 libhts3 113s libhtscodecs2 libslow5-0 libstreamvbyte0 libsz2 nanopolish 113s 0 upgraded, 11 newly installed, 0 to remove and 1 not upgraded. 113s Need to get 4309 kB/4310 kB of archives. 113s After this operation, 15.9 MB of additional disk space will be used. 113s Get:1 /tmp/autopkgtest.bX7TzZ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 114s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 114s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 114s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 114s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 114s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 114s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 114s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 114s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libslow5-0 arm64 0.7.0+dfsg-2ubuntu4 [61.3 kB] 114s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libstreamvbyte0 arm64 0.4.1-4ubuntu1 [6260 B] 114s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 nanopolish arm64 0.14.0-1ubuntu1 [2337 kB] 115s Fetched 4309 kB in 2s (2788 kB/s) 115s Selecting previously unselected package libaec0:arm64. 115s (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.) 115s Preparing to unpack .../00-libaec0_1.1.2-1_arm64.deb ... 115s Unpacking libaec0:arm64 (1.1.2-1) ... 115s Selecting previously unselected package libdeflate0:arm64. 115s Preparing to unpack .../01-libdeflate0_1.19-1_arm64.deb ... 115s Unpacking libdeflate0:arm64 (1.19-1) ... 115s Selecting previously unselected package libgomp1:arm64. 115s Preparing to unpack .../02-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 115s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 115s Selecting previously unselected package libsz2:arm64. 115s Preparing to unpack .../03-libsz2_1.1.2-1_arm64.deb ... 115s Unpacking libsz2:arm64 (1.1.2-1) ... 115s Selecting previously unselected package libhdf5-103-1:arm64. 116s Preparing to unpack .../04-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 116s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 116s Selecting previously unselected package libhtscodecs2:arm64. 116s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_arm64.deb ... 116s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 116s Selecting previously unselected package libhts3:arm64. 116s Preparing to unpack .../06-libhts3_1.18+ds-1_arm64.deb ... 116s Unpacking libhts3:arm64 (1.18+ds-1) ... 116s Selecting previously unselected package libslow5-0:arm64. 116s Preparing to unpack .../07-libslow5-0_0.7.0+dfsg-2ubuntu4_arm64.deb ... 116s Unpacking libslow5-0:arm64 (0.7.0+dfsg-2ubuntu4) ... 116s Selecting previously unselected package libstreamvbyte0:arm64. 116s Preparing to unpack .../08-libstreamvbyte0_0.4.1-4ubuntu1_arm64.deb ... 116s Unpacking libstreamvbyte0:arm64 (0.4.1-4ubuntu1) ... 116s Selecting previously unselected package nanopolish. 116s Preparing to unpack .../09-nanopolish_0.14.0-1ubuntu1_arm64.deb ... 116s Unpacking nanopolish (0.14.0-1ubuntu1) ... 116s Selecting previously unselected package autopkgtest-satdep. 116s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 116s Unpacking autopkgtest-satdep (0) ... 116s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 116s Setting up libstreamvbyte0:arm64 (0.4.1-4ubuntu1) ... 116s Setting up libdeflate0:arm64 (1.19-1) ... 116s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 116s Setting up libaec0:arm64 (1.1.2-1) ... 116s Setting up libslow5-0:arm64 (0.7.0+dfsg-2ubuntu4) ... 116s Setting up libsz2:arm64 (1.1.2-1) ... 116s Setting up libhts3:arm64 (1.18+ds-1) ... 116s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 116s Setting up nanopolish (0.14.0-1ubuntu1) ... 116s Setting up autopkgtest-satdep (0) ... 116s Processing triggers for man-db (2.12.0-3) ... 116s Processing triggers for libc-bin (2.39-0ubuntu2) ... 119s (Reading database ... 74851 files and directories currently installed.) 119s Removing autopkgtest-satdep (0) ... 120s autopkgtest [17:04:10]: test run-unit-test: [----------------------- 120s =============================================================================== 120s All tests passed (636 assertions in 6 test cases) 120s 121s autopkgtest [17:04:11]: test run-unit-test: -----------------------] 121s run-unit-test PASS 121s autopkgtest [17:04:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 121s autopkgtest [17:04:11]: @@@@@@@@@@@@@@@@@@@@ summary 121s run-unit-test PASS 126s Creating nova instance adt-noble-arm64-nanopolish-20240316-170209-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...