0s autopkgtest [05:28:00]: starting date: 2024-03-11 0s autopkgtest [05:28:00]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [05:28:00]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mv4mr0t3/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:cairo,src:glib2.0,src:libpng1.6,src:wp2latex --apt-upgrade bali-phy --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=cairo/1.18.0-1ubuntu1 glib2.0/2.79.3-3ubuntu3 libpng1.6/1.6.43-3 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-2.secgroup --name adt-noble-arm64-bali-phy-20240311-052800-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/ 100s autopkgtest [05:29:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 100s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 100s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [434 kB] 101s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 101s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 101s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2622 kB] 101s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [581 kB] 101s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 101s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 101s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 101s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2967 kB] 101s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 101s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB] 101s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 102s Fetched 6833 kB in 1s (4990 kB/s) 102s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 106s The following packages will be REMOVED: 106s libglib2.0-0 106s The following NEW packages will be installed: 106s libglib2.0-0t64 xdg-user-dirs 106s The following packages will be upgraded: 106s gir1.2-glib-2.0 libglib2.0-data 106s 2 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 106s Need to get 1774 kB of archives. 106s After this operation, 138 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 106s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 106s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 106s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 107s Fetched 1774 kB in 1s (2972 kB/s) 107s (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 ... 74748 files and directories currently installed.) 107s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 107s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 107s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 107s udisks2 depends on libglib2.0-0 (>= 2.77.0). 107s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 107s python3-gi depends on libglib2.0-0 (>= 2.77.0). 107s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 107s netplan.io depends on libglib2.0-0 (>= 2.70.0). 107s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 107s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 107s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 107s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 107s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 107s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 107s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 107s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 107s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 107s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 107s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 107s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 107s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 107s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 107s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 107s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 107s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 107s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 107s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 107s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 107s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 107s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 107s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 107s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 107s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 107s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 107s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 107s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 107s fwupd depends on libglib2.0-0 (>= 2.79.0). 107s bolt depends on libglib2.0-0 (>= 2.56.0). 107s 107s (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 ... 74748 files and directories currently installed.) 107s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 107s Selecting previously unselected package libglib2.0-0t64:arm64. 107s (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 ... 74723 files and directories currently installed.) 107s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 107s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 107s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 107s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 107s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 107s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 107s Selecting previously unselected package xdg-user-dirs. 107s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 107s Unpacking xdg-user-dirs (0.18-1) ... 107s Setting up xdg-user-dirs (0.18-1) ... 107s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 107s No schema files found: doing nothing. 107s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 107s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 107s Processing triggers for man-db (2.12.0-3) ... 108s Processing triggers for libc-bin (2.39-0ubuntu2) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s sh: Attempting to set up Debian/Ubuntu apt sources automatically 110s sh: Distribution appears to be Ubuntu 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s eatmydata is already the newest version (131-1). 111s dbus is already the newest version (1.14.10-4ubuntu1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s rng-tools-debian is already the newest version (2.4). 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s haveged is already the newest version (1.9.14-1ubuntu1). 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 114s The following packages will be REMOVED: 114s cloud-init* python3-configobj* python3-debconf* 114s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 114s After this operation, 3248 kB disk space will be freed. 114s (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 ... 74762 files and directories currently installed.) 114s Removing cloud-init (24.1-0ubuntu1) ... 115s Removing python3-configobj (5.0.8-3) ... 115s Removing python3-debconf (1.5.86) ... 115s Processing triggers for man-db (2.12.0-3) ... 115s (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 ... 74373 files and directories currently installed.) 115s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 116s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 116s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s linux-generic is already the newest version (6.8.0-11.11+1). 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 118s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 118s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 118s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 119s Reading package lists... 119s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Calculating upgrade... 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s autopkgtest [05:30:03]: rebooting testbed after setup commands that affected boot 149s autopkgtest [05:30:29]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 150s autopkgtest [05:30:30]: testbed dpkg architecture: arm64 151s autopkgtest [05:30:31]: @@@@@@@@@@@@@@@@@@@@ apt-source bali-phy 153s Get:1 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (dsc) [2216 B] 153s Get:2 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (tar) [1124 kB] 153s Get:3 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (diff) [5408 B] 153s gpgv: Signature made Tue Dec 19 15:00:40 2023 UTC 153s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 153s gpgv: Can't check signature: No public key 153s dpkg-source: warning: cannot verify inline signature for ./bali-phy_3.6.1+dfsg-2build1.dsc: no acceptable signature found 153s autopkgtest [05:30:33]: testing package bali-phy version 3.6.1+dfsg-2build1 153s autopkgtest [05:30:33]: build not needed 154s autopkgtest [05:30:34]: test run-unit-test: preparing testbed 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 161s Starting 2 pkgProblemResolver with broken count: 0 161s Done 162s Done 162s Starting pkgProblemResolver with broken count: 0 162s Starting 2 pkgProblemResolver with broken count: 0 162s Done 163s The following additional packages will be installed: 163s bali-phy fontconfig-config fonts-dejavu-core fonts-dejavu-mono 163s libboost-chrono1.83.0 libboost-filesystem1.83.0 163s libboost-program-options1.83.0 libboost-random1.83.0 libcairo2 163s libfontconfig1 libpixman-1-0 libpng16-16t64 libxcb-render0 libxcb-shm0 163s libxrender1 163s Suggested packages: 163s figtree seaview 163s Recommended packages: 163s r-base gnuplot 163s The following packages will be REMOVED: 163s libpng16-16 163s The following NEW packages will be installed: 163s bali-phy fontconfig-config fonts-dejavu-core fonts-dejavu-mono 163s libboost-chrono1.83.0 libboost-filesystem1.83.0 163s libboost-program-options1.83.0 libboost-random1.83.0 libcairo2 163s libfontconfig1 libpixman-1-0 libpng16-16t64 libxcb-render0 libxcb-shm0 163s libxrender1 163s 0 upgraded, 15 newly installed, 1 to remove and 0 not upgraded. 163s 1 not fully installed or removed. 163s Need to get 11.5 MB of archives. 163s After this operation, 37.0 MB of additional disk space will be used. 163s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-chrono1.83.0 arm64 1.83.0-2ubuntu1 [322 kB] 163s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-2ubuntu1 [366 kB] 163s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2ubuntu1 [410 kB] 163s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-random1.83.0 arm64 1.83.0-2ubuntu1 [320 kB] 163s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 163s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 163s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 163s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 163s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 163s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 163s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 163s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 163s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 163s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcairo2 arm64 1.18.0-1ubuntu1 [555 kB] 163s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 bali-phy arm64 3.6.1+dfsg-2build1 [7575 kB] 164s Fetched 11.5 MB in 1s (12.3 MB/s) 164s Selecting previously unselected package libboost-chrono1.83.0:arm64. 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 ... 74318 files and directories currently installed.) 164s Preparing to unpack .../0-libboost-chrono1.83.0_1.83.0-2ubuntu1_arm64.deb ... 164s Unpacking libboost-chrono1.83.0:arm64 (1.83.0-2ubuntu1) ... 164s Selecting previously unselected package libboost-filesystem1.83.0:arm64. 164s Preparing to unpack .../1-libboost-filesystem1.83.0_1.83.0-2ubuntu1_arm64.deb ... 164s Unpacking libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 164s Selecting previously unselected package libboost-program-options1.83.0:arm64. 164s Preparing to unpack .../2-libboost-program-options1.83.0_1.83.0-2ubuntu1_arm64.deb ... 164s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 164s Selecting previously unselected package libboost-random1.83.0:arm64. 164s Preparing to unpack .../3-libboost-random1.83.0_1.83.0-2ubuntu1_arm64.deb ... 164s Unpacking libboost-random1.83.0:arm64 (1.83.0-2ubuntu1) ... 164s Selecting previously unselected package fonts-dejavu-mono. 164s Preparing to unpack .../4-fonts-dejavu-mono_2.37-8_all.deb ... 164s Unpacking fonts-dejavu-mono (2.37-8) ... 164s Selecting previously unselected package fonts-dejavu-core. 164s Preparing to unpack .../5-fonts-dejavu-core_2.37-8_all.deb ... 164s Unpacking fonts-dejavu-core (2.37-8) ... 164s Selecting previously unselected package fontconfig-config. 164s Preparing to unpack .../6-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 164s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 164s Selecting previously unselected package libfontconfig1:arm64. 165s Preparing to unpack .../7-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 165s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 165s Selecting previously unselected package libpixman-1-0:arm64. 165s Preparing to unpack .../8-libpixman-1-0_0.42.2-1_arm64.deb ... 165s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 165s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 165s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 165s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 165s 165s (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 ... 74480 files and directories currently installed.) 165s Removing libpng16-16:arm64 (1.6.43-1) ... 165s Selecting previously unselected package libpng16-16t64:arm64. 165s (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 ... 74470 files and directories currently installed.) 165s Preparing to unpack .../0-libpng16-16t64_1.6.43-3_arm64.deb ... 165s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 165s Selecting previously unselected package libxcb-render0:arm64. 165s Preparing to unpack .../1-libxcb-render0_1.15-1_arm64.deb ... 165s Unpacking libxcb-render0:arm64 (1.15-1) ... 165s Selecting previously unselected package libxcb-shm0:arm64. 165s Preparing to unpack .../2-libxcb-shm0_1.15-1_arm64.deb ... 165s Unpacking libxcb-shm0:arm64 (1.15-1) ... 165s Selecting previously unselected package libxrender1:arm64. 165s Preparing to unpack .../3-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 165s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 165s Selecting previously unselected package libcairo2:arm64. 165s Preparing to unpack .../4-libcairo2_1.18.0-1ubuntu1_arm64.deb ... 165s Unpacking libcairo2:arm64 (1.18.0-1ubuntu1) ... 165s Selecting previously unselected package bali-phy. 165s Preparing to unpack .../5-bali-phy_3.6.1+dfsg-2build1_arm64.deb ... 165s Unpacking bali-phy (3.6.1+dfsg-2build1) ... 165s Setting up libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 165s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 165s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 165s Setting up libxcb-render0:arm64 (1.15-1) ... 165s Setting up libboost-random1.83.0:arm64 (1.83.0-2ubuntu1) ... 165s Setting up libxcb-shm0:arm64 (1.15-1) ... 165s Setting up libboost-filesystem1.83.0:arm64 (1.83.0-2ubuntu1) ... 165s Setting up fonts-dejavu-mono (2.37-8) ... 165s Setting up libpng16-16t64:arm64 (1.6.43-3) ... 165s Setting up fonts-dejavu-core (2.37-8) ... 165s Setting up libboost-chrono1.83.0:arm64 (1.83.0-2ubuntu1) ... 165s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 165s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 165s Setting up libcairo2:arm64 (1.18.0-1ubuntu1) ... 165s Setting up bali-phy (3.6.1+dfsg-2build1) ... 165s Setting up autopkgtest-satdep (0) ... 165s Processing triggers for man-db (2.12.0-3) ... 166s Processing triggers for libc-bin (2.39-0ubuntu2) ... 169s (Reading database ... 75044 files and directories currently installed.) 169s Removing autopkgtest-satdep (0) ... 170s autopkgtest [05:30:50]: test run-unit-test: [----------------------- 170s VERSION: 3.6.1 [3.6.1] 170s BUILD: Dec 19 2023 14:51:09 170s ARCH: linux aarch64 170s COMPILER: gcc 13.2.0 aarch64 171s Bayesian Inference of Alignment and Phylogeny 171s Usage: bali-phy [ ...] [OPTIONS] 171s Basic options: 171s 171s General options: 171s -h [ --help ] [=arg(=basic)] Print usage information. 171s -v [ --version ] Print version information. 171s -t [ --test ] Analyze the initial values and exit. 171s -c [ --config ] arg Command file to read. 171s 171s MCMC options: 171s -i [ --iterations ] arg The number of iterations to run. 171s -n [ --name ] arg Name for the output directory to create. 171s 171s Parameter options: 171s --align arg Sequence file & initial alignment. 171s -T [ --tree ] arg File with initial tree 171s 171s Model options: 171s -A [ --alphabet ] arg The alphabet. 171s -S [ --smodel ] arg Substitution model. 171s -I [ --imodel ] arg Insertion-deletion model. 171s -R [ --scale ] arg Prior on the scale. 171s -L [ --link ] arg Link partitions. 171s 171s Showing basic command line options. Not all options are shown! 171s * See `bali-phy help advanced` to see more options. 171s 171s See `bali-phy help option` for help on option. For example, 171s * `bali-phy help alphabet` shows help on the --alphabet command. 171s * `bali-phy help normal` shows help on the normal distribution. 171s * `bali-phy help tn93` shows help on the TN93 model. 171s * `bali-phy help log` shows help on the log function. 171s 171s To see help on one of the following topics, run `bali-phy help topic` 171s 171s alphabets/ commands/ distributions/ functions/ models/ 171s parameters/ 171s 172s T:topology ~ uniform on tree topologies 172s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 172s 172s Partition P1: 172s file = sequences/5S-rRNA/5d.fasta 172s alphabet = DNA 172s subst = tn93 (S1) 172s indel = rs07 (I1) 172s scale ~ gamma[0.5,2] (Scale1) 172s 172s Substitution model S1 priors: 172s tn93:kappaPur ~ log_normal[log[2],0.25] 172s tn93:kappaPyr ~ log_normal[log[2],0.25] 172s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 172s 172s Insertion/deletion model I1 priors: 172s rs07:log_rate ~ laplace[-4,0.707] 172s rs07:mean_length ~ shifted_exponential[10,1] 172s 172s iter = 0 prior = -33.790694740510119 likelihood = -1483.234816657316969 posterior = -1517.025511397827131 prior_A = -37.769371881270153 |A| = 126 #indels = 4 |indels| = 12 #substs = 260 P1/likelihood = -1483.234816657316969 P1/prior_A = -37.769371881270153 P1/|A| = 126 P1/#indels = 4 P1/|indels| = 12 P1/#substs = 260 Scale[1]*|T| = 0.312887353008491 |T| = 0.480024947609822 rs07:log_rate = -4.360922545264546 rs07:mean_length = 4.97131803540848 tn93:kappaPur = 2.674531993935546 tn93:kappaPyr = 1.9206197631901862 tn93:pi[A] = 0.3300618075544738 tn93:pi[C] = 0.1097957500009612 tn93:pi[G] = 0.32253993433256817 tn93:pi[T] = 0.23760250811199682 scale[1] = 0.6518147745579553 scale1 = 0.6518147745579553 173s Created directory '5d-1/' for output files. 174s T:topology ~ uniform on tree topologies 174s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 174s 174s Partition P1: 174s file = sequences/5S-rRNA/5d.fasta 174s alphabet = DNA 174s subst = tn93 (S1) 174s indel = rs07 (I1) 174s scale ~ gamma[0.5,2] (Scale1) 174s 174s Substitution model S1 priors: 174s tn93:kappaPur ~ log_normal[log[2],0.25] 174s tn93:kappaPyr ~ log_normal[log[2],0.25] 174s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 174s 174s Insertion/deletion model I1 priors: 174s rs07:log_rate ~ laplace[-4,0.707] 174s rs07:mean_length ~ shifted_exponential[10,1] 174s 174s Beginning pre-burnin: 3 iterations. 174s Start #1 prior = -33.7907 likelihood = -1483.23 |T| = 0.480025 Scale1*|T| = 0.312887 174s 174s Tree (S)ize #1 prior = -15.3853 likelihood = -918.651 |T| = 0.351153 Scale1*|T| = 13.4823 174s Tree (S)ize #2 prior = -8.67375 likelihood = -921.505 |T| = 0.557146 Scale1*|T| = 11.6476 174s Tree (S)ize #3 prior = -10.9776 likelihood = -916.148 |T| = 1.76036 Scale1*|T| = 17.2445 174s 174s (S)+Branch (L)engths #1 prior = -16.2584 likelihood = -913.26 |T| = 2.47609 Scale1*|T| = 13.0113 174s (S)+Branch (L)engths #2 prior = -16.8078 likelihood = -894.729 |T| = 3.04489 Scale1*|T| = 6.59351 174s (S)+Branch (L)engths #3 prior = -13.1975 likelihood = -886.107 |T| = 2.05444 Scale1*|T| = 5.6581 174s 174s (S)+(L)+(P)arameters #1 prior = -18.8487 likelihood = -843.212 |T| = 1.94953 Scale1*|T| = 5.31078 174s (S)+(L)+(P)arameters #2 prior = -13.6692 likelihood = -799.58 |T| = 1.45035 Scale1*|T| = 5.99899 174s (S)+(L)+(P)arameters #3 prior = -16.2199 likelihood = -794.492 |T| = 1.25891 Scale1*|T| = 6.13717 174s 174s (S)+(L)+(P)+NNI #1 prior = -14.3438 likelihood = -794.463 |T| = 0.950972 Scale1*|T| = 8.25425 174s (S)+(L)+(P)+NNI #2 prior = -13.0194 likelihood = -796.879 |T| = 0.922848 Scale1*|T| = 5.82845 174s (S)+(L)+(P)+NNI #3 prior = -20.7114 likelihood = -793.84 |T| = 2.12375 Scale1*|T| = 5.74906 174s (S)+(L)+(P)+NNI #4 prior = -17.9262 likelihood = -792.257 |T| = 1.86364 Scale1*|T| = 6.4008 174s 174s SPR #1 prior = -17.1706 likelihood = -791.452 |T| = 2.03026 Scale1*|T| = 7.65838 174s 174s (S)+(L)+(P)+NNI #1 prior = -19.9971 likelihood = -792.17 |T| = 2.12702 Scale1*|T| = 8.17853 174s (S)+(L)+(P)+NNI #2 prior = -12.6645 likelihood = -794.309 |T| = 1.28717 Scale1*|T| = 7.80855 174s (S)+(L)+(P)+NNI #3 prior = -14.7901 likelihood = -792.908 |T| = 1.42784 Scale1*|T| = 10.0019 174s 174s Finished pre-burnin in 0.06 seconds. 174s 174s 174s BAli-Phy does NOT detect how many iterations is sufficient: 174s You need to monitor convergence and kill it when done. 174s Maximum number of iterations set to 50. 174s 174s Beginning MCMC computations. 174s - Future screen output sent to '5d-1/C1.out' 174s - Future debugging output sent to '5d-1/C1.err' 174s - Sampled trees logged to '5d-1/C1.trees' 174s - Sampled alignments logged to '5d-1/C1.P.fastas' 174s - Run info written to '5d-1/C1.run.json' 174s - Sampled numerical parameters logged to '5d-1/C1.log' as TSV 174s 174s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 174s See the manual at http://www.bali-phy.org/README.xhtml for further information. 177s Created directory '5d-2/' for output files. 179s T:topology ~ uniform on tree topologies 179s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 179s 179s Partition P1: 179s file = sequences/5S-rRNA/5d.fasta 179s alphabet = DNA 179s subst = tn93 (S1) 179s indel = none 179s scale ~ gamma[0.5,2] (Scale1) 179s 179s Partition #1: 126 columns -> 110 unique patterns. 179s Substitution model S1 priors: 179s tn93:kappaPur ~ log_normal[log[2],0.25] 179s tn93:kappaPyr ~ log_normal[log[2],0.25] 179s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 179s 179s Beginning pre-burnin: 3 iterations. 179s Start #1 prior = 3.66627 likelihood = -1521.58 |T| = 0.596738 Scale1*|T| = 0.388962 179s 179s Tree (S)ize #1 prior = -20.0519 likelihood = -925.895 |T| = 0.882719 Scale1*|T| = 34.6447 179s Tree (S)ize #2 prior = -24.3393 likelihood = -921.384 |T| = 0.882719 Scale1*|T| = 42.0429 179s Tree (S)ize #3 prior = -24.233 likelihood = -921.47 |T| = 0.882719 Scale1*|T| = 41.8591 179s 179s (S)+Branch (L)engths #1 prior = -21.242 likelihood = -918.932 |T| = 2.6265 Scale1*|T| = 54.994 179s (S)+Branch (L)engths #2 prior = -20.0058 likelihood = -915.641 |T| = 2.85599 Scale1*|T| = 52.1019 179s (S)+Branch (L)engths #3 prior = -18.7336 likelihood = -915.654 |T| = 3.4078 Scale1*|T| = 36.1988 179s 179s (S)+(L)+(P)arameters #1 prior = -14.0743 likelihood = -838.854 |T| = 2.16918 Scale1*|T| = 17.0259 179s (S)+(L)+(P)arameters #2 prior = -8.3735 likelihood = -827.845 |T| = 1.26424 Scale1*|T| = 9.98903 179s (S)+(L)+(P)arameters #3 prior = -9.91045 likelihood = -825.447 |T| = 1.00143 Scale1*|T| = 10.5296 179s 179s (S)+(L)+(P)+NNI #1 prior = -15.3467 likelihood = -816.19 |T| = 2.26734 Scale1*|T| = 8.40198 179s (S)+(L)+(P)+NNI #2 prior = -8.19633 likelihood = -792.187 |T| = 1.91628 Scale1*|T| = 6.5609 179s (S)+(L)+(P)+NNI #3 prior = -10.4653 likelihood = -794.019 |T| = 2.00651 Scale1*|T| = 7.691 179s (S)+(L)+(P)+NNI #4 prior = -10.5093 likelihood = -794.981 |T| = 1.83101 Scale1*|T| = 8.14948 179s 179s SPR #1 prior = -9.71503 likelihood = -794.17 |T| = 2.01453 Scale1*|T| = 9.01076 179s 179s (S)+(L)+(P)+NNI #1 prior = -7.67389 likelihood = -790.993 |T| = 0.925182 Scale1*|T| = 6.89699 179s (S)+(L)+(P)+NNI #2 prior = -7.38032 likelihood = -793.615 |T| = 1.83607 Scale1*|T| = 6.24615 179s (S)+(L)+(P)+NNI #3 prior = -6.06074 likelihood = -791.981 |T| = 1.24881 Scale1*|T| = 7.05904 179s 179s Finished pre-burnin in 0.06 seconds. 179s 179s 179s BAli-Phy does NOT detect how many iterations is sufficient: 179s You need to monitor convergence and kill it when done. 179s Maximum number of iterations set to 200. 179s 179s Beginning MCMC computations. 179s - Future screen output sent to '5d-2/C1.out' 179s - Future debugging output sent to '5d-2/C1.err' 179s - Sampled trees logged to '5d-2/C1.trees' 179s - Sampled alignments logged to '5d-2/C1.P.fastas' 179s - Run info written to '5d-2/C1.run.json' 179s - Sampled numerical parameters logged to '5d-2/C1.log' as TSV 179s 179s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 179s See the manual at http://www.bali-phy.org/README.xhtml for further information. 181s Created directory '5d-3/' for output files. 183s T:topology ~ uniform on tree topologies 183s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 183s 183s Partition P1: 183s file = sequences/5S-rRNA/5d.fasta 183s alphabet = DNA 183s subst = tn93 (S1) 183s indel = rs07 (I1) 183s scale ~ gamma[0.5,2] (Scale1) 183s 183s Substitution model S1 priors: 183s tn93:kappaPur ~ log_normal[log[2],0.25] 183s tn93:kappaPyr ~ log_normal[log[2],0.25] 183s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 183s 183s Insertion/deletion model I1 priors: 183s rs07:log_rate ~ laplace[-4,0.707] 183s rs07:mean_length ~ shifted_exponential[10,1] 183s 183s Beginning pre-burnin: 3 iterations. 183s Start #1 prior = -56.3247 likelihood = -1927.42 |T| = 1.5207 Scale1*|T| = 0.0976517 183s 183s Tree (S)ize #1 prior = -18.3491 likelihood = -906.914 |T| = 2.11497 Scale1*|T| = 47.2382 183s Tree (S)ize #2 prior = -22.5222 likelihood = -897.298 |T| = 2.77828 Scale1*|T| = 66.83 183s Tree (S)ize #3 prior = -27.9028 likelihood = -892.7 |T| = 4.59784 Scale1*|T| = 86.4347 183s 183s (S)+Branch (L)engths #1 prior = -19.964 likelihood = -869.162 |T| = 3.05947 Scale1*|T| = 50.5759 183s (S)+Branch (L)engths #2 prior = -14.3515 likelihood = -869.757 |T| = 2.62724 Scale1*|T| = 21.8798 183s (S)+Branch (L)engths #3 prior = -16.7018 likelihood = -866.72 |T| = 2.69974 Scale1*|T| = 26.5967 183s 183s (S)+(L)+(P)arameters #1 prior = -18.9871 likelihood = -817.182 |T| = 2.28378 Scale1*|T| = 45.248 183s (S)+(L)+(P)arameters #2 prior = -15.4959 likelihood = -815.977 |T| = 2.29986 Scale1*|T| = 23.3011 183s (S)+(L)+(P)arameters #3 prior = -13.6538 likelihood = -815.208 |T| = 1.62433 Scale1*|T| = 14.8935 183s 183s (S)+(L)+(P)+NNI #1 prior = -14.6629 likelihood = -812.522 |T| = 1.80065 Scale1*|T| = 18.1032 183s (S)+(L)+(P)+NNI #2 prior = -16.4463 likelihood = -809.915 |T| = 2.56876 Scale1*|T| = 11.5815 183s (S)+(L)+(P)+NNI #3 prior = -13.1505 likelihood = -811.929 |T| = 2.10243 Scale1*|T| = 9.65252 183s (S)+(L)+(P)+NNI #4 prior = -15.6367 likelihood = -811.931 |T| = 2.08843 Scale1*|T| = 11.8715 183s 183s SPR #1 prior = -9.34145 likelihood = -792.232 |T| = 1.16817 Scale1*|T| = 8.04855 183s 183s (S)+(L)+(P)+NNI #1 prior = -9.57398 likelihood = -790.066 |T| = 0.915938 Scale1*|T| = 9.02079 183s (S)+(L)+(P)+NNI #2 prior = -15.1991 likelihood = -791.862 |T| = 2.73586 Scale1*|T| = 7.77048 183s (S)+(L)+(P)+NNI #3 prior = -7.03941 likelihood = -794.234 |T| = 1.22613 Scale1*|T| = 7.88133 183s 183s Finished pre-burnin in 0.07 seconds. 183s 183s 183s BAli-Phy does NOT detect how many iterations is sufficient: 183s You need to monitor convergence and kill it when done. 183s Maximum number of iterations set to 100. 183s 183s Beginning MCMC computations. 183s - Future screen output sent to '5d-3/C1.out' 183s - Future debugging output sent to '5d-3/C1.err' 183s - Sampled trees logged to '5d-3/C1.trees' 183s - Sampled alignments logged to '5d-3/C1.P.fastas' 183s - Run info written to '5d-3/C1.run.json' 183s - Sampled numerical parameters logged to '5d-3/C1.log' as TSV 183s 183s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 183s See the manual at http://www.bali-phy.org/README.xhtml for further information. 188s /usr/bin/bp-analyze:452: SyntaxWarning: invalid escape sequence '\s' 188s self.version = self.find_header_attribute("VERSION").split('\s+')[0] 188s /usr/bin/bp-analyze:1118: SyntaxWarning: invalid escape sequence '\s' 188s m = re.search('([^\s]+) ~ ([^\s]+)\s+\((.+),(.+)\)',line) 188s /usr/bin/bp-analyze:1126: SyntaxWarning: invalid escape sequence '\s' 188s m = re.search('t @ (.+)\s+Ne = ([^ ]+)\s+burnin = (Not Converged!|[^ ]+)', lines[i]) 188s /usr/bin/bp-analyze:1135: SyntaxWarning: invalid escape sequence '\s' 188s m = re.search('PSRF-80%CI = ([^ ]+)\s+PSRF-RCF = ([^ ]+)',lines[i]) 188s /usr/bin/bp-analyze:1142: SyntaxWarning: invalid escape sequence '\s' 188s m = re.search('\s+(.+) = (.+)', line) 188s /usr/bin/bp-analyze:1227: SyntaxWarning: invalid escape sequence '\(' 188s m = re.search(' const.: ([^ ]+) \(([^ ]+)\%\)', line) 188s /usr/bin/bp-analyze:1232: SyntaxWarning: invalid escape sequence '\(' 188s m = re.search('inform.: ([^ ]+) \(([^ ]+)\%\)', line) 188s /usr/bin/bp-analyze:2092: SyntaxWarning: invalid escape sequence '\[' 188s asdsf = self.get_value_from_file('Results/partitions.bs','ASDSF\[min=0.100\] =') 189s Program 'gnuplot' not found: Some graphs will not be generated. 189s 189s Program 'R' not found: Some mixing graphs will not be generated. 189s 189s Creating new directory Results/ for summary files. 189s Summarizing distribution of numerical parameters: done. 189s Analyzing scalar variables: done. 189s 189s Summarizing topology distribution: done. 189s Drawing trees: c50 c66 c80 c90 c95 c99 c100 greedy MAP . done. 189s 189s Generate mixing diagnostics for topologies ... done. 189s Generate SRQ plot for partitions: done. 189s Generate SRQ plot for c50 tree: done. 189s Computing initial alignments: done. 189s 189s Computing WPD alignments: done. 189s Computing ancestral state alignment: done. 189s Drawing alignments: **** done. 189s Generating AU values for 'P1.initial'... done. 189s Generating AU values for 'P1.max'... done. 189s 189s NOTE: burnin (scalar) <= Not Converged! 189s NOTE: min_ESS (scalar) = 8.008 189s NOTE: min_ESS (partition) = 0.000 189s NOTE: ASDSF = NA 189s NOTE: MSDSF = NA 189s NOTE: PSRF-80%CI = NA 189s NOTE: PSRF-RCF = NA 189s 189s Report written to 'Results/index.html 190s autopkgtest [05:31:10]: test run-unit-test: -----------------------] 190s run-unit-test PASS 190s autopkgtest [05:31:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 191s autopkgtest [05:31:11]: @@@@@@@@@@@@@@@@@@@@ summary 191s run-unit-test PASS 202s Creating nova instance adt-noble-arm64-bali-phy-20240311-052800-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240311.img (UUID 900cfff9-7f1a-42c7-81a7-22635cd2a5f9)...