0s autopkgtest [18:11:56]: starting date and time: 2025-03-15 18:11:56+0000 0s autopkgtest [18:11:56]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:11:56]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.992oixst/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade uncalled --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.227 lxd-armhf-10.145.243.227:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [18:12:16]: testbed dpkg architecture: armhf 22s autopkgtest [18:12:18]: testbed apt version: 2.9.33 26s autopkgtest [18:12:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 27s autopkgtest [18:12:23]: testbed release detected to be: None 35s autopkgtest [18:12:31]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 37s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 38s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 38s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 38s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 38s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 38s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 38s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 38s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 39s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 39s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 39s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 39s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 40s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 62s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 62s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 64s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 64s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 64s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 79s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 81s Fetched 41.0 MB in 44s (936 kB/s) 82s Reading package lists... 88s autopkgtest [18:13:24]: upgrading testbed (apt dist-upgrade and autopurge) 89s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 90s Starting 2 pkgProblemResolver with broken count: 0 90s Done 91s Entering ResolveByKeep 91s 91s Calculating upgrade... 92s The following packages will be upgraded: 92s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 92s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Need to get 8683 kB of archives. 92s After this operation, 23.6 kB of additional disk space will be used. 92s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 94s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 95s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 98s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 99s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 99s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 99s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 100s Preconfiguring packages ... 100s Fetched 8683 kB in 8s (1112 kB/s) 100s (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 ... 64655 files and directories currently installed.) 100s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 100s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 100s Setting up libc6:armhf (2.41-1ubuntu2) ... 101s (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 ... 64655 files and directories currently installed.) 101s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 101s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 101s Setting up libc-bin (2.41-1ubuntu2) ... 101s (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 ... 64655 files and directories currently installed.) 101s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 101s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 101s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 101s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 101s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 101s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 101s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 101s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 101s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 102s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 102s Setting up sos (4.9.0-5) ... 102s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 102s Setting up locales (2.41-1ubuntu2) ... 103s Generating locales (this might take a while)... 105s en_US.UTF-8... done 105s Generation complete. 105s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 105s Setting up strace (6.13+ds-1ubuntu1) ... 105s Processing triggers for man-db (2.13.0-1) ... 106s Processing triggers for systemd (257.3-1ubuntu3) ... 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Starting pkgProblemResolver with broken count: 0 109s Starting 2 pkgProblemResolver with broken count: 0 109s Done 109s Solving dependencies... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [18:13:48]: rebooting testbed after setup commands that affected boot 152s autopkgtest [18:14:28]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 177s autopkgtest [18:14:53]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled 188s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-3build2 (dsc) [2141 B] 188s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-3build2 (tar) [155 kB] 188s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-3build2 (diff) [6012 B] 188s gpgv: Signature made Tue Mar 4 16:32:02 2025 UTC 188s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 188s gpgv: Can't check signature: No public key 188s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-3build2.dsc: no acceptable signature found 188s autopkgtest [18:15:04]: testing package uncalled version 2.3+ds-3build2 190s autopkgtest [18:15:06]: build not needed 192s autopkgtest [18:15:08]: test run-unit-test: preparing testbed 194s Reading package lists... 195s Building dependency tree... 195s Reading state information... 195s Starting pkgProblemResolver with broken count: 0 195s Starting 2 pkgProblemResolver with broken count: 0 195s Done 196s The following NEW packages will be installed: 196s libaec0 libblas3 libgfortran5 libhdf5-310 liblapack3 libsz2 python3-numpy 196s python3-numpy-dev uncalled 196s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 196s Need to get 8474 kB of archives. 196s After this operation, 28.9 MB of additional disk space will be used. 196s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy-dev armhf 1:2.2.3+ds-5 [141 kB] 196s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 196s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 197s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 199s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:2.2.3+ds-5 [3725 kB] 203s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 203s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 203s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-310 armhf 1.14.5+repack-3 [1410 kB] 204s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf uncalled armhf 2.3+ds-3build2 [618 kB] 205s Fetched 8474 kB in 9s (927 kB/s) 205s Selecting previously unselected package python3-numpy-dev:armhf. 205s (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 ... 64655 files and directories currently installed.) 205s Preparing to unpack .../0-python3-numpy-dev_1%3a2.2.3+ds-5_armhf.deb ... 205s Unpacking python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 205s Selecting previously unselected package libblas3:armhf. 205s Preparing to unpack .../1-libblas3_3.12.1-2_armhf.deb ... 205s Unpacking libblas3:armhf (3.12.1-2) ... 205s Selecting previously unselected package libgfortran5:armhf. 205s Preparing to unpack .../2-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 205s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 205s Selecting previously unselected package liblapack3:armhf. 205s Preparing to unpack .../3-liblapack3_3.12.1-2_armhf.deb ... 205s Unpacking liblapack3:armhf (3.12.1-2) ... 205s Selecting previously unselected package python3-numpy. 205s Preparing to unpack .../4-python3-numpy_1%3a2.2.3+ds-5_armhf.deb ... 206s Unpacking python3-numpy (1:2.2.3+ds-5) ... 206s Selecting previously unselected package libaec0:armhf. 206s Preparing to unpack .../5-libaec0_1.1.3-1_armhf.deb ... 206s Unpacking libaec0:armhf (1.1.3-1) ... 206s Selecting previously unselected package libsz2:armhf. 206s Preparing to unpack .../6-libsz2_1.1.3-1_armhf.deb ... 206s Unpacking libsz2:armhf (1.1.3-1) ... 206s Selecting previously unselected package libhdf5-310:armhf. 206s Preparing to unpack .../7-libhdf5-310_1.14.5+repack-3_armhf.deb ... 206s Unpacking libhdf5-310:armhf (1.14.5+repack-3) ... 206s Selecting previously unselected package uncalled. 206s Preparing to unpack .../8-uncalled_2.3+ds-3build2_armhf.deb ... 206s Unpacking uncalled (2.3+ds-3build2) ... 206s Setting up libaec0:armhf (1.1.3-1) ... 206s Setting up libblas3:armhf (3.12.1-2) ... 206s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 206s Setting up python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 206s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 206s Setting up libsz2:armhf (1.1.3-1) ... 206s Setting up liblapack3:armhf (3.12.1-2) ... 206s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 206s Setting up python3-numpy (1:2.2.3+ds-5) ... 208s Setting up libhdf5-310:armhf (1.14.5+repack-3) ... 208s Setting up uncalled (2.3+ds-3build2) ... 208s Processing triggers for libc-bin (2.41-1ubuntu2) ... 208s Processing triggers for man-db (2.13.0-1) ... 220s autopkgtest [18:15:36]: test run-unit-test: [----------------------- 222s [bwa_index] Pack FASTA... 0.00 sec 222s [bwa_index] Construct BWT for the packed sequence... 222s [bwa_index] 0.00 seconds elapse. 222s [bwa_index] Update BWT... 0.00 sec 222s [bwa_index] Pack forward-only FASTA... 0.00 sec 222s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 222s Initializing parameter search 223s Computing default parameters 223s Writing default parameters 223s Done 223s Loading fast5s 223s Mapping 223s Finishing 223s 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:14.199282 223s autopkgtest [18:15:39]: test run-unit-test: -----------------------] 227s autopkgtest [18:15:43]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 227s run-unit-test PASS 231s autopkgtest [18:15:47]: @@@@@@@@@@@@@@@@@@@@ summary 231s run-unit-test PASS