0s autopkgtest [20:54:11]: starting date: 2024-03-17 0s autopkgtest [20:54:11]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [20:54:11]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8t9h9r19/out --timeout-copy=6000 --setup-commands 'ls /etc/apt/sources.list.d/*.list 2>/dev/null || true; ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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' -- lxd -r lxd-armhf-10.44.124.165 lxd-armhf-10.44.124.165:autopkgtest/ubuntu/noble/armhf 46s autopkgtest [20:54:57]: @@@@@@@@@@@@@@@@@@@@ test bed setup 48s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 48s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3721 kB] 49s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 49s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 49s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [484 kB] 49s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [573 kB] 49s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 49s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 49s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 49s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3489 kB] 49s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 49s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [33.8 kB] 49s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 60s Fetched 8487 kB in 3s (2525 kB/s) 61s Reading package lists... 74s /etc/apt/sources.list.d/proposed.list 76s tee: /proc/self/fd/2: Permission denied 110s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 110s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 110s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 110s Hit:4 http://ftpmaster.internal/ubuntu noble-updates InRelease 110s Hit:5 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 110s Hit:6 http://ftpmaster.internal/ubuntu noble-security InRelease 110s Hit:7 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 110s Hit:8 http://ftpmaster.internal/ubuntu noble-proposed InRelease 115s Reading package lists... 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s Calculating upgrade... 118s The following packages have been kept back: 118s curl openssl 118s 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 121s 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. 123s autopkgtest [20:56:14]: rebooting testbed after setup commands that affected boot 158s autopkgtest [20:56:49]: testbed running kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 163s autopkgtest [20:56:54]: testbed dpkg architecture: armhf 177s autopkgtest [20:57:08]: @@@@@@@@@@@@@@@@@@@@ apt-source nanopolish 184s Get:1 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (dsc) [2256 B] 184s Get:2 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (tar) [4074 kB] 184s Get:3 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (diff) [9120 B] 185s gpgv: Signature made Wed Jan 25 21:10:28 2023 UTC 185s gpgv: using RSA key 7E6D9F62AD7303887A3C1DD04916D7AB1D7A3804 185s gpgv: Can't check signature: No public key 185s dpkg-source: warning: cannot verify inline signature for ./nanopolish_0.14.0-1ubuntu1.dsc: no acceptable signature found 185s autopkgtest [20:57:16]: testing package nanopolish version 0.14.0-1ubuntu1 185s autopkgtest [20:57:16]: build not needed 198s autopkgtest [20:57:29]: test run-unit-test: preparing testbed 214s Reading package lists... 215s Building dependency tree... 215s Reading state information... 216s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 216s Starting 2 pkgProblemResolver with broken count: 0 216s Done 217s Done 217s Starting pkgProblemResolver with broken count: 0 218s Starting 2 pkgProblemResolver with broken count: 0 218s Done 219s The following additional packages will be installed: 219s libaec0 libdeflate0 libgomp1 libhdf5-103-1 libhts3 libhtscodecs2 libslow5-0 219s libstreamvbyte0 libsz2 nanopolish 219s Recommended packages: 219s python3-biopython python3-pysam 219s The following NEW packages will be installed: 219s libaec0 libdeflate0 libgomp1 libhdf5-103-1 libhts3 libhtscodecs2 libslow5-0 219s libstreamvbyte0 libsz2 nanopolish 220s 0 upgraded, 10 newly installed, 0 to remove and 2 not upgraded. 220s 1 not fully installed or removed. 220s Need to get 4382 kB of archives. 220s After this operation, 13.6 MB of additional disk space will be used. 220s Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libgomp1 armhf 14-20240303-1ubuntu1 [125 kB] 220s Get:2 http://ftpmaster.internal/ubuntu noble/universe armhf libaec0 armhf 1.1.2-1 [20.7 kB] 220s Get:3 http://ftpmaster.internal/ubuntu noble/universe armhf libsz2 armhf 1.1.2-1 [5262 B] 220s Get:4 http://ftpmaster.internal/ubuntu noble/universe armhf libhdf5-103-1 armhf 1.10.10+repack-3ubuntu1 [1336 kB] 220s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB] 220s Get:6 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.6.0-1 [65.9 kB] 220s Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf libhts3 armhf 1.18+ds-1 [385 kB] 220s Get:8 http://ftpmaster.internal/ubuntu noble/universe armhf libslow5-0 armhf 0.7.0+dfsg-2ubuntu4 [63.3 kB] 220s Get:9 http://ftpmaster.internal/ubuntu noble/universe armhf libstreamvbyte0 armhf 0.4.1-4ubuntu1 [5742 B] 220s Get:10 http://ftpmaster.internal/ubuntu noble/universe armhf nanopolish armhf 0.14.0-1ubuntu1 [2333 kB] 222s Fetched 4382 kB in 1s (3449 kB/s) 222s Selecting previously unselected package libgomp1:armhf. 222s (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 ... 58620 files and directories currently installed.) 222s Preparing to unpack .../0-libgomp1_14-20240303-1ubuntu1_armhf.deb ... 222s Unpacking libgomp1:armhf (14-20240303-1ubuntu1) ... 222s Selecting previously unselected package libaec0:armhf. 222s Preparing to unpack .../1-libaec0_1.1.2-1_armhf.deb ... 222s Unpacking libaec0:armhf (1.1.2-1) ... 222s Selecting previously unselected package libsz2:armhf. 222s Preparing to unpack .../2-libsz2_1.1.2-1_armhf.deb ... 222s Unpacking libsz2:armhf (1.1.2-1) ... 222s Selecting previously unselected package libhdf5-103-1:armhf. 222s Preparing to unpack .../3-libhdf5-103-1_1.10.10+repack-3ubuntu1_armhf.deb ... 222s Unpacking libhdf5-103-1:armhf (1.10.10+repack-3ubuntu1) ... 222s Selecting previously unselected package libdeflate0:armhf. 222s Preparing to unpack .../4-libdeflate0_1.19-1_armhf.deb ... 222s Unpacking libdeflate0:armhf (1.19-1) ... 222s Selecting previously unselected package libhtscodecs2:armhf. 222s Preparing to unpack .../5-libhtscodecs2_1.6.0-1_armhf.deb ... 222s Unpacking libhtscodecs2:armhf (1.6.0-1) ... 222s Selecting previously unselected package libhts3:armhf. 222s Preparing to unpack .../6-libhts3_1.18+ds-1_armhf.deb ... 222s Unpacking libhts3:armhf (1.18+ds-1) ... 223s Selecting previously unselected package libslow5-0:armhf. 223s Preparing to unpack .../7-libslow5-0_0.7.0+dfsg-2ubuntu4_armhf.deb ... 223s Unpacking libslow5-0:armhf (0.7.0+dfsg-2ubuntu4) ... 223s Selecting previously unselected package libstreamvbyte0:armhf. 223s Preparing to unpack .../8-libstreamvbyte0_0.4.1-4ubuntu1_armhf.deb ... 223s Unpacking libstreamvbyte0:armhf (0.4.1-4ubuntu1) ... 223s Selecting previously unselected package nanopolish. 223s Preparing to unpack .../9-nanopolish_0.14.0-1ubuntu1_armhf.deb ... 223s Unpacking nanopolish (0.14.0-1ubuntu1) ... 223s Setting up libhtscodecs2:armhf (1.6.0-1) ... 223s Setting up libstreamvbyte0:armhf (0.4.1-4ubuntu1) ... 223s Setting up libdeflate0:armhf (1.19-1) ... 223s Setting up libgomp1:armhf (14-20240303-1ubuntu1) ... 223s Setting up libaec0:armhf (1.1.2-1) ... 223s Setting up libslow5-0:armhf (0.7.0+dfsg-2ubuntu4) ... 223s Setting up libsz2:armhf (1.1.2-1) ... 223s Setting up libhts3:armhf (1.18+ds-1) ... 223s Setting up libhdf5-103-1:armhf (1.10.10+repack-3ubuntu1) ... 223s Setting up nanopolish (0.14.0-1ubuntu1) ... 223s Setting up autopkgtest-satdep (0) ... 223s Processing triggers for man-db (2.12.0-3) ... 225s Processing triggers for libc-bin (2.39-0ubuntu2) ... 239s (Reading database ... 58711 files and directories currently installed.) 239s Removing autopkgtest-satdep (0) ... 248s autopkgtest [20:58:19]: test run-unit-test: [----------------------- 250s =============================================================================== 250s All tests passed (636 assertions in 6 test cases) 250s 251s autopkgtest [20:58:22]: test run-unit-test: -----------------------] 254s run-unit-test PASS 254s autopkgtest [20:58:25]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 258s autopkgtest [20:58:29]: @@@@@@@@@@@@@@@@@@@@ summary 258s run-unit-test PASS