0s autopkgtest [01:23:14]: starting date and time: 2024-03-23 01:23:14+0000 0s autopkgtest [01:23:14]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [01:23:14]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lwzyge2x/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:harvest-tools,src:protobuf --apt-upgrade parsnp --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=harvest-tools/1.3-8build4 protobuf/3.21.12-8.2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-22.secgroup --name adt-noble-s390x-parsnp-20240323-012314-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-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/ 90s autopkgtest [01:24:44]: testbed dpkg architecture: s390x 91s autopkgtest [01:24:45]: testbed apt version: 2.7.12 91s autopkgtest [01:24:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 92s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 92s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 93s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 94s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3979 kB] 99s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 99s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [665 kB] 100s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 100s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 100s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 100s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4162 kB] 103s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 103s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.5 kB] 103s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 105s Fetched 9545 kB in 13s (751 kB/s) 105s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Unknown architecture, assuming PC-style ttyS0 109s sh: Attempting to set up Debian/Ubuntu apt sources automatically 109s sh: Distribution appears to be Ubuntu 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s eatmydata is already the newest version (131-1). 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s dbus is already the newest version (1.14.10-4ubuntu1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s rng-tools-debian is already the newest version (2.4). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s The following packages will be REMOVED: 111s cloud-init* python3-configobj* python3-debconf* 111s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 111s After this operation, 3256 kB disk space will be freed. 111s (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 ... 52170 files and directories currently installed.) 111s Removing cloud-init (24.1.2-0ubuntu1) ... 112s Removing python3-configobj (5.0.8-3) ... 112s Removing python3-debconf (1.5.86) ... 112s Processing triggers for man-db (2.12.0-3) ... 112s (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 ... 51781 files and directories currently installed.) 112s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 113s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 113s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 113s invoke-rc.d: policy-rc.d denied execution of try-restart. 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s linux-generic is already the newest version (6.8.0-11.11+1). 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 114s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 114s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 116s Reading package lists... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Calculating upgrade... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s autopkgtest [01:25:11]: rebooting testbed after setup commands that affected boot 139s autopkgtest [01:25:33]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 142s autopkgtest [01:25:36]: @@@@@@@@@@@@@@@@@@@@ apt-source parsnp 144s Get:1 http://ftpmaster.internal/ubuntu noble/universe parsnp 2.0.3+dfsg-1 (dsc) [2245 B] 144s Get:2 http://ftpmaster.internal/ubuntu noble/universe parsnp 2.0.3+dfsg-1 (tar) [141 kB] 144s Get:3 http://ftpmaster.internal/ubuntu noble/universe parsnp 2.0.3+dfsg-1 (diff) [10.0 kB] 144s gpgv: Signature made Tue Jan 30 19:56:28 2024 UTC 144s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 144s gpgv: issuer "emollier@debian.org" 144s gpgv: Can't check signature: No public key 144s dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.3+dfsg-1.dsc: no acceptable signature found 144s autopkgtest [01:25:38]: testing package parsnp version 2.0.3+dfsg-1 144s autopkgtest [01:25:38]: build not needed 145s autopkgtest [01:25:39]: test run-unit-test: preparing testbed 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Starting pkgProblemResolver with broken count: 0 147s Starting 2 pkgProblemResolver with broken count: 0 147s Done 147s The following additional packages will be installed: 147s fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-extra 147s fonts-dejavu-mono fonts-urw-base35 harvest-tools libblas3 libcairo2 147s libcapnp-1.0.1 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 147s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 147s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 libmuscle1 libopenjp2-7 147s libpixman-1-0 libprotobuf32 libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 147s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 147s mummer parsnp phipack python3-biopython python3-cairo python3-freetype 147s python3-numpy python3-pil python3-pyspoa python3-reportlab python3-rlpycairo 147s python3-tqdm raxml sgml-base w3c-sgml-lib x11-common xfonts-encodings 147s xfonts-utils xml-core 147s Suggested packages: 147s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 147s python3-tk bwa clustalo clustalw dialign dssp emboss mafft muscle3 phylip 147s phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 147s python3-rdflib python3-psycopg2 python3-scipy samtools t-coffee wise gcc 147s gfortran python3-dev python3-pytest python-pil-doc pdf-viewer 147s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 147s sgml-base-doc debhelper 147s Recommended packages: 147s python3-dendropy python-biopython-doc ncbi-blast+ python3-olefile 147s The following NEW packages will be installed: 147s autopkgtest-satdep fasttree fontconfig-config fonts-dejavu-core 147s fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 harvest-tools libblas3 147s libcairo2 libcapnp-1.0.1 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 147s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 147s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 libmuscle1 libopenjp2-7 147s libpixman-1-0 libprotobuf32 libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 147s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 147s mummer parsnp phipack python3-biopython python3-cairo python3-freetype 147s python3-numpy python3-pil python3-pyspoa python3-reportlab python3-rlpycairo 147s python3-tqdm raxml sgml-base w3c-sgml-lib x11-common xfonts-encodings 147s xfonts-utils xml-core 147s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 147s Need to get 36.5 MB/36.5 MB of archives. 147s After this operation, 119 MB of additional disk space will be used. 147s Get:1 /tmp/autopkgtest.xxMLf7/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 148s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x sgml-base all 1.31 [11.4 kB] 148s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 148s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 149s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libfontenc1 s390x 1:1.1.8-1 [14.8 kB] 149s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 150s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] 150s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 150s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-utils s390x 1:7.7+6build2 [94.8 kB] 150s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 152s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 152s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-extra all 2.37-8 [1947 kB] 152s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x libcapnp-1.0.1 s390x 1.0.1-3 [1405 kB] 153s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libprotobuf32 s390x 3.21.12-8ubuntu5 [954 kB] 153s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x harvest-tools s390x 1.3-8build3 [129 kB] 153s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 153s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 153s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 153s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 153s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 153s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 153s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 153s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 153s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 153s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 153s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 153s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 153s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libimagequant0 s390x 2.18.0-1 [42.9 kB] 153s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 153s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 153s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 153s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB] 153s Get:33 http://ftpmaster.internal/ubuntu noble/universe s390x libmuscle1 s390x 3.7+4565-7ubuntu1 [253 kB] 153s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libraqm0 s390x 0.10.1-1 [14.4 kB] 153s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 153s Get:36 http://ftpmaster.internal/ubuntu noble/universe s390x libspoa7.0.0 s390x 4.0.8-1 [61.5 kB] 153s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 153s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 153s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 153s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libwebpdemux2 s390x 1.3.2-0.4 [12.4 kB] 153s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libwebpmux3 s390x 1.3.2-0.4 [25.4 kB] 153s Get:42 http://ftpmaster.internal/ubuntu noble/universe s390x mummer s390x 3.23+dfsg-8 [674 kB] 153s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB] 154s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libopenjp2-7 s390x 2.5.0-2 [169 kB] 154s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x python3-pil s390x 10.2.0-1 [519 kB] 154s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x python3-cairo s390x 1.25.1-2 [150 kB] 154s Get:47 http://ftpmaster.internal/ubuntu noble/universe s390x python3-freetype all 2.4.0-1 [83.1 kB] 154s Get:48 http://ftpmaster.internal/ubuntu noble/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 154s Get:49 http://ftpmaster.internal/ubuntu noble/universe s390x python3-reportlab all 4.1.0-1 [683 kB] 154s Get:50 http://ftpmaster.internal/ubuntu noble/main s390x xml-core all 0.19 [20.3 kB] 154s Get:51 http://ftpmaster.internal/ubuntu noble/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 154s Get:52 http://ftpmaster.internal/ubuntu noble/universe s390x python3-biopython s390x 1.81+dfsg-3 [2234 kB] 154s Get:53 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pyspoa s390x 0.0.10-1build1 [87.2 kB] 154s Get:54 http://ftpmaster.internal/ubuntu noble/universe s390x python3-tqdm all 4.64.1-2 [95.2 kB] 154s Get:55 http://ftpmaster.internal/ubuntu noble/universe s390x fasttree s390x 2.1.11-2 [190 kB] 154s Get:56 http://ftpmaster.internal/ubuntu noble/universe s390x phipack s390x 0.0.20160614-5 [56.5 kB] 154s Get:57 http://ftpmaster.internal/ubuntu noble/universe s390x raxml s390x 8.2.13+dfsg-1 [1218 kB] 154s Get:58 http://ftpmaster.internal/ubuntu noble/universe s390x parsnp s390x 2.0.3+dfsg-1 [193 kB] 155s Fetched 36.5 MB in 7s (5279 kB/s) 155s Selecting previously unselected package sgml-base. 155s (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 ... 51726 files and directories currently installed.) 155s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 155s Unpacking sgml-base (1.31) ... 155s Selecting previously unselected package fonts-dejavu-mono. 155s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 155s Unpacking fonts-dejavu-mono (2.37-8) ... 155s Selecting previously unselected package fonts-dejavu-core. 155s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 155s Unpacking fonts-dejavu-core (2.37-8) ... 155s Selecting previously unselected package libfontenc1:s390x. 155s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1_s390x.deb ... 155s Unpacking libfontenc1:s390x (1:1.1.8-1) ... 155s Selecting previously unselected package libfreetype6:s390x. 155s Preparing to unpack .../04-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 155s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 155s Selecting previously unselected package x11-common. 155s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu2_all.deb ... 155s Unpacking x11-common (1:7.7+23ubuntu2) ... 155s Selecting previously unselected package xfonts-encodings. 155s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 155s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 155s Selecting previously unselected package xfonts-utils. 155s Preparing to unpack .../07-xfonts-utils_1%3a7.7+6build2_s390x.deb ... 155s Unpacking xfonts-utils (1:7.7+6build2) ... 155s Selecting previously unselected package fonts-urw-base35. 155s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 155s Unpacking fonts-urw-base35 (20200910-8) ... 155s Selecting previously unselected package fontconfig-config. 155s Preparing to unpack .../09-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 155s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 155s Selecting previously unselected package fonts-dejavu-extra. 155s Preparing to unpack .../10-fonts-dejavu-extra_2.37-8_all.deb ... 155s Unpacking fonts-dejavu-extra (2.37-8) ... 155s Selecting previously unselected package libcapnp-1.0.1:s390x. 155s Preparing to unpack .../11-libcapnp-1.0.1_1.0.1-3_s390x.deb ... 155s Unpacking libcapnp-1.0.1:s390x (1.0.1-3) ... 155s Selecting previously unselected package libprotobuf32:s390x. 155s Preparing to unpack .../12-libprotobuf32_3.21.12-8ubuntu5_s390x.deb ... 155s Unpacking libprotobuf32:s390x (3.21.12-8ubuntu5) ... 155s Selecting previously unselected package harvest-tools. 155s Preparing to unpack .../13-harvest-tools_1.3-8build3_s390x.deb ... 155s Unpacking harvest-tools (1.3-8build3) ... 155s Selecting previously unselected package libblas3:s390x. 155s Preparing to unpack .../14-libblas3_3.12.0-3_s390x.deb ... 155s Unpacking libblas3:s390x (3.12.0-3) ... 155s Selecting previously unselected package libfontconfig1:s390x. 155s Preparing to unpack .../15-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 155s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 155s Selecting previously unselected package libpixman-1-0:s390x. 155s Preparing to unpack .../16-libpixman-1-0_0.42.2-1_s390x.deb ... 155s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 155s Selecting previously unselected package libxcb-render0:s390x. 155s Preparing to unpack .../17-libxcb-render0_1.15-1_s390x.deb ... 155s Unpacking libxcb-render0:s390x (1.15-1) ... 155s Selecting previously unselected package libxcb-shm0:s390x. 155s Preparing to unpack .../18-libxcb-shm0_1.15-1_s390x.deb ... 155s Unpacking libxcb-shm0:s390x (1.15-1) ... 155s Selecting previously unselected package libxrender1:s390x. 155s Preparing to unpack .../19-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 155s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 155s Selecting previously unselected package libcairo2:s390x. 155s Preparing to unpack .../20-libcairo2_1.18.0-1_s390x.deb ... 155s Unpacking libcairo2:s390x (1.18.0-1) ... 155s Selecting previously unselected package libdeflate0:s390x. 155s Preparing to unpack .../21-libdeflate0_1.19-1_s390x.deb ... 155s Unpacking libdeflate0:s390x (1.19-1) ... 155s Selecting previously unselected package libgfortran5:s390x. 155s Preparing to unpack .../22-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 155s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 155s Selecting previously unselected package libgomp1:s390x. 155s Preparing to unpack .../23-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 155s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 155s Selecting previously unselected package libgraphite2-3:s390x. 155s Preparing to unpack .../24-libgraphite2-3_1.3.14-2_s390x.deb ... 155s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 156s Selecting previously unselected package libharfbuzz0b:s390x. 156s Preparing to unpack .../25-libharfbuzz0b_8.3.0-2_s390x.deb ... 156s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 156s Selecting previously unselected package libimagequant0:s390x. 156s Preparing to unpack .../26-libimagequant0_2.18.0-1_s390x.deb ... 156s Unpacking libimagequant0:s390x (2.18.0-1) ... 156s Selecting previously unselected package libjpeg-turbo8:s390x. 156s Preparing to unpack .../27-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 156s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 156s Selecting previously unselected package libjpeg8:s390x. 156s Preparing to unpack .../28-libjpeg8_8c-2ubuntu11_s390x.deb ... 156s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 156s Selecting previously unselected package liblapack3:s390x. 156s Preparing to unpack .../29-liblapack3_3.12.0-3_s390x.deb ... 156s Unpacking liblapack3:s390x (3.12.0-3) ... 156s Selecting previously unselected package liblcms2-2:s390x. 156s Preparing to unpack .../30-liblcms2-2_2.14-2_s390x.deb ... 156s Unpacking liblcms2-2:s390x (2.14-2) ... 156s Selecting previously unselected package libmuscle1. 156s Preparing to unpack .../31-libmuscle1_3.7+4565-7ubuntu1_s390x.deb ... 156s Unpacking libmuscle1 (3.7+4565-7ubuntu1) ... 156s Selecting previously unselected package libraqm0:s390x. 156s Preparing to unpack .../32-libraqm0_0.10.1-1_s390x.deb ... 156s Unpacking libraqm0:s390x (0.10.1-1) ... 156s Selecting previously unselected package libsharpyuv0:s390x. 156s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_s390x.deb ... 156s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ... 156s Selecting previously unselected package libspoa7.0.0:s390x. 156s Preparing to unpack .../34-libspoa7.0.0_4.0.8-1_s390x.deb ... 156s Unpacking libspoa7.0.0:s390x (4.0.8-1) ... 156s Selecting previously unselected package libjbig0:s390x. 156s Preparing to unpack .../35-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 156s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 156s Selecting previously unselected package libwebp7:s390x. 156s Preparing to unpack .../36-libwebp7_1.3.2-0.4_s390x.deb ... 156s Unpacking libwebp7:s390x (1.3.2-0.4) ... 156s Selecting previously unselected package libtiff6:s390x. 156s Preparing to unpack .../37-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ... 156s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 156s Selecting previously unselected package libwebpdemux2:s390x. 156s Preparing to unpack .../38-libwebpdemux2_1.3.2-0.4_s390x.deb ... 156s Unpacking libwebpdemux2:s390x (1.3.2-0.4) ... 156s Selecting previously unselected package libwebpmux3:s390x. 156s Preparing to unpack .../39-libwebpmux3_1.3.2-0.4_s390x.deb ... 156s Unpacking libwebpmux3:s390x (1.3.2-0.4) ... 156s Selecting previously unselected package mummer. 156s Preparing to unpack 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python3-pyspoa (0.0.10-1build1) ... 157s Selecting previously unselected package python3-tqdm. 157s Preparing to unpack .../52-python3-tqdm_4.64.1-2_all.deb ... 157s Unpacking python3-tqdm (4.64.1-2) ... 157s Selecting previously unselected package fasttree. 157s Preparing to unpack .../53-fasttree_2.1.11-2_s390x.deb ... 157s Unpacking fasttree (2.1.11-2) ... 157s Selecting previously unselected package phipack. 157s Preparing to unpack .../54-phipack_0.0.20160614-5_s390x.deb ... 157s Unpacking phipack (0.0.20160614-5) ... 157s Selecting previously unselected package raxml. 157s Preparing to unpack .../55-raxml_8.2.13+dfsg-1_s390x.deb ... 157s Unpacking raxml (8.2.13+dfsg-1) ... 157s Selecting previously unselected package parsnp. 157s Preparing to unpack .../56-parsnp_2.0.3+dfsg-1_s390x.deb ... 157s Unpacking parsnp (2.0.3+dfsg-1) ... 157s Selecting previously unselected package autopkgtest-satdep. 157s Preparing to unpack .../57-1-autopkgtest-satdep.deb ... 157s Unpacking autopkgtest-satdep (0) ... 157s Setting up libgraphite2-3:s390x (1.3.14-2) ... 157s Setting up liblcms2-2:s390x (2.14-2) ... 157s Setting up libpixman-1-0:s390x (0.42.2-1) ... 157s Setting up libsharpyuv0:s390x (1.3.2-0.4) ... 157s Setting up libxrender1:s390x (1:0.9.10-1.1) ... 157s Setting up libcapnp-1.0.1:s390x (1.0.1-3) ... 157s Setting up libxcb-render0:s390x (1.15-1) ... 157s Setting up python3-tqdm (4.64.1-2) ... 157s Setting up x11-common (1:7.7+23ubuntu2) ... 157s Setting up libdeflate0:s390x (1.19-1) ... 157s Setting up libxcb-shm0:s390x (1.15-1) ... 157s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 157s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ... 157s Setting up libfontenc1:s390x (1:1.1.8-1) ... 157s Setting up libblas3:s390x (3.12.0-3) ... 157s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 157s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 157s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 157s Setting up libimagequant0:s390x (2.18.0-1) ... 157s Setting up fonts-dejavu-mono (2.37-8) ... 157s Setting up libspoa7.0.0:s390x (4.0.8-1) ... 157s Setting up fonts-dejavu-core (2.37-8) ... 157s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 157s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 157s Setting up libwebp7:s390x (1.3.2-0.4) ... 157s Setting up fonts-dejavu-extra (2.37-8) ... 157s Setting up libprotobuf32:s390x (3.21.12-8ubuntu5) ... 157s Setting up mummer (3.23+dfsg-8) ... 157s Setting up libopenjp2-7:s390x (2.5.0-2) ... 157s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 157s Setting up phipack (0.0.20160614-5) ... 157s Setting up fasttree (2.1.11-2) ... 157s Setting up sgml-base (1.31) ... 157s Setting up harvest-tools (1.3-8build3) ... 157s Setting up libwebpmux3:s390x (1.3.2-0.4) ... 157s Setting up raxml (8.2.13+dfsg-1) ... 157s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 157s Setting up python3-pyspoa (0.0.10-1build1) ... 157s Setting up liblapack3:s390x (3.12.0-3) ... 157s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 157s Setting up libmuscle1 (3.7+4565-7ubuntu1) ... 157s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 158s Setting up libwebpdemux2:s390x (1.3.2-0.4) ... 158s Setting up python3-freetype (2.4.0-1) ... 158s Setting up xfonts-utils (1:7.7+6build2) ... 158s Setting up libraqm0:s390x (0.10.1-1) ... 158s Setting up python3-numpy (1:1.24.2-2) ... 159s Setting up libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 159s Setting up xml-core (0.19) ... 160s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 160s Setting up fonts-urw-base35 (20200910-8) ... 160s Setting up libcairo2:s390x (1.18.0-1) ... 160s Setting up python3-pil:s390x (10.2.0-1) ... 160s Setting up python3-cairo (1.25.1-2) ... 160s Setting up python3-rlpycairo (0.3.0-3) ... 160s Setting up python3-reportlab (4.1.0-1) ... 161s Processing triggers for libc-bin (2.39-0ubuntu2) ... 161s Processing triggers for man-db (2.12.0-3) ... 161s Processing triggers for sgml-base (1.31) ... 161s Setting up w3c-sgml-lib (1.3-3) ... 185s Setting up python3-biopython (1.81+dfsg-3) ... 186s Setting up parsnp (2.0.3+dfsg-1) ... 186s Setting up autopkgtest-satdep (0) ... 189s (Reading database ... 55287 files and directories currently installed.) 189s Removing autopkgtest-satdep (0) ... 189s autopkgtest [01:26:23]: test run-unit-test: [----------------------- 190s Test 1: With GenBank Annotations 190s 01:26:24 - INFO - |--Parsnp 2.0.3--| 190s 190s 01:26:24 - INFO - 190s ********************************************************************************** 190s SETTINGS: 190s |-refgenome: mers_virus/ref/England1.gbk 190s |-genomes: 190s mers_virus/genomes/Jordan-N3_2012.fna 190s mers_virus/genomes/KFU-HKU_19Dam.fna 190s ...42 more file(s)... 190s mers_virus/genomes/KFU-HKU_1.fna 190s mers_virus/genomes/Buraidah_1_2013.fna 190s |-aligner: muscle 190s |-outdir: /tmp/autopkgtest.xxMLf7/autopkgtest_tmp/P_2024_03_23_012624271069 190s |-OS: Linux 190s |-threads: 1 190s ********************************************************************************** 190s 190s 01:26:24 - INFO - <> 190s 01:26:24 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 190s 01:26:24 - INFO - Reconstructing core genome phylogeny... 195s 01:26:29 - INFO - Aligned 46 genomes in 5.52 seconds 195s 01:26:29 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.xxMLf7/autopkgtest_tmp/P_2024_03_23_012624271069 195s Passed 195s 195s Test 2: Without GenBank Annotations 196s 01:26:29 - INFO - |--Parsnp 2.0.3--| 196s 196s 01:26:29 - INFO - 196s ********************************************************************************** 196s SETTINGS: 196s |-refgenome: mers_virus/ref/England1.fna 196s |-genomes: 196s mers_virus/genomes/Jordan-N3_2012.fna 196s mers_virus/genomes/KFU-HKU_19Dam.fna 196s ...42 more file(s)... 196s mers_virus/genomes/KFU-HKU_1.fna 196s mers_virus/genomes/Buraidah_1_2013.fna 196s |-aligner: muscle 196s |-outdir: /tmp/autopkgtest.xxMLf7/autopkgtest_tmp/P_2024_03_23_012629988714 196s |-OS: Linux 196s |-threads: 1 196s ********************************************************************************** 196s 196s 01:26:29 - INFO - <> 196s 01:26:29 - INFO - No genbank file provided for reference annotations, skipping.. 196s 01:26:29 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 196s 01:26:30 - INFO - Reconstructing core genome phylogeny... 201s 01:26:35 - INFO - Aligned 46 genomes in 5.37 seconds 201s 01:26:35 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.xxMLf7/autopkgtest_tmp/P_2024_03_23_012629988714 201s Passed 201s 201s autopkgtest [01:26:35]: test run-unit-test: -----------------------] 202s autopkgtest [01:26:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 202s run-unit-test PASS 202s autopkgtest [01:26:36]: @@@@@@@@@@@@@@@@@@@@ summary 202s run-unit-test PASS 213s Creating nova instance adt-noble-s390x-parsnp-20240323-012314-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240322.img (UUID c8671f9a-0e89-48e3-af4f-3c79b89294e8)...