0s autopkgtest [17:43:58]: starting date and time: 2024-03-24 17:43:58+0000 0s autopkgtest [17:43:58]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:43:58]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7fw8or6r/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:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade samtools-legacy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-4.secgroup --name adt-noble-arm64-samtools-legacy-20240324-174358-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/ 68s autopkgtest [17:45:06]: testbed dpkg architecture: arm64 68s autopkgtest [17:45:06]: testbed apt version: 2.7.12 68s autopkgtest [17:45:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 69s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 69s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 69s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 69s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 69s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB] 69s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 69s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 69s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 69s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 69s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 69s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 69s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 71s Fetched 9851 kB in 2s (5077 kB/s) 71s Reading package lists... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 75s Calculating upgrade... 75s The following packages will be REMOVED: 75s libssl3 75s The following NEW packages will be installed: 75s libssl3t64 75s The following packages have been kept back: 75s curl 75s The following packages will be upgraded: 75s openssl 75s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 75s Need to get 2777 kB of archives. 75s After this operation, 139 kB of additional disk space will be used. 75s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 75s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 76s Fetched 2777 kB in 1s (2962 kB/s) 77s (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 ... 74819 files and directories currently installed.) 77s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 77s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 77s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 77s wget depends on libssl3 (>= 3.0.0). 77s u-boot-tools depends on libssl3 (>= 3.0.0). 77s tnftp depends on libssl3 (>= 3.0.0). 77s tcpdump depends on libssl3 (>= 3.0.0). 77s systemd-resolved depends on libssl3 (>= 3.0.0). 77s systemd depends on libssl3 (>= 3.0.0). 77s sudo depends on libssl3 (>= 3.0.0). 77s sbsigntool depends on libssl3 (>= 3.0.0). 77s rsync depends on libssl3 (>= 3.0.0). 77s python3-cryptography depends on libssl3 (>= 3.0.0). 77s openssh-server depends on libssl3 (>= 3.0.10). 77s openssh-client depends on libssl3 (>= 3.0.10). 77s mtd-utils depends on libssl3 (>= 3.0.0). 77s mokutil depends on libssl3 (>= 3.0.0). 77s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 77s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 77s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 77s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 77s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 77s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 77s libnvme1 depends on libssl3 (>= 3.0.0). 77s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 77s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 77s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 77s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 77s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 77s kmod depends on libssl3 (>= 3.0.0). 77s dhcpcd-base depends on libssl3 (>= 3.0.0). 77s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 77s 77s (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 ... 74819 files and directories currently installed.) 77s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 77s Selecting previously unselected package libssl3t64:arm64. 77s (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 ... 74808 files and directories currently installed.) 77s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 77s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 77s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 77s Setting up openssl (3.0.13-0ubuntu2) ... 77s Processing triggers for man-db (2.12.0-3) ... 78s Processing triggers for libc-bin (2.39-0ubuntu6) ... 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 80s sh: Attempting to set up Debian/Ubuntu apt sources automatically 80s sh: Distribution appears to be Ubuntu 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s eatmydata is already the newest version (131-1). 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s dbus is already the newest version (1.14.10-4ubuntu1). 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 83s rng-tools-debian is already the newest version (2.4). 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s The following packages will be REMOVED: 83s cloud-init* python3-configobj* python3-debconf* 84s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 84s After this operation, 3256 kB disk space will be freed. 84s (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 ... 74821 files and directories currently installed.) 84s Removing cloud-init (24.1.2-0ubuntu1) ... 84s Removing python3-configobj (5.0.8-3) ... 84s Removing python3-debconf (1.5.86) ... 84s Processing triggers for man-db (2.12.0-3) ... 85s (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 ... 74432 files and directories currently installed.) 85s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 85s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 85s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 85s invoke-rc.d: policy-rc.d denied execution of try-restart. 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s linux-generic is already the newest version (6.8.0-11.11+1). 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 87s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 87s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 88s Reading package lists... 88s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 91s autopkgtest [17:45:29]: rebooting testbed after setup commands that affected boot 118s autopkgtest [17:45:56]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 121s autopkgtest [17:45:59]: @@@@@@@@@@@@@@@@@@@@ apt-source samtools-legacy 124s Get:1 http://ftpmaster.internal/ubuntu noble/universe samtools-legacy 0.1.19+dfsg-6ubuntu1 (dsc) [2220 B] 124s Get:2 http://ftpmaster.internal/ubuntu noble/universe samtools-legacy 0.1.19+dfsg-6ubuntu1 (tar) [371 kB] 124s Get:3 http://ftpmaster.internal/ubuntu noble/universe samtools-legacy 0.1.19+dfsg-6ubuntu1 (diff) [10.8 kB] 124s gpgv: Signature made Tue Nov 21 23:05:58 2023 UTC 124s gpgv: using RSA key 5C7ABEA20F8630459CC8C8B5E27F2CF8458C2FA4 124s gpgv: Can't check signature: No public key 124s dpkg-source: warning: cannot verify inline signature for ./samtools-legacy_0.1.19+dfsg-6ubuntu1.dsc: no acceptable signature found 124s autopkgtest [17:46:02]: testing package samtools-legacy version 0.1.19+dfsg-6ubuntu1 125s autopkgtest [17:46:03]: build not needed 125s autopkgtest [17:46:03]: test run-unit-test: preparing testbed 127s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Starting pkgProblemResolver with broken count: 0 128s Starting 2 pkgProblemResolver with broken count: 0 128s Done 129s The following additional packages will be installed: 129s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 129s g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 129s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libatomic1 129s libbam-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdeflate0 129s libgcc-13-dev libgomp1 libhts3 libhtscodecs2 libhwasan0 libisl23 libitm1 129s liblsan0 libmpc3 libstdc++-13-dev libtsan2 libubsan1 linux-libc-dev 129s rpcsvc-proto samtools zlib1g-dev 129s Suggested packages: 129s cpp-doc gcc-13-locales cpp-13-doc gcc-13-doc gcc-multilib manpages-dev 129s autoconf automake libtool flex bison gdb gcc-doc gdb-aarch64-linux-gnu 129s glibc-doc libstdc++-13-doc cwltool 129s Recommended packages: 129s manpages manpages-dev libc-devtools 129s The following NEW packages will be installed: 129s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 129s cpp-aarch64-linux-gnu g++ g++-13 g++-13-aarch64-linux-gnu 129s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 129s gcc-aarch64-linux-gnu libasan8 libatomic1 libbam-dev libc-dev-bin libc6-dev 129s libcc1-0 libcrypt-dev libdeflate0 libgcc-13-dev libgomp1 libhts3 129s libhtscodecs2 libhwasan0 libisl23 libitm1 liblsan0 libmpc3 libstdc++-13-dev 129s libtsan2 libubsan1 linux-libc-dev rpcsvc-proto samtools zlib1g-dev 129s 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. 129s Need to get 63.6 MB/63.6 MB of archives. 129s After this operation, 225 MB of additional disk space will be used. 129s Get:1 /tmp/autopkgtest.S1JUyy/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 129s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu6 [19.7 kB] 129s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 130s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 130s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 130s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu6 [1596 kB] 130s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 130s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 130s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 131s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 131s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 131s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 131s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 131s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 131s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 131s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 131s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 131s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 131s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 131s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 132s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 132s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 132s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 132s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 132s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 132s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 132s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 132s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 133s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 133s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 133s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 133s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 133s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 133s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 libbam-dev arm64 0.1.19+dfsg-6ubuntu1 [114 kB] 133s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 133s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 133s Get:37 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 133s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 133s Fetched 63.6 MB in 4s (16.0 MB/s) 134s Selecting previously unselected package libc-dev-bin. 134s (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 ... 74377 files and directories currently installed.) 134s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu6_arm64.deb ... 134s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 134s Selecting previously unselected package linux-libc-dev:arm64. 134s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_arm64.deb ... 134s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 134s Selecting previously unselected package libcrypt-dev:arm64. 134s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 134s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 134s Selecting previously unselected package rpcsvc-proto. 134s Preparing to unpack .../03-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 134s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 134s Selecting previously unselected package libc6-dev:arm64. 134s Preparing to unpack .../04-libc6-dev_2.39-0ubuntu6_arm64.deb ... 134s Unpacking libc6-dev:arm64 (2.39-0ubuntu6) ... 134s Selecting previously unselected package libisl23:arm64. 134s Preparing to unpack .../05-libisl23_0.26-3_arm64.deb ... 134s Unpacking libisl23:arm64 (0.26-3) ... 134s Selecting previously unselected package libmpc3:arm64. 134s Preparing to unpack .../06-libmpc3_1.3.1-1_arm64.deb ... 134s Unpacking libmpc3:arm64 (1.3.1-1) ... 134s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 134s Preparing to unpack .../07-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 134s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 135s Selecting previously unselected package cpp-13. 135s Preparing to unpack .../08-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 135s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 135s Selecting previously unselected package cpp-aarch64-linux-gnu. 135s Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 135s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 135s Selecting previously unselected package cpp. 135s Preparing to unpack .../10-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 135s Unpacking cpp (4:13.2.0-7ubuntu1) ... 135s Selecting previously unselected package libcc1-0:arm64. 135s Preparing to unpack .../11-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 135s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 135s Selecting previously unselected package libgomp1:arm64. 135s Preparing to unpack .../12-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 135s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 135s Selecting previously unselected package libitm1:arm64. 135s Preparing to unpack .../13-libitm1_14-20240303-1ubuntu1_arm64.deb ... 135s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 135s Selecting previously unselected package libatomic1:arm64. 135s Preparing to unpack .../14-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 135s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 135s Selecting previously unselected package libasan8:arm64. 135s Preparing to unpack .../15-libasan8_14-20240303-1ubuntu1_arm64.deb ... 135s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 135s Selecting previously unselected package liblsan0:arm64. 135s Preparing to unpack .../16-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 135s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 135s Selecting previously unselected package libtsan2:arm64. 135s Preparing to unpack .../17-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 135s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 135s Selecting previously unselected package libubsan1:arm64. 135s Preparing to unpack .../18-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 135s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 135s Selecting previously unselected package libhwasan0:arm64. 135s Preparing to unpack .../19-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 135s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package libgcc-13-dev:arm64. 136s Preparing to unpack .../20-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 136s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 136s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 136s Preparing to unpack .../21-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 136s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 136s Selecting previously unselected package gcc-13. 136s Preparing to unpack .../22-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 136s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 136s Selecting previously unselected package gcc-aarch64-linux-gnu. 136s Preparing to unpack .../23-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 136s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 136s Selecting previously unselected package gcc. 136s Preparing to unpack .../24-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 136s Unpacking gcc (4:13.2.0-7ubuntu1) ... 136s Selecting previously unselected package libstdc++-13-dev:arm64. 136s Preparing to unpack .../25-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 136s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 137s Selecting previously unselected package g++-13-aarch64-linux-gnu. 137s Preparing to unpack .../26-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 137s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 137s Selecting previously unselected package g++-13. 137s Preparing to unpack .../27-g++-13_13.2.0-17ubuntu2_arm64.deb ... 137s Unpacking g++-13 (13.2.0-17ubuntu2) ... 137s Selecting previously unselected package g++-aarch64-linux-gnu. 137s Preparing to unpack .../28-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 137s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 137s Selecting previously unselected package g++. 137s Preparing to unpack .../29-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 137s Unpacking g++ (4:13.2.0-7ubuntu1) ... 137s Selecting previously unselected package build-essential. 137s Preparing to unpack .../30-build-essential_12.10ubuntu1_arm64.deb ... 137s Unpacking build-essential (12.10ubuntu1) ... 137s Selecting previously unselected package zlib1g-dev:arm64. 137s Preparing to unpack .../31-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 137s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 137s Selecting previously unselected package libbam-dev. 137s Preparing to unpack .../32-libbam-dev_0.1.19+dfsg-6ubuntu1_arm64.deb ... 137s Unpacking libbam-dev (0.1.19+dfsg-6ubuntu1) ... 137s Selecting previously unselected package libdeflate0:arm64. 137s Preparing to unpack .../33-libdeflate0_1.19-1_arm64.deb ... 137s Unpacking libdeflate0:arm64 (1.19-1) ... 137s Selecting previously unselected package libhtscodecs2:arm64. 137s Preparing to unpack .../34-libhtscodecs2_1.6.0-1_arm64.deb ... 137s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 137s Selecting previously unselected package libhts3:arm64. 137s Preparing to unpack .../35-libhts3_1.18+ds-1_arm64.deb ... 137s Unpacking libhts3:arm64 (1.18+ds-1) ... 138s Selecting previously unselected package samtools. 138s Preparing to unpack .../36-samtools_1.19.2-1_arm64.deb ... 138s Unpacking samtools (1.19.2-1) ... 138s Selecting previously unselected package autopkgtest-satdep. 138s Preparing to unpack .../37-1-autopkgtest-satdep.deb ... 138s Unpacking autopkgtest-satdep (0) ... 138s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 138s Setting up libdeflate0:arm64 (1.19-1) ... 138s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 138s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 138s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 138s Setting up libmpc3:arm64 (1.3.1-1) ... 138s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 138s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 138s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 138s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 138s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 138s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 138s Setting up libisl23:arm64 (0.26-3) ... 138s Setting up libc-dev-bin (2.39-0ubuntu6) ... 138s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 138s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 138s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 138s Setting up libhts3:arm64 (1.18+ds-1) ... 138s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 138s Setting up samtools (1.19.2-1) ... 138s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 138s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 138s Setting up libc6-dev:arm64 (2.39-0ubuntu6) ... 138s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 138s Setting up cpp-13 (13.2.0-17ubuntu2) ... 138s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 138s Setting up gcc-13 (13.2.0-17ubuntu2) ... 138s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 138s Setting up cpp (4:13.2.0-7ubuntu1) ... 138s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 138s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 138s Setting up g++-13 (13.2.0-17ubuntu2) ... 138s Setting up gcc (4:13.2.0-7ubuntu1) ... 138s Setting up libbam-dev (0.1.19+dfsg-6ubuntu1) ... 138s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 138s Setting up g++ (4:13.2.0-7ubuntu1) ... 138s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 138s Setting up build-essential (12.10ubuntu1) ... 138s Setting up autopkgtest-satdep (0) ... 138s Processing triggers for man-db (2.12.0-3) ... 139s Processing triggers for libc-bin (2.39-0ubuntu6) ... 145s (Reading database ... 77261 files and directories currently installed.) 145s autopkgtest [17:46:22]: test run-unit-test: [----------------------- 145s Removing autopkgtest-satdep (0) ... 145s Test 1 -- calDepth 145s ref 7 1 145s ref 8 1 145s ref 9 3 145s ref 10 3 145s ref 11 3 145s ref 12 3 145s ref 13 3 145s ref 14 3 145s ref 15 2 145s ref 16 3 145s ref 17 3 145s ref 18 3 145s ref 19 2 145s ref 20 2 145s ref 21 2 145s ref 22 2 145s ref 23 1 145s ref 24 1 145s ref 25 1 145s ref 26 1 145s ref 27 1 145s ref 28 1 145s ref 29 2 145s ref 30 2 145s ref 31 2 145s ref 32 2 145s ref 33 2 145s ref 34 1 145s ref 35 1 145s ref 36 1 145s ref 37 2 145s ref 38 2 145s ref 39 2 145s ref 40 2 145s ref 41 1 145s ref 42 1 145s ref 43 1 145s ref 44 1 145s ref 45 1 145s ref2 1 1 145s ref2 2 2 145s ref2 3 2 145s ref2 4 2 145s ref2 5 2 145s ref2 6 3 145s ref2 7 3 145s ref2 8 3 145s ref2 9 3 145s ref2 10 4 145s ref2 11 4 145s ref2 12 5 145s ref2 13 5 145s ref2 14 6 145s ref2 15 6 145s ref2 16 6 145s ref2 17 6 145s ref2 18 6 145s ref2 19 6 145s ref2 20 6 145s ref2 21 5 145s ref2 22 5 145s ref2 23 4 145s ref2 24 4 145s ref2 25 4 145s ref2 26 4 145s ref2 27 4 145s ref2 28 3 145s ref2 29 3 145s ref2 30 3 145s ref2 31 3 145s ref2 32 3 145s ref2 33 3 145s ref2 34 3 145s ref2 35 2 145s ref2 36 1 145s =============== PASS ================ 145s Test 2 -- chk_indel 145s =============== PASS ================ 145s Test 3 -- bam2bed 145s ref 6 22 r001 30 + 145s ref 8 18 r002 30 + 145s ref 8 14 r003 30 + 145s ref 15 40 r004 30 + 145s ref 28 33 r003 30 - 145s ref 36 45 r001 30 - 145s ref2 0 20 x1 30 + 145s ref2 1 22 x2 30 + 145s ref2 5 27 x3 30 + 145s ref2 9 34 x4 30 + 145s ref2 11 35 x5 30 + 145s ref2 13 36 x6 30 + 145s =============== PASS ================ 145s autopkgtest [17:46:23]: test run-unit-test: -----------------------] 146s autopkgtest [17:46:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 146s run-unit-test PASS 146s autopkgtest [17:46:24]: @@@@@@@@@@@@@@@@@@@@ summary 146s run-unit-test PASS 150s Creating nova instance adt-noble-arm64-samtools-legacy-20240324-174358-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)...