0s autopkgtest [06:53:36]: starting date and time: 2025-02-21 06:53:36+0000 0s autopkgtest [06:53:36]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [06:53:36]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8n2j11do/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade gubbins --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:2.2.3+ds-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-9.secgroup --name adt-plucky-amd64-gubbins-20250221-065336-juju-7f2275-prod-proposed-migration-environment-15-1786bc5d-57b8-4e84-96c0-5918fbdf5b60 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 46s autopkgtest [06:54:22]: testbed dpkg architecture: amd64 46s autopkgtest [06:54:22]: testbed apt version: 2.9.30ubuntu1 46s autopkgtest [06:54:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 46s autopkgtest [06:54:22]: testbed release detected to be: None 47s autopkgtest [06:54:23]: updating testbed package index (apt update) 47s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 47s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 47s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 47s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 47s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.6 kB] 47s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [722 kB] 47s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 47s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.8 kB] 47s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [115 kB] 47s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [144 kB] 47s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 47s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 47s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [280 kB] 47s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [708 kB] 47s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [22.5 kB] 47s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [9128 B] 47s Fetched 2234 kB in 0s (5801 kB/s) 48s Reading package lists... 48s + lsb_release --codename --short 48s + RELEASE=plucky 48s + cat 48s + [ plucky != trusty ] 48s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 48s Reading package lists... 49s Building dependency tree... 49s Reading state information... 49s Calculating upgrade... 49s Calculating upgrade... 49s The following NEW packages will be installed: 49s libjemalloc2 49s The following packages will be upgraded: 49s apparmor apport apport-core-dump-handler bind9-dnsutils bind9-host 49s bind9-libs cloud-init cloud-init-base libapparmor1 python3-apport 49s python3-problem-report tmux 49s 12 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 49s Need to get 4016 kB of archives. 49s After this operation, 1111 kB of additional disk space will be used. 49s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-problem-report all 2.31.0+git20250220-0ubuntu1 [26.0 kB] 49s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apport all 2.31.0+git20250220-0ubuntu1 [93.5 kB] 49s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 apport-core-dump-handler all 2.31.0+git20250220-0ubuntu1 [18.7 kB] 49s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 apport all 2.31.0+git20250220-0ubuntu1 [83.1 kB] 49s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu4 [54.6 kB] 49s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu4 [700 kB] 49s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-2build1 [256 kB] 49s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 bind9-dnsutils amd64 1:9.20.4-3ubuntu1 [169 kB] 49s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 bind9-host amd64 1:9.20.4-3ubuntu1 [51.9 kB] 49s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 bind9-libs amd64 1:9.20.4-3ubuntu1 [1380 kB] 50s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu1 [616 kB] 50s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 tmux amd64 3.5a-3 [564 kB] 50s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu1 [2088 B] 50s Preconfiguring packages ... 50s Fetched 4016 kB in 0s (32.8 MB/s) 50s (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 ... 108970 files and directories currently installed.) 50s Preparing to unpack .../00-python3-problem-report_2.31.0+git20250220-0ubuntu1_all.deb ... 50s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 50s for fn in glob1(directory, "%s.*" % fname): 50s Unpacking python3-problem-report (2.31.0+git20250220-0ubuntu1) over (2.31.0-0ubuntu5) ... 51s Preparing to unpack .../01-python3-apport_2.31.0+git20250220-0ubuntu1_all.deb ... 51s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 51s for fn in glob1(directory, "%s.*" % fname): 51s Unpacking python3-apport (2.31.0+git20250220-0ubuntu1) over (2.31.0-0ubuntu5) ... 51s Preparing to unpack .../02-apport-core-dump-handler_2.31.0+git20250220-0ubuntu1_all.deb ... 51s Unpacking apport-core-dump-handler (2.31.0+git20250220-0ubuntu1) over (2.31.0-0ubuntu5) ... 51s Preparing to unpack .../03-apport_2.31.0+git20250220-0ubuntu1_all.deb ... 51s Unpacking apport (2.31.0+git20250220-0ubuntu1) over (2.31.0-0ubuntu5) ... 51s Preparing to unpack .../04-libapparmor1_4.1.0~beta5-0ubuntu4_amd64.deb ... 51s Unpacking libapparmor1:amd64 (4.1.0~beta5-0ubuntu4) over (4.1.0~beta5-0ubuntu2) ... 51s Preparing to unpack .../05-apparmor_4.1.0~beta5-0ubuntu4_amd64.deb ... 52s Unpacking apparmor (4.1.0~beta5-0ubuntu4) over (4.1.0~beta5-0ubuntu2) ... 52s Selecting previously unselected package libjemalloc2:amd64. 52s Preparing to unpack .../06-libjemalloc2_5.3.0-2build1_amd64.deb ... 52s Unpacking libjemalloc2:amd64 (5.3.0-2build1) ... 52s Preparing to unpack .../07-bind9-dnsutils_1%3a9.20.4-3ubuntu1_amd64.deb ... 52s Unpacking bind9-dnsutils (1:9.20.4-3ubuntu1) over (1:9.20.0-2ubuntu4) ... 52s Preparing to unpack .../08-bind9-host_1%3a9.20.4-3ubuntu1_amd64.deb ... 52s Unpacking bind9-host (1:9.20.4-3ubuntu1) over (1:9.20.0-2ubuntu4) ... 52s Preparing to unpack .../09-bind9-libs_1%3a9.20.4-3ubuntu1_amd64.deb ... 52s Unpacking bind9-libs:amd64 (1:9.20.4-3ubuntu1) over (1:9.20.0-2ubuntu4) ... 52s Preparing to unpack .../10-cloud-init-base_25.1-0ubuntu1_all.deb ... 52s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 52s for fn in glob1(directory, "%s.*" % fname): 52s Unpacking cloud-init-base (25.1-0ubuntu1) over (25.1~3geb1965a4-0ubuntu1) ... 53s Preparing to unpack .../11-tmux_3.5a-3_amd64.deb ... 53s Unpacking tmux (3.5a-3) over (3.4-7) ... 53s Preparing to unpack .../12-cloud-init_25.1-0ubuntu1_all.deb ... 53s Unpacking cloud-init (25.1-0ubuntu1) over (25.1~3geb1965a4-0ubuntu1) ... 53s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu4) ... 53s Setting up python3-problem-report (2.31.0+git20250220-0ubuntu1) ... 53s Setting up libjemalloc2:amd64 (5.3.0-2build1) ... 53s Setting up cloud-init-base (25.1-0ubuntu1) ... 54s Setting up python3-apport (2.31.0+git20250220-0ubuntu1) ... 54s Setting up apparmor (4.1.0~beta5-0ubuntu4) ... 55s Installing new version of config file /etc/apparmor.d/sbuild ... 55s Installing new version of config file /etc/apparmor.d/sbuild-abort ... 55s Installing new version of config file /etc/apparmor.d/sbuild-adduser ... 55s Installing new version of config file /etc/apparmor.d/sbuild-apt ... 55s Installing new version of config file /etc/apparmor.d/sbuild-checkpackages ... 55s Installing new version of config file /etc/apparmor.d/sbuild-clean ... 55s Installing new version of config file /etc/apparmor.d/sbuild-createchroot ... 55s Installing new version of config file /etc/apparmor.d/sbuild-destroychroot ... 55s Installing new version of config file /etc/apparmor.d/sbuild-distupgrade ... 55s Installing new version of config file /etc/apparmor.d/sbuild-hold ... 55s Installing new version of config file /etc/apparmor.d/sbuild-shell ... 55s Installing new version of config file /etc/apparmor.d/sbuild-unhold ... 55s Installing new version of config file /etc/apparmor.d/sbuild-update ... 55s Installing new version of config file /etc/apparmor.d/sbuild-upgrade ... 56s Reloading AppArmor profiles 57s Setting up tmux (3.5a-3) ... 57s Setting up cloud-init (25.1-0ubuntu1) ... 57s Setting up bind9-libs:amd64 (1:9.20.4-3ubuntu1) ... 57s Setting up bind9-host (1:9.20.4-3ubuntu1) ... 57s Setting up bind9-dnsutils (1:9.20.4-3ubuntu1) ... 57s Setting up apport-core-dump-handler (2.31.0+git20250220-0ubuntu1) ... 59s Setting up apport (2.31.0+git20250220-0ubuntu1) ... 59s apport-autoreport.service is a disabled or a static unit not running, not starting it. 59s Processing triggers for debianutils (5.21) ... 59s Processing triggers for libc-bin (2.40-4ubuntu1) ... 59s Processing triggers for rsyslog (8.2412.0-2ubuntu1) ... 59s Processing triggers for systemd (257.2-3ubuntu1) ... 59s Processing triggers for man-db (2.13.0-1) ... 61s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 61s + /usr/lib/apt/apt-helper analyze-pattern ?true 61s + uname -r 61s + sed s/\./\\./g 61s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 61s + apt list ?obsolete 61s + tail+ cut -d/ -f1 61s -n+2 61s + grep -v ^linux-.*6\.12\.0-15-generic.* 62s Reading package lists...+ true 62s + obsolete_pkgs= 62s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 62s 62s Building dependency tree... 62s Reading state information... 62s Solving dependencies... 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s + grep -q trusty /etc/lsb-release 62s + [ ! -d /usr/share/doc/unattended-upgrades ] 62s + [ ! -d /usr/share/doc/lxd ] 62s + [ ! -d /usr/share/doc/lxd-client ] 62s + [ ! -d /usr/share/doc/snapd ] 62s + type iptables 62s + cat 62s + chmod 755 /etc/rc.local 62s + . /etc/rc.local 62s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 62s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 62s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 62s + uname -m 62s + [ x86_64 = ppc64le ] 62s + [ -d /run/systemd/system ] 62s + systemd-detect-virt --quiet --vm 62s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 62s + cat 62s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 62s + echo COMPRESS=lz4 62s autopkgtest [06:54:38]: upgrading testbed (apt dist-upgrade and autopurge) 62s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 63s Starting 2 pkgProblemResolver with broken count: 0 63s Done 64s Entering ResolveByKeep 64s 64s Calculating upgrade... 64s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Starting pkgProblemResolver with broken count: 0 65s Starting 2 pkgProblemResolver with broken count: 0 65s Done 65s Solving dependencies... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s autopkgtest [06:54:42]: rebooting testbed after setup commands that affected boot 70s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 81s autopkgtest [06:54:57]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 82s autopkgtest [06:54:58]: @@@@@@@@@@@@@@@@@@@@ apt-source gubbins 82s Get:1 http://ftpmaster.internal/ubuntu plucky/universe gubbins 3.4-1 (dsc) [2406 B] 82s Get:2 http://ftpmaster.internal/ubuntu plucky/universe gubbins 3.4-1 (tar) [2878 kB] 82s Get:3 http://ftpmaster.internal/ubuntu plucky/universe gubbins 3.4-1 (diff) [9624 B] 83s gpgv: Signature made Sat Nov 30 18:13:39 2024 UTC 83s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 83s gpgv: issuer "emollier@debian.org" 83s gpgv: Can't check signature: No public key 83s dpkg-source: warning: cannot verify inline signature for ./gubbins_3.4-1.dsc: no acceptable signature found 83s autopkgtest [06:54:59]: testing package gubbins version 3.4-1 83s autopkgtest [06:54:59]: build not needed 83s autopkgtest [06:54:59]: test run-example: preparing testbed 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Starting pkgProblemResolver with broken count: 0 84s Starting 2 pkgProblemResolver with broken count: 0 84s Done 85s The following NEW packages will be installed: 85s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 85s gubbins iqtree libamd-comgr2 libamdhip64-5 libblas3 libcairo2 libdeflate0 85s libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1 libfontenc1 85s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhsa-runtime64-1 85s libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libimagequant0 85s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 85s libllvm17t64 libmunge2 libopenjp2-7 libopenmpi40 libpciaccess0 libpixman-1-0 85s libpmix2t64 libpsm-infinipath1 libpsm2-2 libraqm0 librdmacm1t64 libsharpyuv0 85s libtiff6 libucx0 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 85s libxcb-shm0 libxnvctrl0 libxrender1 ocl-icd-libopencl1 python3-biopython 85s python3-cairo python3-decorator python3-dendropy python3-dill 85s python3-freetype python3-multiprocess python3-numpy python3-numpy-dev 85s python3-pil python3-reportlab python3-rlpycairo python3-scipy raxml 85s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 85s 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 124 MB of archives. 85s After this operation, 506 MB of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2 [147 kB] 85s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 85s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 85s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy amd64 1:2.2.3+ds-2 [8537 kB] 85s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 85s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 85s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 85s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 85s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 85s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 85s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 85s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 85s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 85s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250213-1ubuntu1 [148 kB] 85s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 85s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 85s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 85s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 85s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 85s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 85s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 85s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 85s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 85s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 85s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 85s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 85s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 85s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 85s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 85s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 85s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5 [589 kB] 85s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 86s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 86s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 86s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 86s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 86s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 86s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build1 [143 kB] 86s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 86s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 86s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.3.1-1 [1137 kB] 86s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 86s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 86s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.85+dfsg-2 [1745 kB] 86s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dendropy all 4.6.1-2 [278 kB] 86s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dill all 0.3.9-1 [84.5 kB] 86s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-multiprocess all 0.70.17-1 [108 kB] 86s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 86s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 86s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 87s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB] 87s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 gubbins amd64 3.4-1 [90.6 kB] 87s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 87s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 87s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 87s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 55.0-1ubuntu1 [71.5 kB] 87s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3.1 [789 kB] 87s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB] 87s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 87s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 87s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 87s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 87s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.12.0-1 [16.0 kB] 87s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.6-3 [714 kB] 87s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-20 [26.0 MB] 88s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 88s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 88s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 88s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 88s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 55.0-1ubuntu1 [29.7 kB] 88s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 55.0-1ubuntu1 [42.7 kB] 88s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.17.0+ds-3build1 [1162 kB] 88s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi40 amd64 5.0.7-1 [2526 kB] 88s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 iqtree amd64 2.0.7+dfsg-1build3 [8816 kB] 89s Fetched 124 MB in 4s (30.9 MB/s) 89s Selecting previously unselected package python3-numpy-dev:amd64. 89s (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 ... 108976 files and directories currently installed.) 89s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-2_amd64.deb ... 89s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... 89s Selecting previously unselected package libblas3:amd64. 89s Preparing to unpack .../01-libblas3_3.12.1-2_amd64.deb ... 89s Unpacking libblas3:amd64 (3.12.1-2) ... 89s Selecting previously unselected package libgfortran5:amd64. 89s Preparing to unpack .../02-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 89s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 89s Selecting previously unselected package liblapack3:amd64. 89s Preparing to unpack .../03-liblapack3_3.12.1-2_amd64.deb ... 89s Unpacking liblapack3:amd64 (3.12.1-2) ... 90s Selecting previously unselected package python3-numpy. 90s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-2_amd64.deb ... 90s Unpacking python3-numpy (1:2.2.3+ds-2) ... 90s Selecting previously unselected package sgml-base. 90s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 90s Unpacking sgml-base (1.31) ... 90s Selecting previously unselected package fonts-dejavu-mono. 90s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 90s Unpacking fonts-dejavu-mono (2.37-8) ... 90s Selecting previously unselected package fonts-dejavu-core. 90s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 90s Unpacking fonts-dejavu-core (2.37-8) ... 90s Selecting previously unselected package libfontenc1:amd64. 90s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 90s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 90s Selecting previously unselected package x11-common. 90s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu3_all.deb ... 90s Unpacking x11-common (1:7.7+23ubuntu3) ... 90s Selecting previously unselected package xfonts-encodings. 90s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 90s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 90s Selecting previously unselected package xfonts-utils. 90s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_amd64.deb ... 90s Unpacking xfonts-utils (1:7.7+7) ... 90s Selecting previously unselected package fonts-urw-base35. 90s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 90s Unpacking fonts-urw-base35 (20200910-8) ... 91s Selecting previously unselected package fontconfig-config. 91s Preparing to unpack .../13-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 91s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 91s Selecting previously unselected package libgomp1:amd64. 91s Preparing to unpack .../14-libgomp1_15-20250213-1ubuntu1_amd64.deb ... 91s Unpacking libgomp1:amd64 (15-20250213-1ubuntu1) ... 91s Selecting previously unselected package libimagequant0:amd64. 91s Preparing to unpack .../15-libimagequant0_2.18.0-1build1_amd64.deb ... 91s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 91s Selecting previously unselected package libjpeg-turbo8:amd64. 91s Preparing to unpack .../16-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 91s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 91s Selecting previously unselected package libjpeg8:amd64. 91s Preparing to unpack .../17-libjpeg8_8c-2ubuntu11_amd64.deb ... 91s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 91s Selecting previously unselected package liblcms2-2:amd64. 91s Preparing to unpack .../18-liblcms2-2_2.16-2_amd64.deb ... 91s Unpacking liblcms2-2:amd64 (2.16-2) ... 91s Selecting previously unselected package libopenjp2-7:amd64. 91s Preparing to unpack .../19-libopenjp2-7_2.5.0-2ubuntu3_amd64.deb ... 91s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 91s Selecting previously unselected package libgraphite2-3:amd64. 91s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 91s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 91s Selecting previously unselected package libharfbuzz0b:amd64. 91s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_amd64.deb ... 91s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 91s Selecting previously unselected package libraqm0:amd64. 91s Preparing to unpack .../22-libraqm0_0.10.2-1_amd64.deb ... 91s Unpacking libraqm0:amd64 (0.10.2-1) ... 91s Selecting previously unselected package libdeflate0:amd64. 91s Preparing to unpack .../23-libdeflate0_1.23-1_amd64.deb ... 91s Unpacking libdeflate0:amd64 (1.23-1) ... 91s Selecting previously unselected package libjbig0:amd64. 91s Preparing to unpack .../24-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 91s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 91s Selecting previously unselected package liblerc4:amd64. 91s Preparing to unpack .../25-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 91s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 91s Selecting previously unselected package libsharpyuv0:amd64. 91s Preparing to unpack .../26-libsharpyuv0_1.5.0-0.1_amd64.deb ... 91s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 91s Selecting previously unselected package libwebp7:amd64. 91s Preparing to unpack .../27-libwebp7_1.5.0-0.1_amd64.deb ... 91s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 91s Selecting previously unselected package libtiff6:amd64. 91s Preparing to unpack .../28-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 91s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 91s Selecting previously unselected package libwebpdemux2:amd64. 91s Preparing to unpack .../29-libwebpdemux2_1.5.0-0.1_amd64.deb ... 91s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 91s Selecting previously unselected package libwebpmux3:amd64. 91s Preparing to unpack .../30-libwebpmux3_1.5.0-0.1_amd64.deb ... 91s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 91s Selecting previously unselected package python3-pil:amd64. 91s Preparing to unpack .../31-python3-pil_11.1.0-5_amd64.deb ... 91s Unpacking python3-pil:amd64 (11.1.0-5) ... 91s Selecting previously unselected package libfontconfig1:amd64. 91s Preparing to unpack .../32-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 91s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 91s Selecting previously unselected package libpixman-1-0:amd64. 91s Preparing to unpack .../33-libpixman-1-0_0.44.0-3_amd64.deb ... 91s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 92s Selecting previously unselected package libxcb-render0:amd64. 92s Preparing to unpack .../34-libxcb-render0_1.17.0-2_amd64.deb ... 92s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 92s Selecting previously unselected package libxcb-shm0:amd64. 92s Preparing to unpack .../35-libxcb-shm0_1.17.0-2_amd64.deb ... 92s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 92s Selecting previously unselected package libxrender1:amd64. 92s Preparing to unpack .../36-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 92s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 92s Selecting previously unselected package libcairo2:amd64. 92s Preparing to unpack .../37-libcairo2_1.18.2-2_amd64.deb ... 92s Unpacking libcairo2:amd64 (1.18.2-2) ... 92s Selecting previously unselected package python3-cairo. 92s Preparing to unpack .../38-python3-cairo_1.26.1-2build1_amd64.deb ... 92s Unpacking python3-cairo (1.26.1-2build1) ... 92s Selecting previously unselected package python3-freetype. 92s Preparing to unpack .../39-python3-freetype_2.5.1-1_all.deb ... 92s Unpacking python3-freetype (2.5.1-1) ... 92s Selecting previously unselected package python3-rlpycairo. 92s Preparing to unpack .../40-python3-rlpycairo_0.3.0-3_all.deb ... 92s Unpacking python3-rlpycairo (0.3.0-3) ... 92s Selecting previously unselected package python3-reportlab. 92s Preparing to unpack .../41-python3-reportlab_4.3.1-1_all.deb ... 92s Unpacking python3-reportlab (4.3.1-1) ... 92s Selecting previously unselected package xml-core. 92s Preparing to unpack .../42-xml-core_0.19_all.deb ... 92s Unpacking xml-core (0.19) ... 92s Selecting previously unselected package w3c-sgml-lib. 92s Preparing to unpack .../43-w3c-sgml-lib_1.3-3_all.deb ... 92s Unpacking w3c-sgml-lib (1.3-3) ... 92s Selecting previously unselected package python3-biopython. 92s Preparing to unpack .../44-python3-biopython_1.85+dfsg-2_amd64.deb ... 92s Unpacking python3-biopython (1.85+dfsg-2) ... 92s Selecting previously unselected package python3-dendropy. 92s Preparing to unpack .../45-python3-dendropy_4.6.1-2_all.deb ... 92s Unpacking python3-dendropy (4.6.1-2) ... 92s Selecting previously unselected package python3-dill. 92s Preparing to unpack .../46-python3-dill_0.3.9-1_all.deb ... 92s Unpacking python3-dill (0.3.9-1) ... 92s Selecting previously unselected package python3-multiprocess. 92s Preparing to unpack .../47-python3-multiprocess_0.70.17-1_all.deb ... 92s Unpacking python3-multiprocess (0.70.17-1) ... 92s Selecting previously unselected package python3-decorator. 92s Preparing to unpack .../48-python3-decorator_5.1.1-5_all.deb ... 92s Unpacking python3-decorator (5.1.1-5) ... 92s Selecting previously unselected package liblbfgsb0:amd64. 92s Preparing to unpack .../49-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 92s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 92s Selecting previously unselected package python3-scipy. 92s Preparing to unpack .../50-python3-scipy_1.14.1-4ubuntu1_amd64.deb ... 92s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 93s Selecting previously unselected package raxml. 93s Preparing to unpack .../51-raxml_8.2.13+dfsg-1_amd64.deb ... 93s Unpacking raxml (8.2.13+dfsg-1) ... 93s Selecting previously unselected package gubbins. 93s Preparing to unpack .../52-gubbins_3.4-1_amd64.deb ... 93s Unpacking gubbins (3.4-1) ... 93s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 93s Preparing to unpack .../53-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 93s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 93s Selecting previously unselected package libpsm-infinipath1. 93s Preparing to unpack .../54-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 93s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 93s Selecting previously unselected package libpsm2-2. 93s Preparing to unpack .../55-libpsm2-2_11.2.185-2.1_amd64.deb ... 93s Unpacking libpsm2-2 (11.2.185-2.1) ... 93s Selecting previously unselected package librdmacm1t64:amd64. 93s Preparing to unpack .../56-librdmacm1t64_55.0-1ubuntu1_amd64.deb ... 93s Unpacking librdmacm1t64:amd64 (55.0-1ubuntu1) ... 93s Selecting previously unselected package libfabric1:amd64. 93s Preparing to unpack .../57-libfabric1_1.17.0-3.1_amd64.deb ... 93s Unpacking libfabric1:amd64 (1.17.0-3.1) ... 93s Selecting previously unselected package libhwloc15:amd64. 93s Preparing to unpack .../58-libhwloc15_2.12.0-1_amd64.deb ... 93s Unpacking libhwloc15:amd64 (2.12.0-1) ... 93s Selecting previously unselected package libmunge2:amd64. 93s Preparing to unpack .../59-libmunge2_0.5.16-1_amd64.deb ... 93s Unpacking libmunge2:amd64 (0.5.16-1) ... 93s Selecting previously unselected package libpciaccess0:amd64. 93s Preparing to unpack .../60-libpciaccess0_0.17-3build1_amd64.deb ... 93s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 93s Selecting previously unselected package libxnvctrl0:amd64. 93s Preparing to unpack .../61-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 93s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 93s Selecting previously unselected package ocl-icd-libopencl1:amd64. 94s Preparing to unpack .../62-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 94s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 94s Selecting previously unselected package libhwloc-plugins:amd64. 94s Preparing to unpack .../63-libhwloc-plugins_2.12.0-1_amd64.deb ... 94s Unpacking libhwloc-plugins:amd64 (2.12.0-1) ... 94s Selecting previously unselected package libpmix2t64:amd64. 94s Preparing to unpack .../64-libpmix2t64_5.0.6-3_amd64.deb ... 94s Unpacking libpmix2t64:amd64 (5.0.6-3) ... 94s Selecting previously unselected package libllvm17t64:amd64. 94s Preparing to unpack .../65-libllvm17t64_1%3a17.0.6-20_amd64.deb ... 94s Unpacking libllvm17t64:amd64 (1:17.0.6-20) ... 94s Selecting previously unselected package libamd-comgr2:amd64. 94s Preparing to unpack .../66-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 94s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 95s Selecting previously unselected package libhsakmt1:amd64. 95s Preparing to unpack .../67-libhsakmt1_5.7.0-1build1_amd64.deb ... 95s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 95s Selecting previously unselected package libhsa-runtime64-1. 95s Preparing to unpack .../68-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 95s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 95s Selecting previously unselected package libamdhip64-5. 95s Preparing to unpack .../69-libamdhip64-5_5.7.1-5_amd64.deb ... 95s Unpacking libamdhip64-5 (5.7.1-5) ... 95s Selecting previously unselected package libibumad3:amd64. 95s Preparing to unpack .../70-libibumad3_55.0-1ubuntu1_amd64.deb ... 95s Unpacking libibumad3:amd64 (55.0-1ubuntu1) ... 95s Selecting previously unselected package libibmad5:amd64. 95s Preparing to unpack .../71-libibmad5_55.0-1ubuntu1_amd64.deb ... 95s Unpacking libibmad5:amd64 (55.0-1ubuntu1) ... 95s Selecting previously unselected package libucx0:amd64. 95s Preparing to unpack .../72-libucx0_1.17.0+ds-3build1_amd64.deb ... 95s Unpacking libucx0:amd64 (1.17.0+ds-3build1) ... 95s Selecting previously unselected package libopenmpi40:amd64. 95s Preparing to unpack .../73-libopenmpi40_5.0.7-1_amd64.deb ... 95s Unpacking libopenmpi40:amd64 (5.0.7-1) ... 95s Selecting previously unselected package iqtree. 95s Preparing to unpack .../74-iqtree_2.0.7+dfsg-1build3_amd64.deb ... 95s Unpacking iqtree (2.0.7+dfsg-1build3) ... 95s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 95s Setting up liblcms2-2:amd64 (2.16-2) ... 95s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 95s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 95s Setting up libpciaccess0:amd64 (0.17-3build1) ... 95s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 95s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 95s Setting up libxcb-render0:amd64 (1.17.0-2) ... 95s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 95s Setting up x11-common (1:7.7+23ubuntu3) ... 96s Setting up libibumad3:amd64 (55.0-1ubuntu1) ... 96s Setting up libdeflate0:amd64 (1.23-1) ... 96s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 96s Setting up libibmad5:amd64 (55.0-1ubuntu1) ... 96s Setting up libgomp1:amd64 (15-20250213-1ubuntu1) ... 96s Setting up python3-freetype (2.5.1-1) ... 96s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 96s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 96s Setting up python3-decorator (5.1.1-5) ... 96s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 96s Setting up libblas3:amd64 (3.12.1-2) ... 96s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 96s Setting up libmunge2:amd64 (0.5.16-1) ... 96s Setting up libllvm17t64:amd64 (1:17.0.6-20) ... 96s Setting up python3-dill (0.3.9-1) ... 96s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 96s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 96s Setting up fonts-dejavu-mono (2.37-8) ... 96s Setting up libhwloc15:amd64 (2.12.0-1) ... 96s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... 96s Setting up fonts-dejavu-core (2.37-8) ... 96s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 96s Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 96s Setting up libwebp7:amd64 (1.5.0-0.1) ... 96s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 96s Setting up libpsm2-2 (11.2.185-2.1) ... 96s Setting up librdmacm1t64:amd64 (55.0-1ubuntu1) ... 96s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 96s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 96s Setting up sgml-base (1.31) ... 96s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 96s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 96s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 96s Setting up python3-multiprocess (0.70.17-1) ... 97s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 97s Setting up python3-dendropy (4.6.1-2) ... 97s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 97s Setting up raxml (8.2.13+dfsg-1) ... 97s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 97s Setting up libfabric1:amd64 (1.17.0-3.1) ... 97s Setting up liblapack3:amd64 (3.12.1-2) ... 97s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 97s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 97s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 97s Setting up xfonts-utils (1:7.7+7) ... 97s Setting up libhwloc-plugins:amd64 (2.12.0-1) ... 97s Setting up libraqm0:amd64 (0.10.2-1) ... 97s Setting up libpmix2t64:amd64 (5.0.6-3) ... 97s Setting up python3-numpy (1:2.2.3+ds-2) ... 99s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 99s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 99s Setting up xml-core (0.19) ... 99s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 99s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 99s Setting up python3-scipy (1.14.1-4ubuntu1) ... 103s Setting up fonts-urw-base35 (20200910-8) ... 103s Setting up libcairo2:amd64 (1.18.2-2) ... 103s Setting up python3-pil:amd64 (11.1.0-5) ... 103s Setting up libamdhip64-5 (5.7.1-5) ... 103s Setting up libucx0:amd64 (1.17.0+ds-3build1) ... 103s Setting up python3-cairo (1.26.1-2build1) ... 103s Setting up python3-rlpycairo (0.3.0-3) ... 103s Setting up python3-reportlab (4.3.1-1) ... 104s Setting up libopenmpi40:amd64 (5.0.7-1) ... 104s Setting up iqtree (2.0.7+dfsg-1build3) ... 104s Processing triggers for man-db (2.13.0-1) ... 106s Processing triggers for libc-bin (2.40-4ubuntu1) ... 106s Processing triggers for sgml-base (1.31) ... 106s Setting up w3c-sgml-lib (1.3-3) ... 135s Setting up python3-biopython (1.85+dfsg-2) ... 136s Setting up gubbins (3.4-1) ... 136s Processing triggers for libc-bin (2.40-4ubuntu1) ... 137s autopkgtest [06:55:53]: test run-example: [----------------------- 137s ##### alignment_file_multiple_lines_per_sequence.aln ##### 140s Use raxml with AVX support (1 cpus) 140s 140s WARNING: The number of threads is currently set to 1 140s You can specify the number of threads to run via -T numberOfThreads 140s NumberOfThreads must be set to an integer value greater than 1 140s 140s RAxML, will now set the number of threads automatically to 2 ! 140s 140s Warning, you specified a working directory via "-w" 140s Keep in mind that RAxML only accepts absolute path names, not relative ones! 140s 140s RAxML can't, parse the alignment file as phylip file 140s it will now try to parse it as FASTA file 140s 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 2956_6_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 2956_6_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 2956_6_4 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 2956_6_5 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 2956_6_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 3002_8_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 3002_8_4 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 3002_8_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_2_11 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_2_1 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_2_12 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_2_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_2_5 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_2_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_2_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_2_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_10 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_11 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_12 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_4 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_5 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_6_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_7_10 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_7_11 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_7_1 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_7_12 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_7_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_7_8 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_7_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_8_10 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_8_1 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_8_12 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_8_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_8_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_8_4 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_8_8 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4056_8_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4075_3_11 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4075_3_12 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4075_3_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4075_3_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4075_3_5 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4075_3_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4075_3_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4075_3_8 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4075_3_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_2_11 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_2_12 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_2_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_2_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_2_4 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_2_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_2_8 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_2_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_3_11 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_3_1 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_3_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_3_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 4370_3_8 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_5_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_5_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_5_4 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_5_5 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_5_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_6_1 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_6_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_6_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_6_4 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_6_5 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_6_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_6_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_6_8 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_6_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_7_10 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_7_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_7_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_7_4 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_7_5 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_7_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_7_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_7_8 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_7_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_8_1 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_8_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_8_3 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_8_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_8_8 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 2956_6_1 and 5174_8_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 3002_8_2 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 3002_8_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 4056_2_10 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 4056_8_6 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 5174_5_1 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 5174_5_7 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 5174_5_9 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 5174_6_10 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 5174_7_1 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_1 and 5174_8_5 are exactly identical 140s 140s 140s IMPORTANT WARNING: Sequences 3002_8_5 and 4056_2_3 are exactly identical 140s 140s IMPORTANT WARNING 140s Found 103 sequences that are exactly identical to other sequences in the alignment. 140s Normally they should be excluded from the analysis. 140s 140s Just in case you might need it, an alignment file with 140s sequence duplicates removed is printed to file alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln.reduced 140s 140s 140s Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" 140s 140s 140s This is the RAxML Master Pthread 140s 140s This is RAxML Worker Pthread Number: 1 140s 140s 140s This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018. 140s 140s With greatly appreciated code contributions by: 140s Andre Aberer (HITS) 140s Simon Berger (HITS) 140s Alexey Kozlov (HITS) 140s Kassian Kobert (HITS) 140s David Dao (KIT and HITS) 140s Sarah Lutteropp (KIT and HITS) 140s Nick Pattengale (Sandia) 140s Wayne Pfeiffer (SDSC) 140s Akifumi S. Tanabe (NRIFS) 140s Charlie Taylor (UF) 140s 140s 140s Alignment has 2 distinct alignment patterns 140s 140s Proportion of gaps and completely undetermined characters in this alignment: 0.93% 140s 140s RAxML Model Optimization up to an accuracy of 0.100000 log likelihood units 140s 140s Using 1 distinct models/data partitions with joint branch length optimization 140s 140s 140s All free model parameters will be estimated by RAxML 140s GAMMA model of rate heterogeneity, ML estimate of alpha-parameter 140s 140s GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units 140s 140s Partition: 0 140s Alignment Patterns: 2 140s Name: No Name Provided 140s DataType: DNA 140s Substitution Matrix: GTR 140s 140s 140s 140s 140s RAxML was called as follows: 140s 140s /usr/bin/raxmlHPC-PTHREADS-AVX -T 1 -safe -m GTRGAMMA -p 2938 -s alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln -n alignment_file_multiple_lines_per_sequence.iteration_1_reconstruction -t /tmp/tmp.th3N4CXw75/tmpjiql_591/alignment_file_multiple_lines_per_sequence.iteration_1.tre.rooted -f e -w /tmp/tmp.th3N4CXw75/tmpjiql_591 140s 140s 140s 140s Model parameters (binary file format) written to: /tmp/tmp.th3N4CXw75/tmpjiql_591/RAxML_binaryModelParameters.alignment_file_multiple_lines_per_sequence.iteration_1_reconstruction 140s 0.045489 -11.101028 140s 140s 140s Overall Time for Tree Evaluation 0.045654 140s Final GAMMA likelihood: -11.101028 140s 140s Number of free parameters for AIC-TEST(BR-LEN): 220 140s Number of free parameters for AIC-TEST(NO-BR-LEN): 9 140s 140s 140s Model Parameters of Partition 0, Name: No Name Provided, Type of Data: DNA 140s alpha: 8.441832 140s Tree-Length: 2.162953 140s rate A <-> C: 0.000100 140s rate A <-> G: 0.307258 140s rate A <-> T: 0.000100 140s rate C <-> G: 0.000100 140s rate C <-> T: 2.562609 140s rate G <-> T: 1.000000 140s 140s freq pi(A): 0.438679 140s freq pi(C): 0.500000 140s freq pi(G): 0.056604 140s freq pi(T): 0.004717 140s 140s Final tree written to: /tmp/tmp.th3N4CXw75/tmpjiql_591/RAxML_result.alignment_file_multiple_lines_per_sequence.iteration_1_reconstruction 140s Execution Log File written to: /tmp/tmp.th3N4CXw75/tmpjiql_591/RAxML_log.alignment_file_multiple_lines_per_sequence.iteration_1_reconstruction 140s 140s --- Gubbins 3.4 --- 140s 140s Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R. "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196. 140s 140s Checking dependencies and input files... 140s 140s Checking input alignment file... 140s 140s Filtering input alignment... 140s Excluded sequence Vibrio_parahaemolyticus because it had 98.5 percentage missing data while a maximum of 25.0 is allowed 140s Excluded sequence Vibrio_vulnificus because it had 98.5 percentage missing data while a maximum of 25.0 is allowed 140s ...done. Run time: 0.06 s 140s 140s Running Gubbins to detect SNPs... 140s gubbins "/tmp/tmp.th3N4CXw75/tmpjiql_591/alignment_file_multiple_lines_per_sequence.aln" 140s ...done. Run time: 0.08 s 140s 140s Entering the main loop. 140s 140s *** Iteration 1 *** 140s 140s Constructing the phylogenetic tree with raxmlHPC... 140s raxmlHPC -safe -m GTRGAMMA -p 6101 -f d -p 1 -s /tmp/tmp.th3N4CXw75/alignment_file_multiple_lines_per_sequence.aln.phylip -n alignment_file_multiple_lines_per_sequence.iteration_1 > /dev/null 2>&1 140s ...done. Run time: 2.46 s 140s 140s Reconstructing ancestral sequences with pyjar... 140s 140s Fitting substitution model to tree... 140s raxmlHPC -safe -m GTRGAMMA -p 2938 -s alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln -n alignment_file_multiple_lines_per_sequence.iteration_1_reconstruction -t /tmp/tmp.th3N4CXw75/tmpjiql_591/alignment_file_multiple_lines_per_sequence.iteration_1.tre.rooted -f e -w /tmp/tmp.th3N4CXw75/tmpjiql_591 140s 140s Running joint ancestral reconstruction with pyjar 142s Traceback (most recent call last): 142s File "/usr/bin/run_gubbins", line 33, in 142s sys.exit(load_entry_point('gubbins==3.4', 'console_scripts', 'run_gubbins.py')()) 142s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 142s File "/usr/share/gubbins/gubbins/run_gubbins.py", line 166, in main 142s gubbins.common.parse_and_run(parser.parse_args(), parser.description) 142s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 142s File "/usr/share/gubbins/gubbins/common.py", line 373, in parse_and_run 142s jar(sequence_names = ordered_sequence_names, # complete polymorphism alignment 142s ~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 142s base_patterns = base_pattern_bases_array, # array of unique base patterns in alignment 142s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 142s ...<8 lines>... 142s verbose = input_args.verbose, 142s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 142s max_pos = max_pos) 142s ^^^^^^^^^^^^^^^^^^ 142s File "/usr/share/gubbins/gubbins/pyjar.py", line 646, in jar 142s node_pij = numpy.full((num_nodes,16), numpy.NINF, dtype=numpy.float32) 142s ^^^^^^^^^^ 142s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ 142s raise AttributeError( 142s ...<3 lines>... 142s ) 142s AttributeError: `np.NINF` was removed in the NumPy 2.0 release. Use `-np.inf` instead. 142s autopkgtest [06:55:58]: test run-example: -----------------------] 143s autopkgtest [06:55:59]: test run-example: - - - - - - - - - - results - - - - - - - - - - 143s run-example FAIL non-zero exit status 1 143s autopkgtest [06:55:59]: @@@@@@@@@@@@@@@@@@@@ summary 143s run-example FAIL non-zero exit status 1 159s nova [W] Skipping flock for amd64 159s Creating nova instance adt-plucky-amd64-gubbins-20250221-065336-juju-7f2275-prod-proposed-migration-environment-15-1786bc5d-57b8-4e84-96c0-5918fbdf5b60 from image adt/ubuntu-plucky-amd64-server-20250221.img (UUID c1e73dc6-ac8e-4368-b017-f8cd363a3a68)... 159s nova [W] Timed out waiting for 3465d737-8440-4ed5-ab0b-b850e7936ba0 to get deleted.