0s autopkgtest [17:35:07]: starting date: 2024-03-11
  0s autopkgtest [17:35:07]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline
  0s autopkgtest [17:35:07]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kyojpo7g/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:postgresql-16,src:db5.3,src:gdbm,src:llvm-toolchain-17,src:mmdebstrap,src:openssl,src:perl,src:python3.12,src:readline --apt-upgrade rdkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=postgresql-16/16.2-1ubuntu2 db5.3/5.3.28+dfsg2-5 gdbm/1.23-5.1 llvm-toolchain-17/1:17.0.6-8ubuntu1.1 mmdebstrap/1.4.3-6 openssl/3.0.13-0ubuntu1 perl/5.38.2-3.2 python3.12/3.12.2-4build2 readline/8.2-3.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-25.secgroup --name adt-noble-arm64-rdkit-20240311-173506-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/
 96s autopkgtest [17:36:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 96s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 98s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [38.0 kB]
 98s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2673 kB]
 98s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [452 kB]
 98s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B]
 98s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [593 kB]
 98s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 98s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB]
 98s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 98s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2980 kB]
 98s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 98s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB]
 98s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
100s Fetched 6929 kB in 2s (2776 kB/s)
100s Reading package lists...
103s Reading package lists...
103s Building dependency tree...
103s Reading state information...
104s Calculating upgrade...
104s The following packages will be REMOVED:
104s   libdb5.3 libgdbm-compat4 libgdbm6 libperl5.38 libreadline8 libssl3
104s The following NEW packages will be installed:
104s   libdb5.3t64 libgdbm-compat4t64 libgdbm6t64 libperl5.38t64 libreadline8t64
104s   libssl3t64
104s The following packages will be upgraded:
104s   klibc-utils libklibc libpython3.12-minimal libpython3.12-stdlib openssl perl
104s   perl-base perl-modules-5.38 python3.12 python3.12-minimal readline-common
104s 11 upgraded, 6 newly installed, 6 to remove and 0 not upgraded.
104s Need to get 19.4 MB of archives.
104s After this operation, 275 kB of additional disk space will be used.
104s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
105s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3.12 arm64 3.12.2-4build2 [645 kB]
105s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3.12-minimal arm64 3.12.2-4build2 [2189 kB]
105s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3.12-minimal arm64 3.12.2-4build2 [829 kB]
105s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB]
105s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3.12-stdlib arm64 3.12.2-4build2 [2002 kB]
105s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB]
105s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB]
105s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B]
105s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB]
105s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB]
105s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB]
105s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB]
105s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB]
105s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 klibc-utils arm64 2.0.13-4 [114 kB]
105s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libklibc arm64 2.0.13-4 [51.4 kB]
106s Fetched 19.4 MB in 1s (16.0 MB/s)
107s (Reading database ... 
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107s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
107s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
107s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
107s  wget depends on libssl3 (>= 3.0.0).
107s  u-boot-tools depends on libssl3 (>= 3.0.0).
107s  tnftp depends on libssl3 (>= 3.0.0).
107s  tcpdump depends on libssl3 (>= 3.0.0).
107s  systemd-resolved depends on libssl3 (>= 3.0.0).
107s  systemd depends on libssl3 (>= 3.0.0).
107s  sudo depends on libssl3 (>= 3.0.0).
107s  sbsigntool depends on libssl3 (>= 3.0.0).
107s  rsync depends on libssl3 (>= 3.0.0).
107s  python3-cryptography depends on libssl3 (>= 3.0.0).
107s  openssh-server depends on libssl3 (>= 3.0.10).
107s  openssh-client depends on libssl3 (>= 3.0.10).
107s  mtd-utils depends on libssl3 (>= 3.0.0).
107s  mokutil depends on libssl3 (>= 3.0.0).
107s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
107s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
107s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
107s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
107s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
107s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
107s  libnvme1 depends on libssl3 (>= 3.0.0).
107s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
107s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
107s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
107s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
107s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
107s  kmod depends on libssl3 (>= 3.0.0).
107s  dhcpcd-base depends on libssl3 (>= 3.0.0).
107s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
107s 
107s (Reading database ... 
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(Reading database ... 74748 files and directories currently installed.)
107s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
107s Selecting previously unselected package libssl3t64:arm64.
107s (Reading database ... 
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107s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
107s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
107s Preparing to unpack .../python3.12_3.12.2-4build2_arm64.deb ...
107s Unpacking python3.12 (3.12.2-4build2) over (3.12.2-1) ...
107s Preparing to unpack .../python3.12-minimal_3.12.2-4build2_arm64.deb ...
107s Unpacking python3.12-minimal (3.12.2-4build2) over (3.12.2-1) ...
107s Preparing to unpack .../libpython3.12-minimal_3.12.2-4build2_arm64.deb ...
107s Unpacking libpython3.12-minimal:arm64 (3.12.2-4build2) over (3.12.2-1) ...
107s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested:
107s  parted depends on libreadline8 (>= 6.0).
107s  libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta).
107s  gpgsm depends on libreadline8 (>= 6.0).
107s  gpgconf depends on libreadline8 (>= 6.0).
107s  gpg depends on libreadline8 (>= 6.0).
107s  gawk depends on libreadline8 (>= 6.0).
107s  fdisk depends on libreadline8 (>= 6.0).
107s 
108s (Reading database ... 
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108s Removing libreadline8:arm64 (8.2-3) ...
108s Selecting previously unselected package libreadline8t64:arm64.
108s (Reading database ... 
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(Reading database ... 74738 files and directories currently installed.)
108s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ...
108s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
108s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
108s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
108s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
108s Unpacking libreadline8t64:arm64 (8.2-3.1) ...
108s Preparing to unpack .../libpython3.12-stdlib_3.12.2-4build2_arm64.deb ...
108s Unpacking libpython3.12-stdlib:arm64 (3.12.2-4build2) over (3.12.2-1) ...
108s dpkg: libperl5.38:arm64: dependency problems, but removing anyway as you requested:
108s  perl depends on libperl5.38 (= 5.38.2-3).
108s 
108s (Reading database ... 
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(Reading database ... 74756 files and directories currently installed.)
108s Removing libperl5.38:arm64 (5.38.2-3) ...
108s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested:
108s  libsasl2-modules-db:arm64 depends on libdb5.3.
108s  libpam-modules:arm64 depends on libdb5.3.
108s  iproute2 depends on libdb5.3.
108s  apt-utils depends on libdb5.3.
108s 
108s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ...
108s Selecting previously unselected package libdb5.3t64:arm64.
108s (Reading database ... 
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(Reading database ... 74221 files and directories currently installed.)
108s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_arm64.deb ...
108s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5) ...
108s (Reading database ... 
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(Reading database ... 74227 files and directories currently installed.)
108s Removing libgdbm-compat4:arm64 (1.23-5) ...
108s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested:
108s  python3-gdbm:arm64 depends on libgdbm6 (>= 1.16).
108s  man-db depends on libgdbm6 (>= 1.16).
108s 
108s Removing libgdbm6:arm64 (1.23-5) ...
108s Selecting previously unselected package libgdbm6t64:arm64.
108s (Reading database ... 
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108s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ...
108s Unpacking libgdbm6t64:arm64 (1.23-5.1) ...
108s Selecting previously unselected package libgdbm-compat4t64:arm64.
108s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_arm64.deb ...
108s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ...
108s Selecting previously unselected package libperl5.38t64:arm64.
108s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_arm64.deb ...
108s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ...
108s Preparing to unpack .../perl_5.38.2-3.2_arm64.deb ...
108s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ...
108s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ...
108s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ...
109s Setting up perl-base (5.38.2-3.2) ...
109s (Reading database ... 
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109s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ...
109s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ...
109s Preparing to unpack .../readline-common_8.2-3.1_all.deb ...
109s Unpacking readline-common (8.2-3.1) over (8.2-3) ...
109s Preparing to unpack .../klibc-utils_2.0.13-4_arm64.deb ...
109s Unpacking klibc-utils (2.0.13-4) over (2.0.13-2ubuntu1) ...
109s Preparing to unpack .../libklibc_2.0.13-4_arm64.deb ...
109s Unpacking libklibc:arm64 (2.0.13-4) over (2.0.13-2ubuntu1) ...
109s Setting up libgdbm6t64:arm64 (1.23-5.1) ...
109s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ...
109s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
109s Setting up libpython3.12-minimal:arm64 (3.12.2-4build2) ...
109s Setting up libklibc:arm64 (2.0.13-4) ...
109s Setting up perl-modules-5.38 (5.38.2-3.2) ...
109s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5) ...
109s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ...
109s Setting up klibc-utils (2.0.13-4) ...
109s Setting up openssl (3.0.13-0ubuntu1) ...
109s Setting up readline-common (8.2-3.1) ...
109s Setting up python3.12-minimal (3.12.2-4build2) ...
110s Setting up perl (5.38.2-3.2) ...
110s Setting up libreadline8t64:arm64 (8.2-3.1) ...
110s Setting up libpython3.12-stdlib:arm64 (3.12.2-4build2) ...
110s Setting up python3.12 (3.12.2-4build2) ...
111s Processing triggers for systemd (255.2-3ubuntu2) ...
111s Processing triggers for man-db (2.12.0-3) ...
113s Processing triggers for install-info (7.1-3) ...
113s Processing triggers for initramfs-tools (0.142ubuntu20) ...
113s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic
113s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
127s System running in EFI mode, skipping.
127s Processing triggers for libc-bin (2.39-0ubuntu2) ...
127s Reading package lists...
128s Building dependency tree...
128s Reading state information...
128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
130s sh: Attempting to set up Debian/Ubuntu apt sources automatically
130s sh: Distribution appears to be Ubuntu
131s Reading package lists...
131s Building dependency tree...
131s Reading state information...
132s eatmydata is already the newest version (131-1).
132s dbus is already the newest version (1.14.10-4ubuntu1).
132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
132s Reading package lists...
132s Building dependency tree...
132s Reading state information...
132s rng-tools-debian is already the newest version (2.4).
132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
133s Reading package lists...
133s Building dependency tree...
133s Reading state information...
133s haveged is already the newest version (1.9.14-1ubuntu1).
133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
133s Reading package lists...
134s Building dependency tree...
134s Reading state information...
134s The following packages will be REMOVED:
134s   cloud-init* python3-configobj* python3-debconf*
135s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
135s After this operation, 3248 kB disk space will be freed.
135s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
135s Removing cloud-init (24.1-0ubuntu1) ...
135s Removing python3-configobj (5.0.8-3) ...
136s Removing python3-debconf (1.5.86) ...
136s Processing triggers for man-db (2.12.0-3) ...
136s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74369 files and directories currently installed.)
136s Purging configuration files for cloud-init (24.1-0ubuntu1) ...
137s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
137s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
138s Reading package lists...
138s Building dependency tree...
138s Reading state information...
138s linux-generic is already the newest version (6.8.0-11.11+1).
138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
139s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
139s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
139s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
139s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
140s Reading package lists...
141s Reading package lists...
141s Building dependency tree...
141s Reading state information...
141s Calculating upgrade...
142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
142s Reading package lists...
142s Building dependency tree...
142s Reading state information...
143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
143s autopkgtest [17:37:30]: rebooting testbed after setup commands that affected boot
175s autopkgtest [17:38:02]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
175s autopkgtest [17:38:02]: testbed dpkg architecture: arm64
176s autopkgtest [17:38:03]: @@@@@@@@@@@@@@@@@@@@ apt-source rdkit
182s Get:1 http://ftpmaster.internal/ubuntu noble/universe rdkit 202309.3-3 (dsc) [2884 B]
182s Get:2 http://ftpmaster.internal/ubuntu noble/universe rdkit 202309.3-3 (tar) [61.9 MB]
182s Get:3 http://ftpmaster.internal/ubuntu noble/universe rdkit 202309.3-3 (diff) [24.9 kB]
183s gpgv: Signature made Wed Feb 28 09:56:29 2024 UTC
183s gpgv:                using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287
183s gpgv:                issuer "merkys@debian.org"
183s gpgv: Can't check signature: No public key
183s dpkg-source: warning: cannot verify inline signature for ./rdkit_202309.3-3.dsc: no acceptable signature found
187s autopkgtest [17:38:14]: testing package rdkit version 202309.3-3
187s autopkgtest [17:38:14]: build not needed
194s autopkgtest [17:38:21]: test installcheck: preparing testbed
199s Reading package lists...
200s Building dependency tree...
200s Reading state information...
200s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
200s Starting 2 pkgProblemResolver with broken count: 0
200s Done
200s  Done
201s Starting pkgProblemResolver with broken count: 0
201s Starting 2 pkgProblemResolver with broken count: 0
201s Done
201s The following additional packages will be installed:
201s   fontconfig-config fonts-freefont-ttf libblas3 libboost-iostreams1.83.0
201s   libboost-python1.83.0 libboost-serialization1.83.0 libcairo2 libcoordgen3
201s   libfontconfig1 libgfortran5 libjs-jquery libjs-underscore libjson-perl
201s   liblapack3 libllvm17t64 libmaeparser1 libpixman-1-0 libpq5
201s   libpython3.11-minimal libpython3.11-stdlib libpython3.12t64 librdkit-dev
201s   librdkit1 libxcb-render0 libxcb-shm0 libxrender1 libxslt1.1 postgresql-16
201s   postgresql-16-rdkit postgresql-client-16 postgresql-client-common
201s   postgresql-common python3-numpy python3-rdkit python3.11 python3.11-minimal
201s   rdkit-data rdkit-doc ssl-cert
201s Suggested packages:
201s   postgresql-doc-16 gcc gfortran python3-dev python3-pytest python3.11-venv
201s   python3.11-doc binfmt-support
201s Recommended packages:
201s   javascript-common libjson-xs-perl
202s The following NEW packages will be installed:
202s   fontconfig-config fonts-freefont-ttf libblas3 libboost-iostreams1.83.0
202s   libboost-python1.83.0 libboost-serialization1.83.0 libcairo2 libcoordgen3
202s   libfontconfig1 libgfortran5 libjs-jquery libjs-underscore libjson-perl
202s   liblapack3 libllvm17t64 libmaeparser1 libpixman-1-0 libpq5
202s   libpython3.11-minimal libpython3.11-stdlib libpython3.12t64 librdkit-dev
202s   librdkit1 libxcb-render0 libxcb-shm0 libxrender1 libxslt1.1 postgresql-16
202s   postgresql-16-rdkit postgresql-client-16 postgresql-client-common
202s   postgresql-common python3-numpy python3-rdkit python3.11 python3.11-minimal
202s   rdkit-data rdkit-doc ssl-cert
202s 0 upgraded, 39 newly installed, 0 to remove and 0 not upgraded.
202s 1 not fully installed or removed.
202s Need to get 97.0 MB of archives.
202s After this operation, 469 MB of additional disk space will be used.
202s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB]
202s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 rdkit-data all 202309.3-3 [12.6 MB]
203s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB]
203s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB]
203s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB]
203s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB]
203s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
203s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
203s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
203s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
203s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-python1.83.0 arm64 1.83.0-2ubuntu1 [457 kB]
203s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-serialization1.83.0 arm64 1.83.0-2ubuntu1 [434 kB]
203s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
203s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
203s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
203s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
203s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
203s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
203s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
203s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libcoordgen3 arm64 3.0.2-1 [207 kB]
203s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3.12t64 arm64 3.12.2-4build2 [2279 kB]
203s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-2ubuntu1 [339 kB]
203s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 libmaeparser1 arm64 1.3.1-1build1 [84.5 kB]
203s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 librdkit1 arm64 202309.3-3 [4841 kB]
203s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rdkit arm64 202309.3-3 [4608 kB]
203s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
203s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
203s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 rdkit-doc all 202309.3-3 [8435 kB]
204s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 librdkit-dev arm64 202309.3-3 [305 kB]
204s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpq5 arm64 16.2-1ubuntu2 [137 kB]
204s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 postgresql-client-common all 257 [36.2 kB]
204s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 postgresql-client-16 arm64 16.2-1ubuntu2 [1261 kB]
204s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libjson-perl all 4.10000-1 [81.9 kB]
204s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 ssl-cert all 1.1.2ubuntu1 [17.8 kB]
204s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 postgresql-common all 257 [162 kB]
204s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libllvm17t64 arm64 1:17.0.6-8ubuntu1.1 [25.0 MB]
204s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.35-1 [161 kB]
204s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 postgresql-16 arm64 16.2-1ubuntu2 [15.2 MB]
205s Get:39 http://ftpmaster.internal/ubuntu noble/universe arm64 postgresql-16-rdkit arm64 202309.3-3 [380 kB]
206s Preconfiguring packages ...
206s Fetched 97.0 MB in 3s (32.7 MB/s)
206s Selecting previously unselected package fonts-freefont-ttf.
206s (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 ... 74314 files and directories currently installed.)
206s Preparing to unpack .../00-fonts-freefont-ttf_20211204+svn4273-2_all.deb ...
206s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ...
206s Selecting previously unselected package rdkit-data.
206s Preparing to unpack .../01-rdkit-data_202309.3-3_all.deb ...
206s Unpacking rdkit-data (202309.3-3) ...
207s Selecting previously unselected package libpython3.11-minimal:arm64.
207s Preparing to unpack .../02-libpython3.11-minimal_3.11.8-1_arm64.deb ...
207s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ...
207s Selecting previously unselected package python3.11-minimal.
207s Preparing to unpack .../03-python3.11-minimal_3.11.8-1_arm64.deb ...
207s Unpacking python3.11-minimal (3.11.8-1) ...
207s Selecting previously unselected package libpython3.11-stdlib:arm64.
207s Preparing to unpack .../04-libpython3.11-stdlib_3.11.8-1_arm64.deb ...
207s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ...
207s Selecting previously unselected package python3.11.
207s Preparing to unpack .../05-python3.11_3.11.8-1_arm64.deb ...
207s Unpacking python3.11 (3.11.8-1) ...
208s Selecting previously unselected package libblas3:arm64.
208s Preparing to unpack .../06-libblas3_3.12.0-3_arm64.deb ...
208s Unpacking libblas3:arm64 (3.12.0-3) ...
208s Selecting previously unselected package libgfortran5:arm64.
208s Preparing to unpack .../07-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
208s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
208s Selecting previously unselected package liblapack3:arm64.
208s Preparing to unpack .../08-liblapack3_3.12.0-3_arm64.deb ...
208s Unpacking liblapack3:arm64 (3.12.0-3) ...
208s Selecting previously unselected package python3-numpy.
208s Preparing to unpack .../09-python3-numpy_1%3a1.24.2-2_arm64.deb ...
208s Unpacking python3-numpy (1:1.24.2-2) ...
208s Selecting previously unselected package libboost-python1.83.0.
208s Preparing to unpack .../10-libboost-python1.83.0_1.83.0-2ubuntu1_arm64.deb ...
208s Unpacking libboost-python1.83.0 (1.83.0-2ubuntu1) ...
208s Selecting previously unselected package libboost-serialization1.83.0:arm64.
208s Preparing to unpack .../11-libboost-serialization1.83.0_1.83.0-2ubuntu1_arm64.deb ...
208s Unpacking libboost-serialization1.83.0:arm64 (1.83.0-2ubuntu1) ...
208s Selecting previously unselected package fontconfig-config.
209s Preparing to unpack .../12-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
209s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
209s Selecting previously unselected package libfontconfig1:arm64.
209s Preparing to unpack .../13-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
209s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
209s Selecting previously unselected package libpixman-1-0:arm64.
209s Preparing to unpack .../14-libpixman-1-0_0.42.2-1_arm64.deb ...
209s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
209s Selecting previously unselected package libxcb-render0:arm64.
209s Preparing to unpack .../15-libxcb-render0_1.15-1_arm64.deb ...
209s Unpacking libxcb-render0:arm64 (1.15-1) ...
209s Selecting previously unselected package libxcb-shm0:arm64.
209s Preparing to unpack .../16-libxcb-shm0_1.15-1_arm64.deb ...
209s Unpacking libxcb-shm0:arm64 (1.15-1) ...
209s Selecting previously unselected package libxrender1:arm64.
209s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
209s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
209s Selecting previously unselected package libcairo2:arm64.
209s Preparing to unpack .../18-libcairo2_1.18.0-1_arm64.deb ...
209s Unpacking libcairo2:arm64 (1.18.0-1) ...
209s Selecting previously unselected package libcoordgen3:arm64.
209s Preparing to unpack .../19-libcoordgen3_3.0.2-1_arm64.deb ...
209s Unpacking libcoordgen3:arm64 (3.0.2-1) ...
210s Selecting previously unselected package libpython3.12t64:arm64.
210s Preparing to unpack .../20-libpython3.12t64_3.12.2-4build2_arm64.deb ...
210s Unpacking libpython3.12t64:arm64 (3.12.2-4build2) ...
210s Selecting previously unselected package libboost-iostreams1.83.0:arm64.
210s Preparing to unpack .../21-libboost-iostreams1.83.0_1.83.0-2ubuntu1_arm64.deb ...
210s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-2ubuntu1) ...
210s Selecting previously unselected package libmaeparser1:arm64.
210s Preparing to unpack .../22-libmaeparser1_1.3.1-1build1_arm64.deb ...
210s Unpacking libmaeparser1:arm64 (1.3.1-1build1) ...
210s Selecting previously unselected package librdkit1.
210s Preparing to unpack .../23-librdkit1_202309.3-3_arm64.deb ...
210s Unpacking librdkit1 (202309.3-3) ...
210s Selecting previously unselected package python3-rdkit.
210s Preparing to unpack .../24-python3-rdkit_202309.3-3_arm64.deb ...
210s Unpacking python3-rdkit (202309.3-3) ...
210s Selecting previously unselected package libjs-jquery.
211s Preparing to unpack .../25-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
211s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
211s Selecting previously unselected package libjs-underscore.
211s Preparing to unpack .../26-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
211s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
211s Selecting previously unselected package rdkit-doc.
211s Preparing to unpack .../27-rdkit-doc_202309.3-3_all.deb ...
211s Unpacking rdkit-doc (202309.3-3) ...
212s Selecting previously unselected package librdkit-dev.
212s Preparing to unpack .../28-librdkit-dev_202309.3-3_arm64.deb ...
212s Unpacking librdkit-dev (202309.3-3) ...
212s Selecting previously unselected package libpq5:arm64.
212s Preparing to unpack .../29-libpq5_16.2-1ubuntu2_arm64.deb ...
212s Unpacking libpq5:arm64 (16.2-1ubuntu2) ...
212s Selecting previously unselected package postgresql-client-common.
212s Preparing to unpack .../30-postgresql-client-common_257_all.deb ...
212s Unpacking postgresql-client-common (257) ...
212s Selecting previously unselected package postgresql-client-16.
212s Preparing to unpack .../31-postgresql-client-16_16.2-1ubuntu2_arm64.deb ...
212s Unpacking postgresql-client-16 (16.2-1ubuntu2) ...
212s Selecting previously unselected package libjson-perl.
212s Preparing to unpack .../32-libjson-perl_4.10000-1_all.deb ...
212s Unpacking libjson-perl (4.10000-1) ...
212s Selecting previously unselected package ssl-cert.
212s Preparing to unpack .../33-ssl-cert_1.1.2ubuntu1_all.deb ...
212s Unpacking ssl-cert (1.1.2ubuntu1) ...
212s Selecting previously unselected package postgresql-common.
212s Preparing to unpack .../34-postgresql-common_257_all.deb ...
212s Adding 'diversion of /usr/bin/pg_config to /usr/bin/pg_config.libpq-dev by postgresql-common'
212s Unpacking postgresql-common (257) ...
212s Selecting previously unselected package libllvm17t64:arm64.
212s Preparing to unpack .../35-libllvm17t64_1%3a17.0.6-8ubuntu1.1_arm64.deb ...
212s Unpacking libllvm17t64:arm64 (1:17.0.6-8ubuntu1.1) ...
213s Selecting previously unselected package libxslt1.1:arm64.
213s Preparing to unpack .../36-libxslt1.1_1.1.35-1_arm64.deb ...
213s Unpacking libxslt1.1:arm64 (1.1.35-1) ...
213s Selecting previously unselected package postgresql-16.
213s Preparing to unpack .../37-postgresql-16_16.2-1ubuntu2_arm64.deb ...
213s Unpacking postgresql-16 (16.2-1ubuntu2) ...
214s Selecting previously unselected package postgresql-16-rdkit.
214s Preparing to unpack .../38-postgresql-16-rdkit_202309.3-3_arm64.deb ...
214s Unpacking postgresql-16-rdkit (202309.3-3) ...
214s Setting up postgresql-client-common (257) ...
214s Setting up libboost-python1.83.0 (1.83.0-2ubuntu1) ...
214s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
214s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
214s Setting up libxcb-render0:arm64 (1.15-1) ...
214s Setting up libpq5:arm64 (16.2-1ubuntu2) ...
214s Setting up fonts-freefont-ttf (20211204+svn4273-2) ...
214s Setting up libxcb-shm0:arm64 (1.15-1) ...
214s Setting up rdkit-data (202309.3-3) ...
214s Setting up libpython3.12t64:arm64 (3.12.2-4build2) ...
214s Setting up libboost-serialization1.83.0:arm64 (1.83.0-2ubuntu1) ...
214s Setting up libblas3:arm64 (3.12.0-3) ...
214s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
214s Setting up libllvm17t64:arm64 (1:17.0.6-8ubuntu1.1) ...
214s Setting up ssl-cert (1.1.2ubuntu1) ...
216s Created symlink /etc/systemd/system/multi-user.target.wants/ssl-cert.service → /usr/lib/systemd/system/ssl-cert.service.

218s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-2ubuntu1) ...
218s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
218s Setting up libjson-perl (4.10000-1) ...
218s Setting up libxslt1.1:arm64 (1.1.35-1) ...
218s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ...
218s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
218s Setting up libcoordgen3:arm64 (3.0.2-1) ...
218s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
218s Setting up python3.11-minimal (3.11.8-1) ...
219s Setting up liblapack3:arm64 (3.12.0-3) ...
219s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
219s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
219s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ...
219s Setting up postgresql-client-16 (16.2-1ubuntu2) ...
220s update-alternatives: using /usr/share/postgresql/16/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode
220s Setting up rdkit-doc (202309.3-3) ...
220s Setting up libmaeparser1:arm64 (1.3.1-1build1) ...
220s Setting up postgresql-common (257) ...
221s 
221s Creating config file /etc/postgresql-common/createcluster.conf with new version
221s Building PostgreSQL dictionaries from installed myspell/hunspell packages...
221s Removing obsolete dictionary files:
223s Created symlink /etc/systemd/system/multi-user.target.wants/postgresql.service → /usr/lib/systemd/system/postgresql.service.

224s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
224s Setting up python3.11 (3.11.8-1) ...
225s Setting up postgresql-16 (16.2-1ubuntu2) ...
225s Creating new PostgreSQL cluster 16/main ...
225s /usr/lib/postgresql/16/bin/initdb -D /var/lib/postgresql/16/main --auth-local peer --auth-host scram-sha-256 --no-instructions
226s The files belonging to this database system will be owned by user "postgres".
226s This user must also own the server process.
226s 
226s The database cluster will be initialized with locale "C.UTF-8".
226s The default database encoding has accordingly been set to "UTF8".
226s The default text search configuration will be set to "english".
226s 
226s Data page checksums are disabled.
226s 
226s fixing permissions on existing directory /var/lib/postgresql/16/main ... ok
226s creating subdirectories ... ok
226s selecting dynamic shared memory implementation ... posix
226s selecting default max_connections ... 100
226s selecting default shared_buffers ... 128MB
226s selecting default time zone ... Etc/UTC
226s creating configuration files ... ok
226s running bootstrap script ... ok
226s performing post-bootstrap initialization ... ok
226s syncing data to disk ... ok
230s Setting up libcairo2:arm64 (1.18.0-1) ...
230s Setting up python3-numpy (1:1.24.2-2) ...
233s Setting up librdkit1 (202309.3-3) ...
233s Setting up python3-rdkit (202309.3-3) ...
233s Setting up librdkit-dev (202309.3-3) ...
233s Setting up postgresql-16-rdkit (202309.3-3) ...
233s Setting up autopkgtest-satdep (0) ...
233s Processing triggers for systemd (255.2-3ubuntu2) ...
233s Processing triggers for man-db (2.12.0-3) ...
235s Processing triggers for libc-bin (2.39-0ubuntu2) ...
239s (Reading database ... 84332 files and directories currently installed.)
239s Removing autopkgtest-satdep (0) ...
240s autopkgtest [17:39:07]: test installcheck: [-----------------------
241s ### PostgreSQL 16 installcheck ###
241s Creating new PostgreSQL cluster 16/regress ...
244s make: Entering directory '/tmp/autopkgtest.RuHwdT/build.W9Z/src/Code/PgSQL/rdkit'
244s echo "# +++ regress install-check in  +++" && /usr/lib/postgresql/16/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=/tmp/autopkgtest.RuHwdT/build.W9Z/src --bindir='/usr/lib/postgresql/16/bin'    --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 bfpgin sfpgist slfpgist fps reaction  fmcs query xqm 
244s # +++ regress install-check in  +++
244s # using postmaster on localhost, port 5433
248s ok 1         - rdkit-91                                 3472 ms
248s ok 2         - props                                     169 ms
248s ok 3         - btree                                     443 ms
250s ok 4         - molgist                                  1476 ms
250s ok 5         - bfpgist-91                                159 ms
250s ok 6         - bfpgin                                    162 ms
250s ok 7         - sfpgist                                    72 ms
250s ok 8         - slfpgist                                   76 ms
250s ok 9         - fps                                        82 ms
254s ok 10        - reaction                                 3231 ms
254s ok 11        - fmcs                                      213 ms
254s ok 12        - query                                      53 ms
254s ok 13        - xqm                                       251 ms
254s 1..13
254s # All 13 tests passed.
254s make: Leaving directory '/tmp/autopkgtest.RuHwdT/build.W9Z/src/Code/PgSQL/rdkit'
254s Dropping cluster 16/regress ...
255s ### End 16 installcheck ###
255s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
255s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
255s autopkgtest [17:39:22]: test installcheck: -----------------------]
256s installcheck         PASS
256s autopkgtest [17:39:23]: test installcheck:  - - - - - - - - - - results - - - - - - - - - -
256s autopkgtest [17:39:23]: @@@@@@@@@@@@@@@@@@@@ summary
256s installcheck         PASS
268s Creating nova instance adt-noble-arm64-rdkit-20240311-173506-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240311.img (UUID 900cfff9-7f1a-42c7-81a7-22635cd2a5f9)...