0s autopkgtest [17:08:20]: starting date and time: 2024-03-16 17:08:20+0000 0s autopkgtest [17:08:20]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:08:20]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w1_86taw/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 uncalled --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@bos02-arm64-28.secgroup --name adt-noble-arm64-uncalled-20240316-170820-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/ 142s autopkgtest [17:10:42]: testbed dpkg architecture: arm64 142s autopkgtest [17:10:42]: testbed apt version: 2.7.12 142s autopkgtest [17:10:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 143s 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/multiverse Sources [51.4 kB] 145s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 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] 146s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 146s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 146s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 156s Fetched 9063 kB in 5s (1659 kB/s) 156s Reading package lists... 162s Reading package lists... 163s Building dependency tree... 163s Reading state information... 165s Calculating upgrade... 166s The following packages will be REMOVED: 166s libssl3 166s The following NEW packages will be installed: 166s libssl3t64 166s The following packages have been kept back: 166s curl 166s The following packages will be upgraded: 166s openssl 166s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 166s Need to get 2753 kB of archives. 166s After this operation, 72.7 kB of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 166s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 168s Fetched 2753 kB in 1s (3795 kB/s) 168s (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 ... 75850 files and directories currently installed.) 168s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 168s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 168s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 168s wget depends on libssl3 (>= 3.0.0). 168s u-boot-tools depends on libssl3 (>= 3.0.0). 168s tnftp depends on libssl3 (>= 3.0.0). 168s tcpdump depends on libssl3 (>= 3.0.0). 168s systemd-resolved depends on libssl3 (>= 3.0.0). 168s systemd depends on libssl3 (>= 3.0.0). 168s sudo depends on libssl3 (>= 3.0.0). 168s sbsigntool depends on libssl3 (>= 3.0.0). 168s rsync depends on libssl3 (>= 3.0.0). 168s python3-cryptography depends on libssl3 (>= 3.0.0). 168s openssh-server depends on libssl3 (>= 3.0.10). 168s openssh-client depends on libssl3 (>= 3.0.10). 168s mtd-utils depends on libssl3 (>= 3.0.0). 168s mokutil depends on libssl3 (>= 3.0.0). 168s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 168s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 168s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 168s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 168s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 168s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 168s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 168s libnvme1 depends on libssl3 (>= 3.0.0). 168s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 168s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 168s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 168s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 168s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 168s kmod depends on libssl3 (>= 3.0.0). 168s dhcpcd-base depends on libssl3 (>= 3.0.0). 168s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 168s 169s (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 ... 75850 files and directories currently installed.) 169s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 169s Selecting previously unselected package libssl3t64:arm64. 169s (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 ... 75839 files and directories currently installed.) 169s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 169s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 169s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 169s Setting up openssl (3.0.13-0ubuntu1) ... 169s Processing triggers for man-db (2.12.0-3) ... 170s Processing triggers for libc-bin (2.39-0ubuntu2) ... 171s Reading package lists... 172s Building dependency tree... 172s Reading state information... 174s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 174s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 174s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 175s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 175s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 181s Reading package lists... 181s Reading package lists... 182s Building dependency tree... 182s Reading state information... 184s Calculating upgrade... 185s The following packages have been kept back: 185s curl 185s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 185s Reading package lists... 186s Building dependency tree... 186s Reading state information... 188s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 192s autopkgtest [17:11:32]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 192s autopkgtest [17:11:32]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled 195s Get:1 http://ftpmaster.internal/ubuntu noble/universe uncalled 2.3+ds-1build1 (dsc) [2169 B] 195s Get:2 http://ftpmaster.internal/ubuntu noble/universe uncalled 2.3+ds-1build1 (tar) [155 kB] 195s Get:3 http://ftpmaster.internal/ubuntu noble/universe uncalled 2.3+ds-1build1 (diff) [4964 B] 195s gpgv: Signature made Thu Nov 2 09:23:48 2023 UTC 195s gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 195s gpgv: issuer "doko@ubuntu.com" 195s gpgv: Can't check signature: No public key 195s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-1build1.dsc: no acceptable signature found 196s autopkgtest [17:11:36]: testing package uncalled version 2.3+ds-1build1 196s autopkgtest [17:11:36]: build not needed 197s autopkgtest [17:11:37]: test run-unit-test: preparing testbed 199s Reading package lists... 200s Building dependency tree... 200s Reading state information... 201s Starting pkgProblemResolver with broken count: 0 201s Starting 2 pkgProblemResolver with broken count: 0 201s Done 203s The following additional packages will be installed: 203s libaec0 libblas3 libgfortran5 libhdf5-103-1 liblapack3 libsz2 python3-numpy 203s uncalled 203s Suggested packages: 203s gcc gfortran python3-dev python3-pytest 204s The following NEW packages will be installed: 204s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1 liblapack3 204s libsz2 python3-numpy uncalled 204s 0 upgraded, 9 newly installed, 0 to remove and 1 not upgraded. 204s Need to get 9282 kB/9282 kB of archives. 204s After this operation, 42.4 MB of additional disk space will be used. 204s Get:1 /tmp/autopkgtest.DzUxsl/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 204s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 205s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 205s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 205s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 205s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 205s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 205s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 205s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 uncalled arm64 2.3+ds-1build1 [713 kB] 207s Fetched 9282 kB in 1s (7264 kB/s) 207s Selecting previously unselected package libaec0:arm64. 207s (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 ... 75852 files and directories currently installed.) 207s Preparing to unpack .../0-libaec0_1.1.2-1_arm64.deb ... 207s Unpacking libaec0:arm64 (1.1.2-1) ... 207s Selecting previously unselected package libblas3:arm64. 207s Preparing to unpack .../1-libblas3_3.12.0-3_arm64.deb ... 207s Unpacking libblas3:arm64 (3.12.0-3) ... 207s Selecting previously unselected package libgfortran5:arm64. 207s Preparing to unpack .../2-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 207s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 207s Selecting previously unselected package libsz2:arm64. 207s Preparing to unpack .../3-libsz2_1.1.2-1_arm64.deb ... 207s Unpacking libsz2:arm64 (1.1.2-1) ... 207s Selecting previously unselected package libhdf5-103-1:arm64. 207s Preparing to unpack .../4-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 207s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 207s Selecting previously unselected package liblapack3:arm64. 208s Preparing to unpack .../5-liblapack3_3.12.0-3_arm64.deb ... 208s Unpacking liblapack3:arm64 (3.12.0-3) ... 208s Selecting previously unselected package python3-numpy. 208s Preparing to unpack .../6-python3-numpy_1%3a1.24.2-2_arm64.deb ... 208s Unpacking python3-numpy (1:1.24.2-2) ... 209s Selecting previously unselected package uncalled. 209s Preparing to unpack .../7-uncalled_2.3+ds-1build1_arm64.deb ... 209s Unpacking uncalled (2.3+ds-1build1) ... 209s Selecting previously unselected package autopkgtest-satdep. 209s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 209s Unpacking autopkgtest-satdep (0) ... 209s Setting up libaec0:arm64 (1.1.2-1) ... 209s Setting up libblas3:arm64 (3.12.0-3) ... 209s 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 209s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 209s Setting up libsz2:arm64 (1.1.2-1) ... 209s Setting up liblapack3:arm64 (3.12.0-3) ... 209s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 209s Setting up python3-numpy (1:1.24.2-2) ... 217s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 217s Setting up uncalled (2.3+ds-1build1) ... 218s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' 218s CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") 218s Setting up autopkgtest-satdep (0) ... 218s Processing triggers for man-db (2.12.0-3) ... 218s Processing triggers for libc-bin (2.39-0ubuntu2) ... 227s (Reading database ... 76934 files and directories currently installed.) 227s Removing autopkgtest-satdep (0) ... 228s autopkgtest [17:12:08]: test run-unit-test: [----------------------- 228s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 228s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 228s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 228s port_re = re.compile("grpc_port = (\d+)") 228s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 228s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 229s [bwa_index] Pack FASTA... 0.00 sec 229s [bwa_index] Construct BWT for the packed sequence... 229s [bwa_index] 0.00 seconds elapse. 229s [bwa_index] Update BWT... 0.00 sec 229s [bwa_index] Pack forward-only FASTA... 0.00 sec 229s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 229s Initializing parameter search 229s Computing default parameters 229s Writing default parameters 229s Done 230s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 230s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 230s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 230s port_re = re.compile("grpc_port = (\d+)") 230s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 230s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 230s Loading fast5s 230s Mapping 230s Finishing 230s f41a60f7-de4a-4b17-9f54-387e52d60b65 106 73 106 - Escherichia_coli_chromosome:2400000-2410000 10000 6938 6976 38 39 255 ch:i:486 st:i:257117 mt:f:28.017185 231s autopkgtest [17:12:11]: test run-unit-test: -----------------------] 231s autopkgtest [17:12:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 231s run-unit-test PASS 232s autopkgtest [17:12:12]: @@@@@@@@@@@@@@@@@@@@ summary 232s run-unit-test PASS 250s Creating nova instance adt-noble-arm64-uncalled-20240316-170820-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...