0s autopkgtest [04:02:04]: starting date and time: 2024-03-23 04:02:04+0000 0s autopkgtest [04:02:04]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [04:02:04]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hwqj2bxx/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-ppc64el-16.secgroup --name adt-noble-ppc64el-parsnp-20240323-040204-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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/ 246s autopkgtest [04:06:10]: testbed dpkg architecture: ppc64el 246s autopkgtest [04:06:10]: testbed apt version: 2.7.12 246s autopkgtest [04:06:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 247s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 247s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4001 kB] 247s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 247s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 247s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 247s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [668 kB] 247s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 247s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 247s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 247s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4259 kB] 248s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 248s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.5 kB] 248s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 251s Fetched 9679 kB in 2s (3922 kB/s) 252s Reading package lists... 254s Reading package lists... 254s Building dependency tree... 254s Reading state information... 255s Calculating upgrade... 255s The following packages will be upgraded: 255s libbsd0 255s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 255s Need to get 56.9 kB of archives. 255s After this operation, 0 B of additional disk space will be used. 255s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 255s Fetched 56.9 kB in 0s (191 kB/s) 256s (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 ... 70156 files and directories currently installed.) 256s Preparing to unpack .../libbsd0_0.12.1-1_ppc64el.deb ... 256s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 256s Setting up libbsd0:ppc64el (0.12.1-1) ... 256s Processing triggers for libc-bin (2.39-0ubuntu2) ... 256s Reading package lists... 256s Building dependency tree... 256s Reading state information... 256s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 257s sh: Attempting to set up Debian/Ubuntu apt sources automatically 257s sh: Distribution appears to be Ubuntu 258s Reading package lists... 258s Building dependency tree... 258s Reading state information... 258s eatmydata is already the newest version (131-1). 258s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 258s Reading package lists... 258s Building dependency tree... 258s Reading state information... 259s dbus is already the newest version (1.14.10-4ubuntu1). 259s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 259s Reading package lists... 259s Building dependency tree... 259s Reading state information... 259s rng-tools-debian is already the newest version (2.4). 259s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 259s Reading package lists... 259s Building dependency tree... 259s Reading state information... 259s The following packages will be REMOVED: 259s cloud-init* python3-configobj* python3-debconf* 260s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 260s After this operation, 3256 kB disk space will be freed. 260s (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 ... 70156 files and directories currently installed.) 260s Removing cloud-init (24.1.2-0ubuntu1) ... 260s Removing python3-configobj (5.0.8-3) ... 260s Removing python3-debconf (1.5.86) ... 260s Processing triggers for man-db (2.12.0-3) ... 261s (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 ... 69767 files and directories currently installed.) 261s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 262s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 262s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 262s invoke-rc.d: policy-rc.d denied execution of try-restart. 262s Reading package lists... 262s Building dependency tree... 262s Reading state information... 262s linux-generic is already the newest version (6.8.0-11.11+1). 262s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 263s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 263s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 263s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 266s Reading package lists... 266s Reading package lists... 266s Building dependency tree... 266s Reading state information... 266s Calculating upgrade... 266s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 266s Reading package lists... 266s Building dependency tree... 266s Reading state information... 266s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 267s autopkgtest [04:06:31]: rebooting testbed after setup commands that affected boot 444s autopkgtest [04:09:28]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 447s autopkgtest [04:09:31]: @@@@@@@@@@@@@@@@@@@@ apt-source parsnp 449s Get:1 http://ftpmaster.internal/ubuntu noble/universe parsnp 2.0.3+dfsg-1 (dsc) [2245 B] 449s Get:2 http://ftpmaster.internal/ubuntu noble/universe parsnp 2.0.3+dfsg-1 (tar) [141 kB] 449s Get:3 http://ftpmaster.internal/ubuntu noble/universe parsnp 2.0.3+dfsg-1 (diff) [10.0 kB] 449s gpgv: Signature made Tue Jan 30 19:56:28 2024 UTC 449s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 449s gpgv: issuer "emollier@debian.org" 449s gpgv: Can't check signature: No public key 449s dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.3+dfsg-1.dsc: no acceptable signature found 449s autopkgtest [04:09:33]: testing package parsnp version 2.0.3+dfsg-1 450s autopkgtest [04:09:34]: build not needed 450s autopkgtest [04:09:34]: test run-unit-test: preparing testbed 451s Reading package lists... 451s Building dependency tree... 451s Reading state information... 452s Starting pkgProblemResolver with broken count: 0 452s Starting 2 pkgProblemResolver with broken count: 0 452s Done 452s The following additional packages will be installed: 452s fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-extra 452s fonts-dejavu-mono fonts-urw-base35 harvest-tools libblas3 libcairo2 452s libcapnp-1.0.1 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 452s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 452s liblapack3 liblcms2-2 liblerc4 libmuscle1 libopenjp2-7 libpixman-1-0 452s libprotobuf32 libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 libwebp7 452s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mummer 452s parsnp phipack python3-biopython python3-cairo python3-freetype 452s python3-numpy python3-pil python3-pyspoa python3-reportlab python3-rlpycairo 452s python3-tqdm raxml sgml-base w3c-sgml-lib x11-common xfonts-encodings 452s xfonts-utils xml-core 452s Suggested packages: 452s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 452s python3-tk bwa clustalo clustalw dialign dssp emboss mafft muscle3 phylip 452s phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 452s python3-rdflib python3-psycopg2 python3-scipy samtools t-coffee wise gcc 452s gfortran python3-dev python3-pytest python-pil-doc pdf-viewer 452s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 452s sgml-base-doc debhelper 452s Recommended packages: 452s python3-dendropy python-biopython-doc ncbi-blast+ python3-olefile 452s The following NEW packages will be installed: 452s autopkgtest-satdep fasttree fontconfig-config fonts-dejavu-core 452s fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 harvest-tools libblas3 452s libcairo2 libcapnp-1.0.1 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 452s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 452s libjpeg8 liblapack3 liblcms2-2 liblerc4 libmuscle1 libopenjp2-7 452s libpixman-1-0 libprotobuf32 libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 452s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 452s mummer parsnp phipack python3-biopython python3-cairo python3-freetype 452s python3-numpy python3-pil python3-pyspoa python3-reportlab python3-rlpycairo 452s python3-tqdm raxml sgml-base w3c-sgml-lib x11-common xfonts-encodings 452s xfonts-utils xml-core 452s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 452s Need to get 37.1 MB/37.1 MB of archives. 452s After this operation, 132 MB of additional disk space will be used. 452s Get:1 /tmp/autopkgtest.rVmRMq/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 452s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el sgml-base all 1.31 [11.4 kB] 452s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 452s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 452s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontenc1 ppc64el 1:1.1.8-1 [15.7 kB] 452s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 452s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 452s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-utils ppc64el 1:7.7+6build2 [112 kB] 452s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 453s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 453s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-extra all 2.37-8 [1947 kB] 453s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libcapnp-1.0.1 ppc64el 1.0.1-3 [1544 kB] 453s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libprotobuf32 ppc64el 3.21.12-8ubuntu5 [982 kB] 453s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el harvest-tools ppc64el 1.3-8build3 [139 kB] 453s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 453s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 453s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 453s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 453s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 453s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 453s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 453s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 453s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 453s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 453s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 453s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 453s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libimagequant0 ppc64el 2.18.0-1 [42.5 kB] 453s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 453s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 453s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 453s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 453s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 453s Get:33 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmuscle1 ppc64el 3.7+4565-7ubuntu1 [280 kB] 453s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libraqm0 ppc64el 0.10.1-1 [18.9 kB] 453s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 453s Get:36 http://ftpmaster.internal/ubuntu noble/universe ppc64el libspoa7.0.0 ppc64el 4.0.8-1 [59.7 kB] 453s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 453s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 453s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 453s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpdemux2 ppc64el 1.3.2-0.4 [14.4 kB] 453s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpmux3 ppc64el 1.3.2-0.4 [31.2 kB] 453s Get:42 http://ftpmaster.internal/ubuntu noble/universe ppc64el mummer ppc64el 3.23+dfsg-8 [714 kB] 453s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 453s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libopenjp2-7 ppc64el 2.5.0-2 [233 kB] 453s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-pil ppc64el 10.2.0-1 [526 kB] 453s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-cairo ppc64el 1.25.1-2 [162 kB] 453s Get:47 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-freetype all 2.4.0-1 [83.1 kB] 453s Get:48 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 453s Get:49 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-reportlab all 4.1.0-1 [683 kB] 453s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el xml-core all 0.19 [20.3 kB] 453s Get:51 http://ftpmaster.internal/ubuntu noble/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 453s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-biopython ppc64el 1.81+dfsg-3 [1738 kB] 454s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pyspoa ppc64el 0.0.10-1build1 [89.0 kB] 454s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-tqdm all 4.64.1-2 [95.2 kB] 454s Get:55 http://ftpmaster.internal/ubuntu noble/universe ppc64el fasttree ppc64el 2.1.11-2 [218 kB] 454s Get:56 http://ftpmaster.internal/ubuntu noble/universe ppc64el phipack ppc64el 0.0.20160614-5 [58.6 kB] 454s Get:57 http://ftpmaster.internal/ubuntu noble/universe ppc64el raxml ppc64el 8.2.13+dfsg-1 [1068 kB] 454s Get:58 http://ftpmaster.internal/ubuntu noble/universe ppc64el parsnp ppc64el 2.0.3+dfsg-1 [224 kB] 454s Fetched 37.1 MB in 2s (20.4 MB/s) 454s Selecting previously unselected package sgml-base. 454s (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 ... 69712 files and directories currently installed.) 454s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 454s Unpacking sgml-base (1.31) ... 454s Selecting previously unselected package fonts-dejavu-mono. 454s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 454s Unpacking fonts-dejavu-mono (2.37-8) ... 454s Selecting previously unselected package fonts-dejavu-core. 454s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 454s Unpacking fonts-dejavu-core (2.37-8) ... 454s Selecting previously unselected package libfontenc1:ppc64el. 454s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1_ppc64el.deb ... 454s Unpacking libfontenc1:ppc64el (1:1.1.8-1) ... 454s Selecting previously unselected package x11-common. 454s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu2_all.deb ... 454s Unpacking x11-common (1:7.7+23ubuntu2) ... 454s Selecting previously unselected package xfonts-encodings. 454s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 454s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 454s Selecting previously unselected package xfonts-utils. 454s Preparing to unpack .../06-xfonts-utils_1%3a7.7+6build2_ppc64el.deb ... 454s Unpacking xfonts-utils (1:7.7+6build2) ... 454s Selecting previously unselected package fonts-urw-base35. 454s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 454s Unpacking fonts-urw-base35 (20200910-8) ... 454s Selecting previously unselected package fontconfig-config. 454s Preparing to unpack .../08-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 455s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 455s Selecting previously unselected package fonts-dejavu-extra. 455s Preparing to unpack .../09-fonts-dejavu-extra_2.37-8_all.deb ... 455s Unpacking fonts-dejavu-extra (2.37-8) ... 455s Selecting previously unselected package libcapnp-1.0.1:ppc64el. 455s Preparing to unpack .../10-libcapnp-1.0.1_1.0.1-3_ppc64el.deb ... 455s Unpacking libcapnp-1.0.1:ppc64el (1.0.1-3) ... 455s Selecting previously unselected package libprotobuf32:ppc64el. 455s Preparing to unpack .../11-libprotobuf32_3.21.12-8ubuntu5_ppc64el.deb ... 455s Unpacking libprotobuf32:ppc64el (3.21.12-8ubuntu5) ... 455s Selecting previously unselected package harvest-tools. 455s Preparing to unpack .../12-harvest-tools_1.3-8build3_ppc64el.deb ... 455s Unpacking harvest-tools (1.3-8build3) ... 455s Selecting previously unselected package libblas3:ppc64el. 455s Preparing to unpack .../13-libblas3_3.12.0-3_ppc64el.deb ... 455s Unpacking libblas3:ppc64el (3.12.0-3) ... 455s Selecting previously unselected package libfontconfig1:ppc64el. 455s Preparing to unpack .../14-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 455s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 455s Selecting previously unselected package libpixman-1-0:ppc64el. 455s Preparing to unpack .../15-libpixman-1-0_0.42.2-1_ppc64el.deb ... 455s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 455s Selecting previously unselected package libxcb-render0:ppc64el. 455s Preparing to unpack .../16-libxcb-render0_1.15-1_ppc64el.deb ... 455s Unpacking libxcb-render0:ppc64el (1.15-1) ... 455s Selecting previously unselected package libxcb-shm0:ppc64el. 455s Preparing to unpack .../17-libxcb-shm0_1.15-1_ppc64el.deb ... 455s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 455s Selecting previously unselected package libxrender1:ppc64el. 455s Preparing to unpack .../18-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 455s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 455s Selecting previously unselected package libcairo2:ppc64el. 455s Preparing to unpack .../19-libcairo2_1.18.0-1_ppc64el.deb ... 455s Unpacking libcairo2:ppc64el (1.18.0-1) ... 455s Selecting previously unselected package libdeflate0:ppc64el. 455s Preparing to unpack .../20-libdeflate0_1.19-1_ppc64el.deb ... 455s Unpacking libdeflate0:ppc64el (1.19-1) ... 455s Selecting previously unselected package libgfortran5:ppc64el. 455s Preparing to unpack .../21-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 455s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 455s Selecting previously unselected package libgomp1:ppc64el. 455s Preparing to unpack .../22-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 455s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 455s Selecting previously unselected package libgraphite2-3:ppc64el. 455s Preparing to unpack .../23-libgraphite2-3_1.3.14-2_ppc64el.deb ... 455s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 455s Selecting previously unselected package libharfbuzz0b:ppc64el. 455s Preparing to unpack .../24-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 455s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 455s Selecting previously unselected package libimagequant0:ppc64el. 455s Preparing to unpack .../25-libimagequant0_2.18.0-1_ppc64el.deb ... 455s Unpacking libimagequant0:ppc64el (2.18.0-1) ... 455s Selecting previously unselected package libjpeg-turbo8:ppc64el. 455s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 455s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 455s Selecting previously unselected package libjpeg8:ppc64el. 455s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 455s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 455s Selecting previously unselected package liblapack3:ppc64el. 455s Preparing to unpack .../28-liblapack3_3.12.0-3_ppc64el.deb ... 455s Unpacking liblapack3:ppc64el (3.12.0-3) ... 455s Selecting previously unselected package liblcms2-2:ppc64el. 455s Preparing to unpack .../29-liblcms2-2_2.14-2_ppc64el.deb ... 455s Unpacking liblcms2-2:ppc64el (2.14-2) ... 455s Selecting previously unselected package liblerc4:ppc64el. 455s Preparing to unpack .../30-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 455s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 455s Selecting previously unselected package libmuscle1. 455s Preparing to unpack .../31-libmuscle1_3.7+4565-7ubuntu1_ppc64el.deb ... 455s Unpacking libmuscle1 (3.7+4565-7ubuntu1) ... 455s Selecting previously unselected package libraqm0:ppc64el. 455s Preparing to unpack .../32-libraqm0_0.10.1-1_ppc64el.deb ... 455s Unpacking libraqm0:ppc64el (0.10.1-1) ... 455s Selecting previously unselected package libsharpyuv0:ppc64el. 455s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 455s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 455s Selecting previously unselected package libspoa7.0.0:ppc64el. 455s Preparing to unpack .../34-libspoa7.0.0_4.0.8-1_ppc64el.deb ... 455s Unpacking libspoa7.0.0:ppc64el (4.0.8-1) ... 455s Selecting previously unselected package libjbig0:ppc64el. 455s Preparing to unpack .../35-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 455s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 455s Selecting previously unselected package libwebp7:ppc64el. 455s Preparing to unpack .../36-libwebp7_1.3.2-0.4_ppc64el.deb ... 455s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 455s Selecting previously unselected package libtiff6:ppc64el. 455s Preparing to unpack .../37-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 455s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 455s Selecting previously unselected package libwebpdemux2:ppc64el. 455s Preparing to unpack .../38-libwebpdemux2_1.3.2-0.4_ppc64el.deb ... 455s Unpacking libwebpdemux2:ppc64el (1.3.2-0.4) ... 455s Selecting previously unselected package libwebpmux3:ppc64el. 455s Preparing to unpack .../39-libwebpmux3_1.3.2-0.4_ppc64el.deb ... 455s Unpacking libwebpmux3:ppc64el (1.3.2-0.4) ... 455s Selecting previously unselected package mummer. 455s Preparing to unpack .../40-mummer_3.23+dfsg-8_ppc64el.deb ... 455s Unpacking mummer (3.23+dfsg-8) ... 456s Selecting previously unselected package python3-numpy. 456s Preparing to unpack .../41-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 456s Unpacking python3-numpy (1:1.24.2-2) ... 456s Selecting previously unselected package libopenjp2-7:ppc64el. 456s Preparing to unpack .../42-libopenjp2-7_2.5.0-2_ppc64el.deb ... 456s Unpacking libopenjp2-7:ppc64el (2.5.0-2) ... 456s Selecting previously unselected package python3-pil:ppc64el. 456s Preparing to unpack .../43-python3-pil_10.2.0-1_ppc64el.deb ... 456s Unpacking python3-pil:ppc64el (10.2.0-1) ... 456s Selecting previously unselected package python3-cairo. 456s Preparing to unpack .../44-python3-cairo_1.25.1-2_ppc64el.deb ... 456s Unpacking python3-cairo (1.25.1-2) ... 456s Selecting previously unselected package python3-freetype. 456s Preparing to unpack .../45-python3-freetype_2.4.0-1_all.deb ... 456s Unpacking python3-freetype (2.4.0-1) ... 456s Selecting previously unselected package python3-rlpycairo. 456s Preparing to unpack .../46-python3-rlpycairo_0.3.0-3_all.deb ... 456s Unpacking python3-rlpycairo (0.3.0-3) ... 456s Selecting previously unselected package python3-reportlab. 456s Preparing to unpack .../47-python3-reportlab_4.1.0-1_all.deb ... 456s Unpacking python3-reportlab (4.1.0-1) ... 456s Selecting previously unselected package xml-core. 456s Preparing to unpack .../48-xml-core_0.19_all.deb ... 456s Unpacking xml-core (0.19) ... 456s Selecting previously unselected package w3c-sgml-lib. 456s Preparing to unpack .../49-w3c-sgml-lib_1.3-3_all.deb ... 456s Unpacking w3c-sgml-lib (1.3-3) ... 456s Selecting previously unselected package python3-biopython. 456s Preparing to unpack .../50-python3-biopython_1.81+dfsg-3_ppc64el.deb ... 456s Unpacking python3-biopython (1.81+dfsg-3) ... 456s Selecting previously unselected package python3-pyspoa. 456s Preparing to unpack .../51-python3-pyspoa_0.0.10-1build1_ppc64el.deb ... 456s Unpacking python3-pyspoa (0.0.10-1build1) ... 456s Selecting previously unselected package python3-tqdm. 456s Preparing to unpack .../52-python3-tqdm_4.64.1-2_all.deb ... 456s Unpacking python3-tqdm (4.64.1-2) ... 456s Selecting previously unselected package fasttree. 456s Preparing to unpack .../53-fasttree_2.1.11-2_ppc64el.deb ... 456s Unpacking fasttree (2.1.11-2) ... 457s Selecting previously unselected package phipack. 457s Preparing to unpack .../54-phipack_0.0.20160614-5_ppc64el.deb ... 457s Unpacking phipack (0.0.20160614-5) ... 457s Selecting previously unselected package raxml. 457s Preparing to unpack .../55-raxml_8.2.13+dfsg-1_ppc64el.deb ... 457s Unpacking raxml (8.2.13+dfsg-1) ... 457s Selecting previously unselected package parsnp. 457s Preparing to unpack .../56-parsnp_2.0.3+dfsg-1_ppc64el.deb ... 457s Unpacking parsnp (2.0.3+dfsg-1) ... 457s Selecting previously unselected package autopkgtest-satdep. 457s Preparing to unpack .../57-1-autopkgtest-satdep.deb ... 457s Unpacking autopkgtest-satdep (0) ... 457s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 457s Setting up liblcms2-2:ppc64el (2.14-2) ... 457s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 457s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 457s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 457s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 457s Setting up libcapnp-1.0.1:ppc64el (1.0.1-3) ... 457s Setting up libxcb-render0:ppc64el (1.15-1) ... 457s Setting up python3-tqdm (4.64.1-2) ... 457s Setting up x11-common (1:7.7+23ubuntu2) ... 457s Setting up libdeflate0:ppc64el (1.19-1) ... 457s Setting up libxcb-shm0:ppc64el (1.15-1) ... 457s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 457s Setting up python3-freetype (2.4.0-1) ... 457s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 457s Setting up libfontenc1:ppc64el (1:1.1.8-1) ... 457s Setting up libblas3:ppc64el (3.12.0-3) ... 457s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 457s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 458s Setting up libimagequant0:ppc64el (2.18.0-1) ... 458s Setting up fonts-dejavu-mono (2.37-8) ... 458s Setting up libspoa7.0.0:ppc64el (4.0.8-1) ... 458s Setting up fonts-dejavu-core (2.37-8) ... 458s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 458s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 458s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 458s Setting up fonts-dejavu-extra (2.37-8) ... 458s Setting up libprotobuf32:ppc64el (3.21.12-8ubuntu5) ... 458s Setting up mummer (3.23+dfsg-8) ... 458s Setting up libopenjp2-7:ppc64el (2.5.0-2) ... 458s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 458s Setting up phipack (0.0.20160614-5) ... 458s Setting up fasttree (2.1.11-2) ... 458s Setting up sgml-base (1.31) ... 458s Setting up harvest-tools (1.3-8build3) ... 458s Setting up libwebpmux3:ppc64el (1.3.2-0.4) ... 458s Setting up raxml (8.2.13+dfsg-1) ... 458s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 458s Setting up python3-pyspoa (0.0.10-1build1) ... 458s Setting up liblapack3:ppc64el (3.12.0-3) ... 458s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 458s Setting up libmuscle1 (3.7+4565-7ubuntu1) ... 458s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 458s Setting up libwebpdemux2:ppc64el (1.3.2-0.4) ... 458s Setting up xfonts-utils (1:7.7+6build2) ... 458s Setting up libraqm0:ppc64el (0.10.1-1) ... 458s Setting up python3-numpy (1:1.24.2-2) ... 460s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 460s Setting up xml-core (0.19) ... 460s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 460s Setting up fonts-urw-base35 (20200910-8) ... 460s Setting up libcairo2:ppc64el (1.18.0-1) ... 460s Setting up python3-pil:ppc64el (10.2.0-1) ... 461s Setting up python3-cairo (1.25.1-2) ... 461s Setting up python3-rlpycairo (0.3.0-3) ... 461s Setting up python3-reportlab (4.1.0-1) ... 462s Processing triggers for libc-bin (2.39-0ubuntu2) ... 462s Processing triggers for man-db (2.12.0-3) ... 463s Processing triggers for sgml-base (1.31) ... 463s Setting up w3c-sgml-lib (1.3-3) ... 494s Setting up python3-biopython (1.81+dfsg-3) ... 495s Setting up parsnp (2.0.3+dfsg-1) ... 495s Setting up autopkgtest-satdep (0) ... 498s (Reading database ... 73272 files and directories currently installed.) 498s Removing autopkgtest-satdep (0) ... 499s autopkgtest [04:10:23]: test run-unit-test: [----------------------- 499s Test 1: With GenBank Annotations 499s 04:10:23 - INFO - |--Parsnp 2.0.3--| 499s 499s 04:10:23 - INFO - 499s ********************************************************************************** 499s SETTINGS: 499s |-refgenome: mers_virus/ref/England1.gbk 499s |-genomes: 499s mers_virus/genomes/KSA-CAMEL-505.fna 499s mers_virus/genomes/KSA-CAMEL-376.fna 499s ...42 more file(s)... 499s mers_virus/genomes/KF192507.1.fna 499s mers_virus/genomes/Riyadh_2_2012.fna 499s |-aligner: muscle 499s |-outdir: /tmp/autopkgtest.rVmRMq/autopkgtest_tmp/P_2024_03_23_041023880060 499s |-OS: Linux 499s |-threads: 1 499s ********************************************************************************** 499s 499s 04:10:23 - INFO - <> 499s 04:10:23 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 500s 04:10:24 - INFO - Reconstructing core genome phylogeny... 506s 04:10:30 - INFO - Aligned 46 genomes in 6.86 seconds 506s 04:10:30 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.rVmRMq/autopkgtest_tmp/P_2024_03_23_041023880060 506s Passed 506s 506s Test 2: Without GenBank Annotations 507s 04:10:30 - INFO - |--Parsnp 2.0.3--| 507s 507s 04:10:30 - INFO - 507s ********************************************************************************** 507s SETTINGS: 507s |-refgenome: mers_virus/ref/England1.fna 507s |-genomes: 507s mers_virus/genomes/KSA-CAMEL-505.fna 507s mers_virus/genomes/KSA-CAMEL-376.fna 507s ...42 more file(s)... 507s mers_virus/genomes/KF192507.1.fna 507s mers_virus/genomes/Riyadh_2_2012.fna 507s |-aligner: muscle 507s |-outdir: /tmp/autopkgtest.rVmRMq/autopkgtest_tmp/P_2024_03_23_041030984141 507s |-OS: Linux 507s |-threads: 1 507s ********************************************************************************** 507s 507s 04:10:30 - INFO - <> 507s 04:10:30 - INFO - No genbank file provided for reference annotations, skipping.. 507s 04:10:30 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 507s 04:10:31 - INFO - Reconstructing core genome phylogeny... 513s 04:10:37 - INFO - Aligned 46 genomes in 6.85 seconds 513s 04:10:37 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.rVmRMq/autopkgtest_tmp/P_2024_03_23_041030984141 513s Passed 513s 514s autopkgtest [04:10:38]: test run-unit-test: -----------------------] 514s autopkgtest [04:10:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 514s run-unit-test PASS 515s autopkgtest [04:10:39]: @@@@@@@@@@@@@@@@@@@@ summary 515s run-unit-test PASS 534s Creating nova instance adt-noble-ppc64el-parsnp-20240323-040204-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240322.img (UUID 8499323f-6fcd-4f77-8a53-77410adea6d3)...