0s autopkgtest [15:09:51]: starting date and time: 2025-03-15 15:09:51+0000 0s autopkgtest [15:09:51]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:09:51]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.79yuekjm/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 parsnp --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.160 lxd-armhf-10.145.243.160:autopkgtest/ubuntu/plucky/armhf 22s autopkgtest [15:10:13]: testbed dpkg architecture: armhf 24s autopkgtest [15:10:15]: testbed apt version: 2.9.33 28s autopkgtest [15:10:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [15:10:21]: testbed release detected to be: None 38s autopkgtest [15:10:29]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 40s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 40s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 41s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 41s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 42s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 42s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 42s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 42s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 43s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 44s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 66s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 67s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 67s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 67s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 83s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 85s Fetched 41.0 MB in 45s (903 kB/s) 86s Reading package lists... 92s autopkgtest [15:11:23]: upgrading testbed (apt dist-upgrade and autopurge) 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 95s Starting 2 pkgProblemResolver with broken count: 0 95s Done 95s Entering ResolveByKeep 96s 96s Calculating upgrade... 96s The following packages will be upgraded: 96s libc-bin libc6 locales python3-jinja2 sos strace 97s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 8642 kB of archives. 97s After this operation, 23.6 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 100s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 101s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 106s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 106s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 106s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 108s Preconfiguring packages ... 108s Fetched 8642 kB in 10s (835 kB/s) 108s (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.) 108s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 108s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 108s Setting up libc6:armhf (2.41-1ubuntu2) ... 108s (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.) 108s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 108s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 108s Setting up libc-bin (2.41-1ubuntu2) ... 108s (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.) 108s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 108s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 109s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 109s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 109s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 109s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 109s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 109s Setting up sos (4.9.0-5) ... 110s Setting up locales (2.41-1ubuntu2) ... 110s Generating locales (this might take a while)... 112s en_US.UTF-8... done 112s Generation complete. 112s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 113s Setting up strace (6.13+ds-1ubuntu1) ... 113s Processing triggers for man-db (2.13.0-1) ... 114s Processing triggers for systemd (257.3-1ubuntu3) ... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 117s Solving dependencies... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [15:11:51]: rebooting testbed after setup commands that affected boot 164s autopkgtest [15:12:35]: 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 188s autopkgtest [15:12:59]: @@@@@@@@@@@@@@@@@@@@ apt-source parsnp 198s Get:1 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.6+dfsg-1ubuntu1 (dsc) [2221 B] 198s Get:2 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.6+dfsg-1ubuntu1 (tar) [142 kB] 198s Get:3 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.6+dfsg-1ubuntu1 (diff) [10.5 kB] 199s gpgv: Signature made Thu Feb 20 04:03:51 2025 UTC 199s gpgv: using RSA key 5C7ABEA20F8630459CC8C8B5E27F2CF8458C2FA4 199s gpgv: Can't check signature: No public key 199s dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.6+dfsg-1ubuntu1.dsc: no acceptable signature found 199s autopkgtest [15:13:10]: testing package parsnp version 2.0.6+dfsg-1ubuntu1 201s autopkgtest [15:13:12]: build not needed 204s autopkgtest [15:13:15]: test run-unit-test: preparing testbed 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 206s Starting pkgProblemResolver with broken count: 0 206s Starting 2 pkgProblemResolver with broken count: 0 207s Done 207s The following NEW packages will be installed: 207s fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono 207s fonts-urw-base35 harvest-tools libblas3 libcairo2 libcapnp-1.1.0 libdeflate0 207s libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 207s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 207s liblcms2-2 liblerc4 libmuscle1 libopenjp2-7 libpixman-1-0 libprotobuf32t64 207s libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 libwebp7 libwebpdemux2 207s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mummer parsnp phipack 207s python3-biopython python3-cairo python3-freetype python3-numpy 207s python3-numpy-dev python3-pil python3-pyspoa python3-reportlab 207s python3-rlpycairo python3-tqdm raxml sgml-base w3c-sgml-lib x11-common 207s xfonts-encodings xfonts-utils xml-core 207s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 207s Need to get 31.2 MB of archives. 207s After this operation, 90.7 MB of additional disk space will be used. 207s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy-dev armhf 1:2.2.3+ds-5 [141 kB] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 208s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 208s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 210s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:2.2.3+ds-5 [3725 kB] 214s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 214s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 214s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 215s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 215s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 215s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 215s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 216s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 216s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 225s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 225s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf libcapnp-1.1.0 armhf 1.1.0-2 [1456 kB] 226s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libprotobuf32t64 armhf 3.21.12-10build2 [912 kB] 227s Get:18 http://ftpmaster.internal/ubuntu plucky/universe armhf harvest-tools armhf 1.3-8build6 [136 kB] 227s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 227s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 227s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 227s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 227s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 227s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 227s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 227s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 227s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 227s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 228s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 228s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 228s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 228s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 228s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 228s Get:34 http://ftpmaster.internal/ubuntu plucky/universe armhf libmuscle1 armhf 3.7+4565-8 [228 kB] 228s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.2-1 [12.4 kB] 228s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 228s Get:37 http://ftpmaster.internal/ubuntu plucky/universe armhf libspoa7.0.0 armhf 4.1.4-2 [67.2 kB] 229s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 229s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 229s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 229s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 229s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 229s Get:43 http://ftpmaster.internal/ubuntu plucky/universe armhf mummer armhf 3.23+dfsg-8 [678 kB] 230s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.3-2 [172 kB] 230s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 11.1.0-5build1 [435 kB] 230s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2build2 [114 kB] 230s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 230s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 230s Get:49 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.3.1-1 [1137 kB] 231s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 231s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 232s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.85+dfsg-2build1 [1692 kB] 233s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyspoa armhf 0.2.1-2build1 [62.7 kB] 233s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.1-2 [92.5 kB] 233s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf fasttree armhf 2.1.11-2 [162 kB] 234s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf phipack armhf 0.0.20160614-5 [45.9 kB] 234s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf raxml armhf 8.2.13+dfsg-2 [1006 kB] 235s Get:58 http://ftpmaster.internal/ubuntu plucky/universe armhf parsnp armhf 2.0.6+dfsg-1ubuntu1 [209 kB] 235s Fetched 31.2 MB in 27s (1141 kB/s) 235s Selecting previously unselected package python3-numpy-dev:armhf. 235s (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.) 235s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_armhf.deb ... 235s Unpacking python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 235s Selecting previously unselected package libblas3:armhf. 235s Preparing to unpack .../01-libblas3_3.12.1-2_armhf.deb ... 235s Unpacking libblas3:armhf (3.12.1-2) ... 235s Selecting previously unselected package libgfortran5:armhf. 235s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 235s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 235s Selecting previously unselected package liblapack3:armhf. 235s Preparing to unpack .../03-liblapack3_3.12.1-2_armhf.deb ... 235s Unpacking liblapack3:armhf (3.12.1-2) ... 235s Selecting previously unselected package python3-numpy. 235s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_armhf.deb ... 236s Unpacking python3-numpy (1:2.2.3+ds-5) ... 236s Selecting previously unselected package sgml-base. 236s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 236s Unpacking sgml-base (1.31) ... 236s Selecting previously unselected package fonts-dejavu-mono. 236s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 236s Unpacking fonts-dejavu-mono (2.37-8) ... 236s Selecting previously unselected package fonts-dejavu-core. 236s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 236s Unpacking fonts-dejavu-core (2.37-8) ... 236s Selecting previously unselected package libfontenc1:armhf. 236s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 236s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 236s Selecting previously unselected package libfreetype6:armhf. 236s Preparing to unpack .../09-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 236s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 236s Selecting previously unselected package x11-common. 236s Preparing to unpack .../10-x11-common_1%3a7.7+23ubuntu3_all.deb ... 236s Unpacking x11-common (1:7.7+23ubuntu3) ... 236s Selecting previously unselected package xfonts-encodings. 236s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 236s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 236s Selecting previously unselected package xfonts-utils. 236s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7_armhf.deb ... 236s Unpacking xfonts-utils (1:7.7+7) ... 236s Selecting previously unselected package fonts-urw-base35. 236s Preparing to unpack .../13-fonts-urw-base35_20200910-8_all.deb ... 236s Unpacking fonts-urw-base35 (20200910-8) ... 236s Selecting previously unselected package fontconfig-config. 236s Preparing to unpack .../14-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 237s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 237s Selecting previously unselected package libcapnp-1.1.0:armhf. 237s Preparing to unpack .../15-libcapnp-1.1.0_1.1.0-2_armhf.deb ... 237s Unpacking libcapnp-1.1.0:armhf (1.1.0-2) ... 237s Selecting previously unselected package libprotobuf32t64:armhf. 237s Preparing to unpack .../16-libprotobuf32t64_3.21.12-10build2_armhf.deb ... 237s Unpacking libprotobuf32t64:armhf (3.21.12-10build2) ... 237s Selecting previously unselected package harvest-tools. 237s Preparing to unpack .../17-harvest-tools_1.3-8build6_armhf.deb ... 237s Unpacking harvest-tools (1.3-8build6) ... 237s Selecting previously unselected package libfontconfig1:armhf. 237s Preparing to unpack .../18-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 237s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 237s Selecting previously unselected package libpixman-1-0:armhf. 237s Preparing to unpack .../19-libpixman-1-0_0.44.0-3_armhf.deb ... 237s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 237s Selecting previously unselected package libxcb-render0:armhf. 237s Preparing to unpack .../20-libxcb-render0_1.17.0-2_armhf.deb ... 237s Unpacking libxcb-render0:armhf (1.17.0-2) ... 237s Selecting previously unselected package libxcb-shm0:armhf. 237s Preparing to unpack .../21-libxcb-shm0_1.17.0-2_armhf.deb ... 237s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 237s Selecting previously unselected package libxrender1:armhf. 237s Preparing to unpack .../22-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 237s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 237s Selecting previously unselected package libcairo2:armhf. 237s Preparing to unpack .../23-libcairo2_1.18.2-2_armhf.deb ... 237s Unpacking libcairo2:armhf (1.18.2-2) ... 237s Selecting previously unselected package libdeflate0:armhf. 237s Preparing to unpack .../24-libdeflate0_1.23-1_armhf.deb ... 237s Unpacking libdeflate0:armhf (1.23-1) ... 237s Selecting previously unselected package libgomp1:armhf. 237s Preparing to unpack .../25-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 237s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 237s Selecting previously unselected package libgraphite2-3:armhf. 237s Preparing to unpack .../26-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 237s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 237s Selecting previously unselected package libharfbuzz0b:armhf. 237s Preparing to unpack .../27-libharfbuzz0b_10.2.0-1_armhf.deb ... 237s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 237s Selecting previously unselected package libimagequant0:armhf. 237s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_armhf.deb ... 237s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 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... 239s 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 239s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 239s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 239s Setting up libimagequant0:armhf (2.18.0-1build1) ... 239s Setting up fonts-dejavu-mono (2.37-8) ... 239s Setting up libspoa7.0.0:armhf (4.1.4-2) ... 239s Setting up python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 239s Setting up fonts-dejavu-core (2.37-8) ... 239s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 239s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 239s Setting up libwebp7:armhf (1.5.0-0.1) ... 239s Setting up mummer (3.23+dfsg-8) ... 239s Setting up libopenjp2-7:armhf (2.5.3-2) ... 239s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 239s Setting up phipack (0.0.20160614-5) ... 239s Setting up fasttree (2.1.11-2) ... 239s Setting up sgml-base (1.31) ... 239s Setting up libcapnp-1.1.0:armhf (1.1.0-2) ... 239s Setting up harvest-tools (1.3-8build6) ... 239s Setting up libwebpmux3:armhf (1.5.0-0.1) ... 239s Setting up raxml (8.2.13+dfsg-2) ... 239s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 239s Setting up python3-pyspoa (0.2.1-2build1) ... 239s Setting up liblapack3:armhf (3.12.1-2) ... 239s 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 239s Setting up libmuscle1 (3.7+4565-8) ... 239s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 239s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 239s Setting up python3-freetype (2.5.1-1) ... 240s Setting up xfonts-utils (1:7.7+7) ... 240s Setting up libraqm0:armhf (0.10.2-1) ... 240s Setting up python3-numpy (1:2.2.3+ds-5) ... 242s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 242s Setting up xml-core (0.19) ... 242s Setting up libfontconfig1:armhf (2.15.0-2ubuntu1) ... 242s Setting up fonts-urw-base35 (20200910-8) ... 242s Setting up libcairo2:armhf (1.18.2-2) ... 242s Setting up python3-pil:armhf (11.1.0-5build1) ... 242s Setting up python3-cairo (1.26.1-2build2) ... 242s Setting up python3-rlpycairo (0.3.0-3) ... 243s Setting up python3-reportlab (4.3.1-1) ... 243s Processing triggers for libc-bin (2.41-1ubuntu2) ... 243s Processing triggers for man-db (2.13.0-1) ... 244s Processing triggers for sgml-base (1.31) ... 244s Setting up w3c-sgml-lib (1.3-3) ... 272s Setting up python3-biopython (1.85+dfsg-2build1) ... 273s Setting up parsnp (2.0.6+dfsg-1ubuntu1) ... 282s autopkgtest [15:14:33]: test run-unit-test: [----------------------- 284s Test 1: With GenBank Annotations 284s 15:14:35 - INFO - |--Parsnp 2.0.6--| 284s 284s 15:14:35 - INFO - 284s ********************************************************************************** 284s SETTINGS: 284s |-refgenome: mers_virus/ref/England1.gbk 284s |-genomes: 284s mers_virus/genomes/Al-Hasa_12_2013.fna 284s mers_virus/genomes/Al-Hasa_15_2013.fna 284s ...42 more file(s)... 284s mers_virus/genomes/Taif_1_2013.fna 284s mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna 284s |-aligner: muscle 284s |-outdir: /tmp/autopkgtest.maMEAh/autopkgtest_tmp/P_2025_03_15_151435466218 284s |-OS: Linux 284s |-threads: 1 284s ********************************************************************************** 284s 284s 15:14:35 - INFO - <> 284s 15:14:35 - INFO - Too few genomes to run partitions of size >50. Running all genomes at once. 284s 15:14:35 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 285s 15:14:36 - INFO - Reconstructing core genome phylogeny... 290s 15:14:41 - INFO - Aligned 47 genomes in 6.17 seconds 290s 15:14:41 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.maMEAh/autopkgtest_tmp/P_2025_03_15_151435466218 290s Passed 290s 290s Test 2: Without GenBank Annotations 290s 15:14:41 - INFO - |--Parsnp 2.0.6--| 290s 290s 15:14:41 - INFO - 290s ********************************************************************************** 290s SETTINGS: 290s |-refgenome: mers_virus/ref/England1.fna 290s |-genomes: 290s mers_virus/genomes/Al-Hasa_12_2013.fna 290s mers_virus/genomes/Al-Hasa_15_2013.fna 290s ...42 more file(s)... 290s mers_virus/genomes/Taif_1_2013.fna 290s mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna 290s |-aligner: muscle 290s |-outdir: /tmp/autopkgtest.maMEAh/autopkgtest_tmp/P_2025_03_15_151441922387 290s |-OS: Linux 290s |-threads: 1 290s ********************************************************************************** 290s 290s 15:14:41 - INFO - <> 290s 15:14:41 - INFO - No genbank file provided for reference annotations, skipping.. 290s 15:14:41 - INFO - Too few genomes to run partitions of size >50. Running all genomes at once. 290s 15:14:41 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 291s 15:14:42 - INFO - Reconstructing core genome phylogeny... 296s 15:14:47 - INFO - Aligned 47 genomes in 6.03 seconds 296s 15:14:47 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.maMEAh/autopkgtest_tmp/P_2025_03_15_151441922387 297s Passed 297s 297s autopkgtest [15:14:48]: test run-unit-test: -----------------------] 301s autopkgtest [15:14:52]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 301s run-unit-test PASS 305s autopkgtest [15:14:56]: @@@@@@@@@@@@@@@@@@@@ summary 305s run-unit-test PASS