0s autopkgtest [17:10:56]: starting date and time: 2024-03-16 17:10:56+0000 0s autopkgtest [17:10:56]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:10:56]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.y10ttt59/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:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade delly --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-3@bos03-arm64-25.secgroup --name adt-noble-arm64-delly-20240316-171056-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 90s autopkgtest [17:12:26]: testbed dpkg architecture: arm64 90s autopkgtest [17:12:26]: testbed apt version: 2.7.12 90s autopkgtest [17:12:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 91s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 92s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 92s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 93s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 93s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 93s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 93s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 93s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 93s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 93s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 93s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 93s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 93s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 95s Fetched 9063 kB in 3s (3019 kB/s) 96s Reading package lists... 99s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade... 101s The following packages will be REMOVED: 101s libssl3 101s The following NEW packages will be installed: 101s libssl3t64 101s The following packages have been kept back: 101s curl 101s The following packages will be upgraded: 101s openssl ubuntu-minimal ubuntu-standard 101s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 101s Need to get 2775 kB of archives. 101s After this operation, 72.7 kB of additional disk space will be used. 101s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 102s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 102s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 102s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 103s Fetched 2775 kB in 1s (2791 kB/s) 104s (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.) 104s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 104s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 104s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 104s wget depends on libssl3 (>= 3.0.0). 104s u-boot-tools depends on libssl3 (>= 3.0.0). 104s tnftp depends on libssl3 (>= 3.0.0). 104s tcpdump depends on libssl3 (>= 3.0.0). 104s systemd-resolved depends on libssl3 (>= 3.0.0). 104s systemd depends on libssl3 (>= 3.0.0). 104s sudo depends on libssl3 (>= 3.0.0). 104s sbsigntool depends on libssl3 (>= 3.0.0). 104s rsync depends on libssl3 (>= 3.0.0). 104s python3-cryptography depends on libssl3 (>= 3.0.0). 104s openssh-server depends on libssl3 (>= 3.0.10). 104s openssh-client depends on libssl3 (>= 3.0.10). 104s mtd-utils depends on libssl3 (>= 3.0.0). 104s mokutil depends on libssl3 (>= 3.0.0). 104s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 104s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 104s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 104s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 104s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 104s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 104s libnvme1 depends on libssl3 (>= 3.0.0). 104s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 104s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 104s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 104s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 104s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 104s kmod depends on libssl3 (>= 3.0.0). 104s dhcpcd-base depends on libssl3 (>= 3.0.0). 104s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 104s 104s (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.) 104s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 104s Selecting previously unselected package libssl3t64:arm64. 104s (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.) 104s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 104s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 104s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ... 104s Unpacking ubuntu-minimal (1.536) over (1.535) ... 104s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ... 104s Unpacking ubuntu-standard (1.536) over (1.535) ... 104s Setting up ubuntu-minimal (1.536) ... 104s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 104s Setting up ubuntu-standard (1.536) ... 104s Setting up openssl (3.0.13-0ubuntu1) ... 104s Processing triggers for man-db (2.12.0-3) ... 105s Processing triggers for libc-bin (2.39-0ubuntu2) ... 106s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 109s sh: Attempting to set up Debian/Ubuntu apt sources automatically 109s sh: Distribution appears to be Ubuntu 109s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s eatmydata is already the newest version (131-1). 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s dbus is already the newest version (1.14.10-4ubuntu1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s rng-tools-debian is already the newest version (2.4). 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 114s The following packages will be REMOVED: 114s cloud-init* python3-configobj* python3-debconf* 118s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 118s After this operation, 3252 kB disk space will be freed. 118s (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.) 118s Removing cloud-init (24.1.1-0ubuntu1) ... 120s Removing python3-configobj (5.0.8-3) ... 121s Removing python3-debconf (1.5.86) ... 121s Processing triggers for man-db (2.12.0-3) ... 122s (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 ... 74371 files and directories currently installed.) 122s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 123s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 123s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 123s invoke-rc.d: policy-rc.d denied execution of try-restart. 123s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s linux-generic is already the newest version (6.8.0-11.11+1). 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 125s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 125s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 127s Reading package lists... 127s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Calculating upgrade... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s autopkgtest [17:13:06]: rebooting testbed after setup commands that affected boot 375s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 394s autopkgtest [17:17:30]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 401s autopkgtest [17:17:37]: @@@@@@@@@@@@@@@@@@@@ apt-source delly 404s Get:1 http://ftpmaster.internal/ubuntu noble/universe delly 1.1.8-1build1 (dsc) [2113 B] 404s Get:2 http://ftpmaster.internal/ubuntu noble/universe delly 1.1.8-1build1 (tar) [3744 kB] 404s Get:3 http://ftpmaster.internal/ubuntu noble/universe delly 1.1.8-1build1 (diff) [5312 B] 405s gpgv: Signature made Tue Dec 19 15:01:08 2023 UTC 405s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 405s gpgv: Can't check signature: No public key 405s dpkg-source: warning: cannot verify inline signature for ./delly_1.1.8-1build1.dsc: no acceptable signature found 405s autopkgtest [17:17:41]: testing package delly version 1.1.8-1build1 405s autopkgtest [17:17:41]: build not needed 406s autopkgtest [17:17:42]: test run-unit-test: preparing testbed 408s Reading package lists... 408s Building dependency tree... 408s Reading state information... 409s Starting pkgProblemResolver with broken count: 0 409s Starting 2 pkgProblemResolver with broken count: 0 409s Done 410s The following additional packages will be installed: 410s delly libboost-filesystem1.83.0 libboost-iostreams1.83.0 410s libboost-program-options1.83.0 libdeflate0 libgomp1 libhts3 libhtscodecs2 410s The following NEW packages will be installed: 410s autopkgtest-satdep delly libboost-filesystem1.83.0 libboost-iostreams1.83.0 410s libboost-program-options1.83.0 libdeflate0 libgomp1 libhts3 libhtscodecs2 411s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 411s Need to get 2202 kB/2203 kB of archives. 411s After this operation, 10.0 MB of additional disk space will be used. 411s Get:1 /tmp/autopkgtest.5B69dj/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 411s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-2ubuntu1 [366 kB] 411s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-2ubuntu1 [339 kB] 411s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2ubuntu1 [410 kB] 411s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 411s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 411s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 411s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 411s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 delly arm64 1.1.8-1build1 [400 kB] 415s Fetched 2202 kB in 1s (2319 kB/s) 415s Selecting previously unselected package libboost-filesystem1.83.0:arm64. 415s (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 ... 74316 files and directories currently installed.) 415s Preparing to unpack .../0-libboost-filesystem1.83.0_1.83.0-2ubuntu1_arm64.deb ... 415s Unpacking libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 415s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 415s Preparing to unpack .../1-libboost-iostreams1.83.0_1.83.0-2ubuntu1_arm64.deb ... 415s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-2ubuntu1) ... 415s Selecting previously unselected package libboost-program-options1.83.0:arm64. 415s Preparing to unpack .../2-libboost-program-options1.83.0_1.83.0-2ubuntu1_arm64.deb ... 415s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 415s Selecting previously unselected package libgomp1:arm64. 415s Preparing to unpack .../3-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 415s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 415s Selecting previously unselected package libdeflate0:arm64. 415s Preparing to unpack .../4-libdeflate0_1.19-1_arm64.deb ... 415s Unpacking libdeflate0:arm64 (1.19-1) ... 415s Selecting previously unselected package libhtscodecs2:arm64. 415s Preparing to unpack .../5-libhtscodecs2_1.6.0-1_arm64.deb ... 415s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 415s Selecting previously unselected package libhts3:arm64. 416s Preparing to unpack .../6-libhts3_1.18+ds-1_arm64.deb ... 416s Unpacking libhts3:arm64 (1.18+ds-1) ... 416s Selecting previously unselected package delly. 416s Preparing to unpack .../7-delly_1.1.8-1build1_arm64.deb ... 416s Unpacking delly (1.1.8-1build1) ... 416s Selecting previously unselected package autopkgtest-satdep. 416s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 416s Unpacking autopkgtest-satdep (0) ... 416s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 416s Setting up libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 416s Setting up libdeflate0:arm64 (1.19-1) ... 416s Setting up libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 416s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 416s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-2ubuntu1) ... 416s Setting up libhts3:arm64 (1.18+ds-1) ... 416s Setting up delly (1.1.8-1build1) ... 416s Setting up autopkgtest-satdep (0) ... 416s Processing triggers for man-db (2.12.0-3) ... 417s Processing triggers for libc-bin (2.39-0ubuntu2) ... 423s (Reading database ... 74363 files and directories currently installed.) 423s Removing autopkgtest-satdep (0) ... 423s autopkgtest [17:17:59]: test run-unit-test: [----------------------- 424s Running Tests 424s Test 1 424s [2024-Mar-16 17:18:00] delly call -o sr.bcf -g ref.fa sr.bam 424s [2024-Mar-16 17:18:00] Paired-end and split-read scanning 424s [2024-Mar-16 17:18:00] Split-read clustering 424s [2024-Mar-16 17:18:00] Paired-end clustering 424s [2024-Mar-16 17:18:00] Split-read assembly 424s [2024-Mar-16 17:18:00] Generate REF and ALT probes 424s [2024-Mar-16 17:18:00] SV annotation 424s [2024-Mar-16 17:18:00] Genotyping 424s [2024-Mar-16 17:18:00] Sample statistics 424s Sample:sr,ReadSize=150,Median=501,MAD=33,UniqueDiscordantPairs=9 424s [2024-Mar-16 17:18:00] Done. 424s Test 2 424s [2024-Mar-16 17:18:00] delly lr -g ref.fa lr.bam -o lr.vcf 424s [2024-Mar-16 17:18:00] Split-read scanning 425s [2024-Mar-16 17:18:00] Split-read assembly 425s [2024-Mar-16 17:18:01] SV annotation 425s [2024-Mar-16 17:18:01] Genotyping 425s [2024-Mar-16 17:18:01] Done. 425s Test 3 425s [2024-Mar-16 17:18:01] delly cnv -g ref.fa -m map.fa.gz sr.bam -o cnv.vcf 425s [2024-Mar-16 17:18:01] Scanning Windows 425s [2024-Mar-16 17:18:01] Estimate GC bias 425s [2024-Mar-16 17:18:01] Count fragments 425s [2024-Mar-16 17:18:01] Genotyping 425s [2024-Mar-16 17:18:01] Done. 425s PASS 426s autopkgtest [17:18:02]: test run-unit-test: -----------------------] 427s run-unit-test PASS 427s autopkgtest [17:18:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 427s autopkgtest [17:18:03]: @@@@@@@@@@@@@@@@@@@@ summary 427s run-unit-test PASS 438s Creating nova instance adt-noble-arm64-delly-20240316-171056-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...