0s autopkgtest [22:54:21]: starting date: 2024-03-17 0s autopkgtest [22:54:21]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [22:54:21]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.85nfwsqo/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: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' -- lxd -r lxd-armhf-10.44.124.112 lxd-armhf-10.44.124.112:autopkgtest/ubuntu/noble/armhf 93s autopkgtest [22:55:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 96s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 96s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 96s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3726 kB] 99s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 99s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [574 kB] 99s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 99s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 99s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 99s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3500 kB] 100s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 100s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [33.8 kB] 100s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 115s Fetched 8505 kB in 6s (1343 kB/s) 115s Reading package lists... 131s /etc/apt/sources.list.d/proposed.list 134s tee: /proc/self/fd/2: Permission denied 173s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 173s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 173s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 173s Hit:4 http://ftpmaster.internal/ubuntu noble-updates InRelease 173s Hit:5 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 174s Hit:6 http://ftpmaster.internal/ubuntu noble-security InRelease 174s Hit:7 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 174s Hit:8 http://ftpmaster.internal/ubuntu noble-proposed InRelease 185s Reading package lists... 185s Reading package lists... 187s Building dependency tree... 187s Reading state information... 189s Calculating upgrade... 191s The following packages have been kept back: 191s curl openssl 191s 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. 191s Reading package lists... 192s Building dependency tree... 192s Reading state information... 195s 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. 198s autopkgtest [22:57:39]: rebooting testbed after setup commands that affected boot 242s autopkgtest [22:58:23]: testbed running kernel: Linux 5.4.0-170-generic #188-Ubuntu SMP Wed Jan 10 09:51:10 UTC 2024 246s autopkgtest [22:58:27]: testbed dpkg architecture: armhf 260s autopkgtest [22:58:41]: @@@@@@@@@@@@@@@@@@@@ apt-source nanopolish 269s Get:1 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (dsc) [2256 B] 269s Get:2 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (tar) [4074 kB] 269s Get:3 http://ftpmaster.internal/ubuntu noble/universe nanopolish 0.14.0-1ubuntu1 (diff) [9120 B] 270s gpgv: Signature made Wed Jan 25 21:10:28 2023 UTC 270s gpgv: using RSA key 7E6D9F62AD7303887A3C1DD04916D7AB1D7A3804 270s gpgv: Can't check signature: No public key 270s dpkg-source: warning: cannot verify inline signature for ./nanopolish_0.14.0-1ubuntu1.dsc: no acceptable signature found 272s autopkgtest [22:58:52]: testing package nanopolish version 0.14.0-1ubuntu1 272s autopkgtest [22:58:53]: build not needed 278s autopkgtest [22:58:59]: test run-unit-test: preparing testbed 292s Reading package lists... 293s Building dependency tree... 293s Reading state information... 295s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 296s Done 298s Starting pkgProblemResolver with broken count: 0 298s Starting 2 pkgProblemResolver with broken count: 0 298s Done 300s The following additional packages will be installed: 300s libaec0 libdeflate0 libgomp1 libhdf5-103-1 libhts3 libhtscodecs2 libslow5-0 300s libstreamvbyte0 libsz2 nanopolish 300s Recommended packages: 300s python3-biopython python3-pysam 301s The following NEW packages will be installed: 301s libaec0 libdeflate0 libgomp1 libhdf5-103-1 libhts3 libhtscodecs2 libslow5-0 301s libstreamvbyte0 libsz2 nanopolish 301s 0 upgraded, 10 newly installed, 0 to remove and 2 not upgraded. 301s 1 not fully installed or removed. 301s Need to get 4385 kB of archives. 301s After this operation, 13.6 MB of additional disk space will be used. 301s Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libgomp1 armhf 14-20240303-1ubuntu1 [125 kB] 301s Get:2 http://ftpmaster.internal/ubuntu noble/universe armhf libaec0 armhf 1.1.2-1 [20.7 kB] 301s Get:3 http://ftpmaster.internal/ubuntu noble/universe armhf libsz2 armhf 1.1.2-1 [5262 B] 301s Get:4 http://ftpmaster.internal/ubuntu noble/universe armhf libhdf5-103-1 armhf 1.10.10+repack-3ubuntu1 [1336 kB] 302s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB] 302s Get:6 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.6.0-1 [65.9 kB] 302s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libhts3 armhf 1.19+ds-1 [388 kB] 302s Get:8 http://ftpmaster.internal/ubuntu noble/universe armhf libslow5-0 armhf 0.7.0+dfsg-2ubuntu4 [63.3 kB] 302s Get:9 http://ftpmaster.internal/ubuntu noble/universe armhf libstreamvbyte0 armhf 0.4.1-4ubuntu1 [5742 B] 302s Get:10 http://ftpmaster.internal/ubuntu noble/universe armhf nanopolish armhf 0.14.0-1ubuntu1 [2333 kB] 304s Fetched 4385 kB in 1s (3961 kB/s) 304s Selecting previously unselected package libgomp1:armhf. 304s (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.) 304s Preparing to unpack .../0-libgomp1_14-20240303-1ubuntu1_armhf.deb ... 304s Unpacking libgomp1:armhf (14-20240303-1ubuntu1) ... 304s Selecting previously unselected package libaec0:armhf. 304s Preparing to unpack .../1-libaec0_1.1.2-1_armhf.deb ... 304s Unpacking libaec0:armhf (1.1.2-1) ... 304s Selecting previously unselected package libsz2:armhf. 304s Preparing to unpack .../2-libsz2_1.1.2-1_armhf.deb ... 304s Unpacking libsz2:armhf (1.1.2-1) ... 305s Selecting previously unselected package libhdf5-103-1:armhf. 305s Preparing to unpack .../3-libhdf5-103-1_1.10.10+repack-3ubuntu1_armhf.deb ... 305s Unpacking libhdf5-103-1:armhf (1.10.10+repack-3ubuntu1) ... 305s Selecting previously unselected package libdeflate0:armhf. 305s Preparing to unpack .../4-libdeflate0_1.19-1_armhf.deb ... 305s Unpacking libdeflate0:armhf (1.19-1) ... 305s Selecting previously unselected package libhtscodecs2:armhf. 305s Preparing to unpack .../5-libhtscodecs2_1.6.0-1_armhf.deb ... 305s Unpacking libhtscodecs2:armhf (1.6.0-1) ... 305s Selecting previously unselected package libhts3:armhf. 305s Preparing to unpack .../6-libhts3_1.19+ds-1_armhf.deb ... 305s Unpacking libhts3:armhf (1.19+ds-1) ... 306s Selecting previously unselected package libslow5-0:armhf. 306s Preparing to unpack .../7-libslow5-0_0.7.0+dfsg-2ubuntu4_armhf.deb ... 306s Unpacking libslow5-0:armhf (0.7.0+dfsg-2ubuntu4) ... 306s Selecting previously unselected package libstreamvbyte0:armhf. 306s Preparing to unpack .../8-libstreamvbyte0_0.4.1-4ubuntu1_armhf.deb ... 306s Unpacking libstreamvbyte0:armhf (0.4.1-4ubuntu1) ... 306s Selecting previously unselected package nanopolish. 306s Preparing to unpack .../9-nanopolish_0.14.0-1ubuntu1_armhf.deb ... 306s Unpacking nanopolish (0.14.0-1ubuntu1) ... 306s Setting up libhtscodecs2:armhf (1.6.0-1) ... 306s Setting up libstreamvbyte0:armhf (0.4.1-4ubuntu1) ... 307s Setting up libdeflate0:armhf (1.19-1) ... 307s Setting up libgomp1:armhf (14-20240303-1ubuntu1) ... 307s Setting up libaec0:armhf (1.1.2-1) ... 307s Setting up libslow5-0:armhf (0.7.0+dfsg-2ubuntu4) ... 307s Setting up libsz2:armhf (1.1.2-1) ... 307s Setting up libhts3:armhf (1.19+ds-1) ... 307s Setting up libhdf5-103-1:armhf (1.10.10+repack-3ubuntu1) ... 307s Setting up nanopolish (0.14.0-1ubuntu1) ... 307s Setting up autopkgtest-satdep (0) ... 307s Processing triggers for man-db (2.12.0-3) ... 312s Processing triggers for libc-bin (2.39-0ubuntu2) ... 335s (Reading database ... 58711 files and directories currently installed.) 335s Removing autopkgtest-satdep (0) ... 346s autopkgtest [23:00:07]: test run-unit-test: [----------------------- 350s =============================================================================== 350s All tests passed (636 assertions in 6 test cases) 350s 350s autopkgtest [23:00:11]: test run-unit-test: -----------------------] 355s autopkgtest [23:00:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 355s run-unit-test PASS 359s autopkgtest [23:00:20]: @@@@@@@@@@@@@@@@@@@@ summary 359s run-unit-test PASS