0s autopkgtest [21:31:13]: starting date and time: 2024-03-23 21:31:13+0000 0s autopkgtest [21:31:13]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [21:31:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4seel1k1/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-arm64-4.secgroup --name adt-noble-arm64-parsnp-20240323-213113-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 108s autopkgtest [21:33:01]: testbed dpkg architecture: arm64 109s autopkgtest [21:33:02]: testbed apt version: 2.7.12 109s autopkgtest [21:33:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 110s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 111s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 111s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 111s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3975 kB] 111s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 111s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [668 kB] 111s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 111s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 111s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 111s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4401 kB] 111s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 111s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [69.8 kB] 111s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 119s Fetched 9834 kB in 3s (2859 kB/s) 120s Reading package lists... 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s Calculating upgrade... 128s The following packages will be upgraded: 128s fonts-ubuntu-console libbsd0 libc-bin libc6 locales 129s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Need to get 7658 kB of archives. 129s After this operation, 2048 B of additional disk space will be used. 129s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libc6 arm64 2.39-0ubuntu6 [2776 kB] 130s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-bin arm64 2.39-0ubuntu6 [591 kB] 130s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libbsd0 arm64 0.12.1-1 [41.0 kB] 130s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 locales all 2.39-0ubuntu6 [4232 kB] 131s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 132s Preconfiguring packages ... 132s Fetched 7658 kB in 3s (3005 kB/s) 132s (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 ... 75911 files and directories currently installed.) 133s Preparing to unpack .../libc6_2.39-0ubuntu6_arm64.deb ... 133s Unpacking libc6:arm64 (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 134s Setting up libc6:arm64 (2.39-0ubuntu6) ... 135s (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 ... 75911 files and directories currently installed.) 135s Preparing to unpack .../libc-bin_2.39-0ubuntu6_arm64.deb ... 135s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 135s Setting up libc-bin (2.39-0ubuntu6) ... 135s (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 ... 75911 files and directories currently installed.) 136s Preparing to unpack .../libbsd0_0.12.1-1_arm64.deb ... 136s Unpacking libbsd0:arm64 (0.12.1-1) over (0.11.8-1) ... 136s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 136s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 136s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 136s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 136s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 136s Setting up locales (2.39-0ubuntu6) ... 139s Generating locales (this might take a while)... 145s en_US.UTF-8... done 145s Generation complete. 145s Setting up libbsd0:arm64 (0.12.1-1) ... 145s Processing triggers for man-db (2.12.0-3) ... 147s Processing triggers for libc-bin (2.39-0ubuntu6) ... 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s sh: Attempting to set up Debian/Ubuntu apt sources automatically 152s sh: Distribution appears to be Ubuntu 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 156s eatmydata is already the newest version (131-1). 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s dbus is already the newest version (1.14.10-4ubuntu1). 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s rng-tools-debian is already the newest version (2.4). 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 163s The following packages will be REMOVED: 163s cloud-init* python3-configobj* python3-debconf* 164s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 164s After this operation, 3256 kB disk space will be freed. 164s (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 ... 75911 files and directories currently installed.) 164s Removing cloud-init (24.1.2-0ubuntu1) ... 165s Removing python3-configobj (5.0.8-3) ... 166s Removing python3-debconf (1.5.86) ... 166s Processing triggers for man-db (2.12.0-3) ... 166s (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 ... 75522 files and directories currently installed.) 166s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 168s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 168s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 168s invoke-rc.d: policy-rc.d denied execution of try-restart. 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 171s linux-generic is already the newest version (6.8.0-11.11+1). 171s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 172s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 172s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 179s Reading package lists... 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 181s Calculating upgrade... 183s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 185s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 185s autopkgtest [21:34:18]: rebooting testbed after setup commands that affected boot 355s autopkgtest [21:37:08]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 359s autopkgtest [21:37:12]: @@@@@@@@@@@@@@@@@@@@ apt-source parsnp 361s Get:1 http://ftpmaster.internal/ubuntu noble/universe parsnp 2.0.3+dfsg-1 (dsc) [2245 B] 361s Get:2 http://ftpmaster.internal/ubuntu noble/universe parsnp 2.0.3+dfsg-1 (tar) [141 kB] 361s Get:3 http://ftpmaster.internal/ubuntu noble/universe parsnp 2.0.3+dfsg-1 (diff) [10.0 kB] 362s gpgv: Signature made Tue Jan 30 19:56:28 2024 UTC 362s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 362s gpgv: issuer "emollier@debian.org" 362s gpgv: Can't check signature: No public key 362s dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.3+dfsg-1.dsc: no acceptable signature found 362s autopkgtest [21:37:15]: testing package parsnp version 2.0.3+dfsg-1 363s autopkgtest [21:37:16]: build not needed 363s autopkgtest [21:37:16]: test run-unit-test: preparing testbed 372s Reading package lists... 373s Building dependency tree... 373s Reading state information... 374s Starting pkgProblemResolver with broken count: 0 374s Starting 2 pkgProblemResolver with broken count: 0 374s Done 376s The following additional packages will be installed: 376s fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-extra 376s fonts-dejavu-mono fonts-urw-base35 harvest-tools libblas3 libcairo2 376s libcapnp-1.0.1 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 376s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 376s liblapack3 liblcms2-2 liblerc4 libmuscle1 libopenjp2-7 libpixman-1-0 376s libprotobuf32 libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 libwebp7 376s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mummer 376s parsnp phipack python3-biopython python3-cairo python3-freetype 376s python3-numpy python3-pil python3-pyspoa python3-reportlab python3-rlpycairo 376s python3-tqdm raxml sgml-base w3c-sgml-lib x11-common xfonts-encodings 376s xfonts-utils xml-core 376s Suggested packages: 376s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 376s python3-tk bwa clustalo clustalw dialign dssp emboss mafft muscle3 phylip 376s phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 376s python3-rdflib python3-psycopg2 python3-scipy samtools t-coffee wise gcc 376s gfortran python3-dev python3-pytest python-pil-doc pdf-viewer 376s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 376s sgml-base-doc debhelper 376s Recommended packages: 376s python3-dendropy python-biopython-doc ncbi-blast+ python3-olefile 376s The following NEW packages will be installed: 376s autopkgtest-satdep fasttree fontconfig-config fonts-dejavu-core 376s fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 harvest-tools libblas3 376s libcairo2 libcapnp-1.0.1 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 376s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 376s libjpeg8 liblapack3 liblcms2-2 liblerc4 libmuscle1 libopenjp2-7 376s libpixman-1-0 libprotobuf32 libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 376s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 376s mummer parsnp phipack python3-biopython python3-cairo python3-freetype 376s python3-numpy python3-pil python3-pyspoa python3-reportlab python3-rlpycairo 376s python3-tqdm raxml sgml-base w3c-sgml-lib x11-common xfonts-encodings 376s xfonts-utils xml-core 376s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 376s Need to get 33.4 MB/33.4 MB of archives. 376s After this operation, 114 MB of additional disk space will be used. 376s Get:1 /tmp/autopkgtest.JCbq6q/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 376s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 376s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 377s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 377s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 377s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 377s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 377s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 377s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 379s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 379s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 380s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libcapnp-1.0.1 arm64 1.0.1-3 [1326 kB] 380s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libprotobuf32 arm64 3.21.12-8ubuntu5 [860 kB] 380s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 harvest-tools arm64 1.3-8build3 [119 kB] 380s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 380s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 380s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 380s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 380s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 380s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 380s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 380s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 380s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 380s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 380s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 380s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 380s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 380s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 380s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 380s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 381s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 381s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 381s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 libmuscle1 arm64 3.7+4565-7ubuntu1 [231 kB] 381s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 381s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 381s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 libspoa7.0.0 arm64 4.0.8-1 [53.6 kB] 381s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 381s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 381s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 381s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 381s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 381s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 381s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 381s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 381s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 382s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 382s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 382s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 382s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 382s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 382s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 382s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 382s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyspoa arm64 0.0.10-1build1 [75.8 kB] 382s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tqdm all 4.64.1-2 [95.2 kB] 382s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 382s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 phipack arm64 0.0.20160614-5 [49.9 kB] 382s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 raxml arm64 8.2.13+dfsg-1 [999 kB] 382s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 parsnp arm64 2.0.3+dfsg-1 [200 kB] 383s Fetched 33.4 MB in 6s (5410 kB/s) 383s Selecting previously unselected package sgml-base. 384s (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 ... 75467 files and directories currently installed.) 384s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 384s Unpacking sgml-base (1.31) ... 384s Selecting previously unselected package fonts-dejavu-mono. 384s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 384s Unpacking fonts-dejavu-mono (2.37-8) ... 384s Selecting previously unselected package fonts-dejavu-core. 384s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 384s Unpacking fonts-dejavu-core (2.37-8) ... 384s Selecting previously unselected package libfontenc1:arm64. 384s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1_arm64.deb ... 384s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 384s Selecting previously unselected package x11-common. 384s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu2_all.deb ... 384s Unpacking x11-common (1:7.7+23ubuntu2) ... 384s Selecting previously unselected package xfonts-encodings. 384s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 384s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 384s Selecting previously unselected package xfonts-utils. 384s Preparing to unpack .../06-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 384s Unpacking xfonts-utils (1:7.7+6build2) ... 384s Selecting previously unselected package fonts-urw-base35. 384s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 385s Unpacking fonts-urw-base35 (20200910-8) ... 385s Selecting previously unselected package fontconfig-config. 385s Preparing to unpack .../08-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 386s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 386s Selecting previously unselected package fonts-dejavu-extra. 386s Preparing to unpack .../09-fonts-dejavu-extra_2.37-8_all.deb ... 386s Unpacking fonts-dejavu-extra (2.37-8) ... 386s Selecting previously unselected package libcapnp-1.0.1:arm64. 386s Preparing to unpack .../10-libcapnp-1.0.1_1.0.1-3_arm64.deb ... 386s Unpacking libcapnp-1.0.1:arm64 (1.0.1-3) ... 386s Selecting previously unselected package libprotobuf32:arm64. 386s Preparing to unpack .../11-libprotobuf32_3.21.12-8ubuntu5_arm64.deb ... 386s Unpacking libprotobuf32:arm64 (3.21.12-8ubuntu5) ... 386s Selecting previously unselected package harvest-tools. 386s Preparing to unpack .../12-harvest-tools_1.3-8build3_arm64.deb ... 386s Unpacking harvest-tools (1.3-8build3) ... 386s Selecting previously unselected package libblas3:arm64. 386s Preparing to 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libxrender1:arm64 (1:0.9.10-1.1) ... 387s Selecting previously unselected package libcairo2:arm64. 387s Preparing to unpack .../19-libcairo2_1.18.0-1_arm64.deb ... 387s Unpacking libcairo2:arm64 (1.18.0-1) ... 387s Selecting previously unselected package libdeflate0:arm64. 387s Preparing to unpack .../20-libdeflate0_1.19-1_arm64.deb ... 387s Unpacking libdeflate0:arm64 (1.19-1) ... 387s Selecting previously unselected package libgfortran5:arm64. 387s Preparing to unpack .../21-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 387s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 387s Selecting previously unselected package libgomp1:arm64. 387s Preparing to unpack .../22-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 387s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 387s Selecting previously unselected package libgraphite2-3:arm64. 387s Preparing to unpack .../23-libgraphite2-3_1.3.14-2_arm64.deb ... 387s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 387s Selecting previously unselected package libharfbuzz0b:arm64. 387s Preparing to unpack .../24-libharfbuzz0b_8.3.0-2_arm64.deb ... 387s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 387s Selecting previously unselected package libimagequant0:arm64. 387s Preparing to unpack .../25-libimagequant0_2.18.0-1_arm64.deb ... 387s Unpacking libimagequant0:arm64 (2.18.0-1) ... 387s Selecting previously unselected package libjpeg-turbo8:arm64. 387s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 387s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 387s Selecting previously unselected package libjpeg8:arm64. 388s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_arm64.deb ... 388s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 388s Selecting previously unselected package liblapack3:arm64. 388s Preparing to unpack .../28-liblapack3_3.12.0-3_arm64.deb ... 388s Unpacking liblapack3:arm64 (3.12.0-3) ... 388s Selecting previously unselected package liblcms2-2:arm64. 388s Preparing to unpack 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python3-pyspoa (0.0.10-1build1) ... 391s Selecting previously unselected package python3-tqdm. 391s Preparing to unpack .../52-python3-tqdm_4.64.1-2_all.deb ... 391s Unpacking python3-tqdm (4.64.1-2) ... 392s Selecting previously unselected package fasttree. 392s Preparing to unpack .../53-fasttree_2.1.11-2_arm64.deb ... 392s Unpacking fasttree (2.1.11-2) ... 392s Selecting previously unselected package phipack. 392s Preparing to unpack .../54-phipack_0.0.20160614-5_arm64.deb ... 392s Unpacking phipack (0.0.20160614-5) ... 392s Selecting previously unselected package raxml. 392s Preparing to unpack .../55-raxml_8.2.13+dfsg-1_arm64.deb ... 392s Unpacking raxml (8.2.13+dfsg-1) ... 392s Selecting previously unselected package parsnp. 392s Preparing to unpack .../56-parsnp_2.0.3+dfsg-1_arm64.deb ... 392s Unpacking parsnp (2.0.3+dfsg-1) ... 392s Selecting previously unselected package autopkgtest-satdep. 392s Preparing to unpack .../57-1-autopkgtest-satdep.deb ... 392s Unpacking autopkgtest-satdep (0) ... 392s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 392s Setting up liblcms2-2:arm64 (2.14-2) ... 392s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 392s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 392s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 392s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 392s Setting up libcapnp-1.0.1:arm64 (1.0.1-3) ... 392s Setting up libxcb-render0:arm64 (1.15-1) ... 392s Setting up python3-tqdm (4.64.1-2) ... 392s Setting up x11-common (1:7.7+23ubuntu2) ... 394s Setting up libdeflate0:arm64 (1.19-1) ... 394s Setting up libxcb-shm0:arm64 (1.15-1) ... 394s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 394s Setting up python3-freetype (2.4.0-1) ... 394s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 394s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 394s Setting up libblas3:arm64 (3.12.0-3) ... 394s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 394s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 394s Setting up libimagequant0:arm64 (2.18.0-1) ... 394s Setting up fonts-dejavu-mono (2.37-8) ... 394s Setting up libspoa7.0.0:arm64 (4.0.8-1) ... 394s Setting up fonts-dejavu-core (2.37-8) ... 394s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 394s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 394s Setting up libwebp7:arm64 (1.3.2-0.4) ... 394s Setting up fonts-dejavu-extra (2.37-8) ... 394s Setting up libprotobuf32:arm64 (3.21.12-8ubuntu5) ... 394s Setting up mummer (3.23+dfsg-8) ... 394s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 394s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 394s Setting up phipack (0.0.20160614-5) ... 394s Setting up fasttree (2.1.11-2) ... 394s Setting up sgml-base (1.31) ... 394s Setting up harvest-tools (1.3-8build3) ... 394s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 394s Setting up raxml (8.2.13+dfsg-1) ... 394s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 394s Setting up python3-pyspoa (0.0.10-1build1) ... 394s Setting up liblapack3:arm64 (3.12.0-3) ... 394s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 394s Setting up libmuscle1 (3.7+4565-7ubuntu1) ... 394s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 395s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 395s Setting up xfonts-utils (1:7.7+6build2) ... 395s Setting up libraqm0:arm64 (0.10.1-1) ... 395s Setting up python3-numpy (1:1.24.2-2) ... 400s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 400s Setting up xml-core (0.19) ... 401s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 401s Setting up fonts-urw-base35 (20200910-8) ... 401s Setting up libcairo2:arm64 (1.18.0-1) ... 401s Setting up python3-pil:arm64 (10.2.0-1) ... 402s Setting up python3-cairo (1.25.1-2) ... 403s Setting up python3-rlpycairo (0.3.0-3) ... 403s Setting up python3-reportlab (4.1.0-1) ... 405s Processing triggers for libc-bin (2.39-0ubuntu6) ... 405s Processing triggers for man-db (2.12.0-3) ... 408s Processing triggers for sgml-base (1.31) ... 408s Setting up w3c-sgml-lib (1.3-3) ... 492s Setting up python3-biopython (1.81+dfsg-3) ... 495s Setting up parsnp (2.0.3+dfsg-1) ... 496s Setting up autopkgtest-satdep (0) ... 504s (Reading database ... 79027 files and directories currently installed.) 504s Removing autopkgtest-satdep (0) ... 505s autopkgtest [21:39:38]: test run-unit-test: [----------------------- 505s Test 1: With GenBank Annotations 506s 21:39:39 - INFO - |--Parsnp 2.0.3--| 506s 506s 21:39:39 - INFO - 506s ********************************************************************************** 506s SETTINGS: 506s |-refgenome: mers_virus/ref/England1.gbk 506s |-genomes: 506s mers_virus/genomes/Riyadh_2_2012.fna 506s mers_virus/genomes/Riyadh_4_2013.fna 506s ...42 more file(s)... 506s mers_virus/genomes/Al-Hasa_3_2013.fna 506s mers_virus/genomes/Bisha_1_2012.fna 506s |-aligner: muscle 506s |-outdir: /tmp/autopkgtest.JCbq6q/autopkgtest_tmp/P_2024_03_23_213939439008 506s |-OS: Linux 506s |-threads: 1 506s ********************************************************************************** 506s 506s 21:39:39 - INFO - <> 506s 21:39:39 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 507s 21:39:40 - INFO - Reconstructing core genome phylogeny... 521s 21:39:54 - INFO - Aligned 46 genomes in 15.22 seconds 521s 21:39:54 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.JCbq6q/autopkgtest_tmp/P_2024_03_23_213939439008 521s Passed 521s 521s Test 2: Without GenBank Annotations 522s 21:39:55 - INFO - |--Parsnp 2.0.3--| 522s 522s 21:39:55 - INFO - 522s ********************************************************************************** 522s SETTINGS: 522s |-refgenome: mers_virus/ref/England1.fna 522s |-genomes: 522s mers_virus/genomes/Riyadh_2_2012.fna 522s mers_virus/genomes/Riyadh_4_2013.fna 522s ...42 more file(s)... 522s mers_virus/genomes/Al-Hasa_3_2013.fna 522s mers_virus/genomes/Bisha_1_2012.fna 522s |-aligner: muscle 522s |-outdir: /tmp/autopkgtest.JCbq6q/autopkgtest_tmp/P_2024_03_23_213955366231 522s |-OS: Linux 522s |-threads: 1 522s ********************************************************************************** 522s 522s 21:39:55 - INFO - <> 522s 21:39:55 - INFO - No genbank file provided for reference annotations, skipping.. 522s 21:39:55 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 523s 21:39:56 - INFO - Reconstructing core genome phylogeny... 536s 21:40:09 - INFO - Aligned 46 genomes in 14.55 seconds 536s 21:40:09 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.JCbq6q/autopkgtest_tmp/P_2024_03_23_213955366231 537s Passed 537s 537s autopkgtest [21:40:10]: test run-unit-test: -----------------------] 538s autopkgtest [21:40:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 538s run-unit-test PASS 538s autopkgtest [21:40:11]: @@@@@@@@@@@@@@@@@@@@ summary 538s run-unit-test PASS 559s Creating nova instance adt-noble-arm64-parsnp-20240323-213113-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240322.img (UUID 30e11504-94c3-4021-bd9a-a4301970c682)...