0s autopkgtest [17:00:40]: starting date and time: 2024-03-16 17:00:40+0000 0s autopkgtest [17:00:40]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:00:40]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f5iqkiu0/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 mindthegap --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-arm64-6.secgroup --name adt-noble-arm64-mindthegap-20240316-170040-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/ 143s autopkgtest [17:03:03]: testbed dpkg architecture: arm64 143s autopkgtest [17:03:03]: testbed apt version: 2.7.12 143s autopkgtest [17:03:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 144s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 144s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 145s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 145s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 145s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 145s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 145s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 145s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 145s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 145s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 145s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 145s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 145s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 147s Fetched 9063 kB in 2s (4347 kB/s) 147s Reading package lists... 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 151s Calculating upgrade... 151s The following packages will be REMOVED: 151s libssl3 151s The following NEW packages will be installed: 151s libssl3t64 151s The following packages have been kept back: 151s curl 151s The following packages will be upgraded: 151s openssl ubuntu-minimal ubuntu-standard 151s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 151s Need to get 2775 kB of archives. 151s After this operation, 72.7 kB of additional disk space will be used. 151s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 152s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 152s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 152s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 153s Fetched 2775 kB in 1s (3692 kB/s) 153s (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.) 153s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 153s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 153s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 153s wget depends on libssl3 (>= 3.0.0). 153s u-boot-tools depends on libssl3 (>= 3.0.0). 153s tnftp depends on libssl3 (>= 3.0.0). 153s tcpdump depends on libssl3 (>= 3.0.0). 153s systemd-resolved depends on libssl3 (>= 3.0.0). 153s systemd depends on libssl3 (>= 3.0.0). 153s sudo depends on libssl3 (>= 3.0.0). 153s sbsigntool depends on libssl3 (>= 3.0.0). 153s rsync depends on libssl3 (>= 3.0.0). 153s python3-cryptography depends on libssl3 (>= 3.0.0). 153s openssh-server depends on libssl3 (>= 3.0.10). 153s openssh-client depends on libssl3 (>= 3.0.10). 153s mtd-utils depends on libssl3 (>= 3.0.0). 153s mokutil depends on libssl3 (>= 3.0.0). 153s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 153s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 153s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 153s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 153s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 153s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 153s libnvme1 depends on libssl3 (>= 3.0.0). 153s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 153s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 153s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 153s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 153s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 153s kmod depends on libssl3 (>= 3.0.0). 153s dhcpcd-base depends on libssl3 (>= 3.0.0). 153s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 153s 153s (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.) 153s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 153s Selecting previously unselected package libssl3t64:arm64. 153s (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.) 153s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 153s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 153s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ... 153s Unpacking ubuntu-minimal (1.536) over (1.535) ... 153s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ... 153s Unpacking ubuntu-standard (1.536) over (1.535) ... 153s Setting up ubuntu-minimal (1.536) ... 153s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 153s Setting up ubuntu-standard (1.536) ... 153s Setting up openssl (3.0.13-0ubuntu1) ... 153s Processing triggers for man-db (2.12.0-3) ... 154s Processing triggers for libc-bin (2.39-0ubuntu2) ... 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 156s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 156s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 156s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 156s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 158s Reading package lists... 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s Calculating upgrade... 159s The following packages have been kept back: 159s curl 159s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 161s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 163s autopkgtest [17:03:23]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 164s autopkgtest [17:03:24]: @@@@@@@@@@@@@@@@@@@@ apt-source mindthegap 168s Get:1 http://ftpmaster.internal/ubuntu noble/universe mindthegap 2.3.0-3 (dsc) [2281 B] 168s Get:2 http://ftpmaster.internal/ubuntu noble/universe mindthegap 2.3.0-3 (tar) [778 kB] 168s Get:3 http://ftpmaster.internal/ubuntu noble/universe mindthegap 2.3.0-3 (diff) [7572 B] 168s gpgv: Signature made Sat Jan 6 10:53:54 2024 UTC 168s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 168s gpgv: issuer "tille@debian.org" 168s gpgv: Can't check signature: No public key 168s dpkg-source: warning: cannot verify inline signature for ./mindthegap_2.3.0-3.dsc: no acceptable signature found 169s autopkgtest [17:03:29]: testing package mindthegap version 2.3.0-3 170s autopkgtest [17:03:30]: build not needed 170s autopkgtest [17:03:30]: test run-unit-test: preparing testbed 171s Reading package lists... 172s Building dependency tree... 172s Reading state information... 172s Starting pkgProblemResolver with broken count: 0 172s Starting 2 pkgProblemResolver with broken count: 0 172s Done 173s The following additional packages will be installed: 173s libaec0 libgatbcore3 libhdf5-103-1 libsz2 mindthegap mindthegap-examples 173s The following NEW packages will be installed: 173s autopkgtest-satdep libaec0 libgatbcore3 libhdf5-103-1 libsz2 mindthegap 173s mindthegap-examples 173s 0 upgraded, 7 newly installed, 0 to remove and 1 not upgraded. 173s Need to get 3520 kB/3521 kB of archives. 173s After this operation, 12.7 MB of additional disk space will be used. 173s Get:1 /tmp/autopkgtest.3W1Knp/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 173s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 174s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libgatbcore3 arm64 1.4.2+dfsg-13 [1446 kB] 174s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 174s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 174s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 mindthegap arm64 2.3.0-3 [217 kB] 174s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 mindthegap-examples all 2.3.0-3 [641 kB] 175s Fetched 3520 kB in 1s (4989 kB/s) 175s Selecting previously unselected package libaec0:arm64. 175s (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.) 175s Preparing to unpack .../0-libaec0_1.1.2-1_arm64.deb ... 175s Unpacking libaec0:arm64 (1.1.2-1) ... 175s Selecting previously unselected package libgatbcore3:arm64. 175s Preparing to unpack .../1-libgatbcore3_1.4.2+dfsg-13_arm64.deb ... 175s Unpacking libgatbcore3:arm64 (1.4.2+dfsg-13) ... 175s Selecting previously unselected package libsz2:arm64. 175s Preparing to unpack .../2-libsz2_1.1.2-1_arm64.deb ... 175s Unpacking libsz2:arm64 (1.1.2-1) ... 175s Selecting previously unselected package libhdf5-103-1:arm64. 175s Preparing to unpack .../3-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 175s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 175s Selecting previously unselected package mindthegap. 175s Preparing to unpack .../4-mindthegap_2.3.0-3_arm64.deb ... 175s Unpacking mindthegap (2.3.0-3) ... 175s Selecting previously unselected package mindthegap-examples. 176s Preparing to unpack .../5-mindthegap-examples_2.3.0-3_all.deb ... 176s Unpacking mindthegap-examples (2.3.0-3) ... 176s Selecting previously unselected package autopkgtest-satdep. 176s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 176s Unpacking autopkgtest-satdep (0) ... 176s Setting up libaec0:arm64 (1.1.2-1) ... 176s Setting up mindthegap-examples (2.3.0-3) ... 176s Setting up libgatbcore3:arm64 (1.4.2+dfsg-13) ... 176s Setting up libsz2:arm64 (1.1.2-1) ... 176s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 176s Setting up mindthegap (2.3.0-3) ... 176s Setting up autopkgtest-satdep (0) ... 176s Processing triggers for man-db (2.12.0-3) ... 176s Processing triggers for libc-bin (2.39-0ubuntu2) ... 180s (Reading database ... 74890 files and directories currently installed.) 180s Removing autopkgtest-satdep (0) ... 181s autopkgtest [17:03:41]: test run-unit-test: [----------------------- 182s Invoking simple_test.sh: 190s clean-insert : passed 190s 13-inserts-ref10k : passed 190s 1-SNP : passed 190s 3-SNP*2 : passed 190s snp-before-clean-insert : passed 190s hetero-insert : passed 190s deletion : passed 190s fuzzy-deletion : passed 190s n-in-solid-stretch : passed 190s n-in-before-clean-insert : passed 190s n-after-clean-insert : passed 190s Invoking simple_full_test.sh: 191s full-test find vcf : PASS 191s full-test find breakpoints : PASS 191s full-test find with bed option vcf : PASS 191s full-test find breakpoints with bed otpion : PASS 191s full-test fill fasta : PASS 191s full-test fill vcf : PASS 192s contig-test fill fasta : PASS 192s contig-test fill gfa : PASS 192s autopkgtest [17:03:52]: test run-unit-test: -----------------------] 193s autopkgtest [17:03:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 193s run-unit-test PASS 193s autopkgtest [17:03:53]: @@@@@@@@@@@@@@@@@@@@ summary 193s run-unit-test PASS 197s Creating nova instance adt-noble-arm64-mindthegap-20240316-170040-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...