0s autopkgtest [17:06:30]: starting date and time: 2024-03-16 17:06:30+0000 0s autopkgtest [17:06:30]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:06:30]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jmuazhk5/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 scrappie --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-arm64-20.secgroup --name adt-noble-arm64-scrappie-20240316-170630-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/ 135s autopkgtest [17:08:45]: testbed dpkg architecture: arm64 136s autopkgtest [17:08:46]: testbed apt version: 2.7.12 136s autopkgtest [17:08:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 136s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 137s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 137s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 137s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 137s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 137s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 137s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 137s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 137s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 137s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 137s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 137s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 137s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 139s Fetched 9063 kB in 2s (4647 kB/s) 139s Reading package lists... 142s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Calculating upgrade... 143s The following packages will be REMOVED: 143s libssl3 143s The following NEW packages will be installed: 143s libssl3t64 143s The following packages have been kept back: 143s curl 143s The following packages will be upgraded: 143s openssl ubuntu-minimal ubuntu-standard 144s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 144s Need to get 2775 kB of archives. 144s After this operation, 72.7 kB of additional disk space will be used. 144s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 144s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 144s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 144s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 145s Fetched 2775 kB in 1s (4107 kB/s) 145s (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.) 145s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 145s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 146s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 146s wget depends on libssl3 (>= 3.0.0). 146s u-boot-tools depends on libssl3 (>= 3.0.0). 146s tnftp depends on libssl3 (>= 3.0.0). 146s tcpdump depends on libssl3 (>= 3.0.0). 146s systemd-resolved depends on libssl3 (>= 3.0.0). 146s systemd depends on libssl3 (>= 3.0.0). 146s sudo depends on libssl3 (>= 3.0.0). 146s sbsigntool depends on libssl3 (>= 3.0.0). 146s rsync depends on libssl3 (>= 3.0.0). 146s python3-cryptography depends on libssl3 (>= 3.0.0). 146s openssh-server depends on libssl3 (>= 3.0.10). 146s openssh-client depends on libssl3 (>= 3.0.10). 146s mtd-utils depends on libssl3 (>= 3.0.0). 146s mokutil depends on libssl3 (>= 3.0.0). 146s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 146s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 146s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 146s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 146s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 146s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 146s libnvme1 depends on libssl3 (>= 3.0.0). 146s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 146s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 146s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 146s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 146s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 146s kmod depends on libssl3 (>= 3.0.0). 146s dhcpcd-base depends on libssl3 (>= 3.0.0). 146s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 146s 146s (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.) 146s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 146s Selecting previously unselected package libssl3t64:arm64. 146s (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.) 146s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 146s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 146s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ... 146s Unpacking ubuntu-minimal (1.536) over (1.535) ... 146s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ... 146s Unpacking ubuntu-standard (1.536) over (1.535) ... 146s Setting up ubuntu-minimal (1.536) ... 146s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 146s Setting up ubuntu-standard (1.536) ... 146s Setting up openssl (3.0.13-0ubuntu1) ... 146s Processing triggers for man-db (2.12.0-3) ... 147s Processing triggers for libc-bin (2.39-0ubuntu2) ... 147s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 149s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 149s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 149s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 149s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 151s Reading package lists... 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s Calculating upgrade... 152s The following packages have been kept back: 152s curl 152s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 157s autopkgtest [17:09:07]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 157s autopkgtest [17:09:07]: @@@@@@@@@@@@@@@@@@@@ apt-source scrappie 172s Get:1 http://ftpmaster.internal/ubuntu noble/universe scrappie 1.4.2-8 (dsc) [2106 B] 172s Get:2 http://ftpmaster.internal/ubuntu noble/universe scrappie 1.4.2-8 (tar) [21.8 MB] 172s Get:3 http://ftpmaster.internal/ubuntu noble/universe scrappie 1.4.2-8 (diff) [14.3 kB] 172s gpgv: Signature made Fri Oct 1 15:05:18 2021 UTC 172s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 172s gpgv: issuer "tille@debian.org" 172s gpgv: Can't check signature: No public key 172s dpkg-source: warning: cannot verify inline signature for ./scrappie_1.4.2-8.dsc: no acceptable signature found 174s autopkgtest [17:09:24]: testing package scrappie version 1.4.2-8 174s autopkgtest [17:09:24]: build not needed 176s autopkgtest [17:09:26]: test run-unit-test: preparing testbed 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Starting pkgProblemResolver with broken count: 0 179s Starting 2 pkgProblemResolver with broken count: 0 179s Done 179s The following additional packages will be installed: 179s libaec0 libblas3 libgomp1 libhdf5-103-1 libsz2 scrappie 179s The following NEW packages will be installed: 179s autopkgtest-satdep libaec0 libblas3 libgomp1 libhdf5-103-1 libsz2 scrappie 179s 0 upgraded, 7 newly installed, 0 to remove and 1 not upgraded. 179s Need to get 19.1 MB/19.1 MB of archives. 179s After this operation, 27.9 MB of additional disk space will be used. 179s Get:1 /tmp/autopkgtest.717u78/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 180s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 180s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 180s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 180s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 180s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 180s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 scrappie arm64 1.4.2-8 [17.6 MB] 182s Fetched 19.1 MB in 1s (14.9 MB/s) 182s Selecting previously unselected package libaec0:arm64. 183s (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.) 183s Preparing to unpack .../0-libaec0_1.1.2-1_arm64.deb ... 183s Unpacking libaec0:arm64 (1.1.2-1) ... 183s Selecting previously unselected package libblas3:arm64. 183s Preparing to unpack .../1-libblas3_3.12.0-3_arm64.deb ... 183s Unpacking libblas3:arm64 (3.12.0-3) ... 183s Selecting previously unselected package libgomp1:arm64. 183s Preparing to unpack .../2-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 183s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 183s Selecting previously unselected package libsz2:arm64. 183s Preparing to unpack .../3-libsz2_1.1.2-1_arm64.deb ... 183s Unpacking libsz2:arm64 (1.1.2-1) ... 183s Selecting previously unselected package libhdf5-103-1:arm64. 183s Preparing to unpack .../4-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 183s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 183s Selecting previously unselected package scrappie. 183s Preparing to unpack .../5-scrappie_1.4.2-8_arm64.deb ... 183s Unpacking scrappie (1.4.2-8) ... 183s Selecting previously unselected package autopkgtest-satdep. 184s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 184s Unpacking autopkgtest-satdep (0) ... 184s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 184s Setting up libaec0:arm64 (1.1.2-1) ... 184s Setting up libblas3:arm64 (3.12.0-3) ... 184s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 184s Setting up libsz2:arm64 (1.1.2-1) ... 184s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 184s Setting up scrappie (1.4.2-8) ... 184s Setting up autopkgtest-satdep (0) ... 184s Processing triggers for man-db (2.12.0-3) ... 184s Processing triggers for libc-bin (2.39-0ubuntu2) ... 188s (Reading database ... 74799 files and directories currently installed.) 188s Removing autopkgtest-satdep (0) ... 189s autopkgtest [17:09:39]: test run-unit-test: [----------------------- 189s Test functionality 189s Test 1 198s >read_ch228_file118.fast5 { "filename" : "read_ch228_file118.fast5", "uuid" : "e47468bf-12e3-4208-a866-babdd780e9c0", "normalised_score" : 0.479833, "nblock" : 5778, "sequence_length" : 2448, "blocks_per_base" : 2.360294, "nsample" : 29150, "trim" : [ 200, 29090 ] } 198s PASS 198s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 198s Test 2 205s >read_ch228_file118.fast5 { "filename" : "read_ch228_file118.fast5", "uuid" : "e47468bf-12e3-4208-a866-babdd780e9c0", "normalised_score" : 0.458548, "nevent" : 5787, "sequence_length" : 1675, "events_per_base" : 3.454925 } 205s PASS 205s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 205s Test 3 211s filename uuid normalised_score nblock sequence_length blocks_per_base nsample trim 211s read_ch228_file118.fast5 e47468bf-12e3-4208-a866-babdd780e9c0 0.611628 5778 2439 2.369004 29150 [200, 29090] 211s MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch174_read172_strand.fast5 c99357df-c74f-4ac0-bb2b-10d0414866c0 0.295786 16158 9512 1.698696 81106 [200, 80990] 211s MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch271_read66_strand.fast5 06c8e9fa-170e-4fcc-9050-c98f8880cad7 0.179309 12818 4723 2.713953 64395 [200, 64290] 211s PASS 212s autopkgtest [17:10:02]: test run-unit-test: -----------------------] 213s run-unit-test PASS 213s autopkgtest [17:10:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 213s autopkgtest [17:10:03]: @@@@@@@@@@@@@@@@@@@@ summary 213s run-unit-test PASS 239s Creating nova instance adt-noble-arm64-scrappie-20240316-170630-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...