0s autopkgtest [17:09:41]: starting date and time: 2025-03-15 17:09:41+0000
  0s autopkgtest [17:09:41]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [17:09:41]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w5wuho9r/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade trinculo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-8.secgroup --name adt-plucky-arm64-trinculo-20250315-170941-juju-7f2275-prod-proposed-migration-environment-2-493ac98f-66fb-4c06-847e-c77bbfed6a91 --image adt/ubuntu-plucky-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,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/
181s autopkgtest [17:12:42]: testbed dpkg architecture: arm64
181s autopkgtest [17:12:42]: testbed apt version: 2.9.33
181s autopkgtest [17:12:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup
181s autopkgtest [17:12:42]: testbed release detected to be: None
182s autopkgtest [17:12:43]: updating testbed package index (apt update)
183s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
183s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
183s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
183s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
183s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB]
184s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
184s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB]
184s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB]
184s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B]
184s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B]
184s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB]
184s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB]
184s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B]
184s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B]
185s Fetched 1078 kB in 2s (585 kB/s)
186s Reading package lists...
187s Reading package lists...
187s Building dependency tree...
187s Reading state information...
188s Calculating upgrade...
188s Calculating upgrade...
188s The following packages will be upgraded:
188s   pinentry-curses python3-jinja2 strace
188s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
188s Need to get 647 kB of archives.
188s After this operation, 11.3 kB of additional disk space will be used.
188s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB]
189s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB]
189s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
190s Fetched 647 kB in 1s (603 kB/s)
190s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
190s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ...
190s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
190s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ...
190s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ...
190s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
190s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
190s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
190s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
191s Setting up strace (6.13+ds-1ubuntu1) ...
191s Processing triggers for man-db (2.13.0-1) ...
191s Reading package lists...
192s Building dependency tree...
192s Reading state information...
192s Solving dependencies...
192s The following packages will be REMOVED:
192s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
192s   libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
192s   linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic*
192s   linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic*
193s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded.
193s After this operation, 267 MB disk space will be freed.
193s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
193s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
193s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
193s Removing libpython3.12t64:arm64 (3.12.9-1) ...
193s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ...
193s Removing libnsl2:arm64 (1.3.0-3build3) ...
193s Removing libpython3.12-minimal:arm64 (3.12.9-1) ...
193s Removing libunwind8:arm64 (1.6.2-3.1) ...
193s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
194s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
195s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
195s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic
195s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic
195s /etc/kernel/postrm.d/initramfs-tools:
195s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
195s /etc/kernel/postrm.d/zz-flash-kernel:
195s flash-kernel: Kernel 6.11.0-8-generic has been removed.
195s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required.
196s /etc/kernel/postrm.d/zz-update-grub:
196s Sourcing file `/etc/default/grub'
196s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
196s Generating grub configuration file ...
196s Found linux image: /boot/vmlinuz-6.14.0-10-generic
196s Found initrd image: /boot/initrd.img-6.14.0-10-generic
196s Warning: os-prober will not be executed to detect other bootable partitions.
196s Systems on them will not be added to the GRUB boot configuration.
196s Check GRUB_DISABLE_OS_PROBER documentation entry.
196s Adding boot menu entry for UEFI Firmware Settings ...
196s done
196s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
197s Processing triggers for libc-bin (2.41-1ubuntu1) ...
197s (Reading database ... 
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(Reading database ... 81650 files and directories currently installed.)
197s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
197s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ...
197s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
197s autopkgtest [17:12:58]: upgrading testbed (apt dist-upgrade and autopurge)
197s Reading package lists...
198s Building dependency tree...
198s Reading state information...
198s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
198s Starting 2 pkgProblemResolver with broken count: 0
198s Done
199s Entering ResolveByKeep
199s 
199s Calculating upgrade...
200s The following packages will be upgraded:
200s   libc-bin libc-dev-bin libc6 libc6-dev locales
200s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
200s Need to get 9530 kB of archives.
200s After this operation, 0 B of additional disk space will be used.
200s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB]
202s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB]
202s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB]
205s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB]
206s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB]
211s Preconfiguring packages ...
211s Fetched 9530 kB in 11s (884 kB/s)
211s (Reading database ... 
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(Reading database ... 81647 files and directories currently installed.)
211s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ...
211s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
211s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ...
211s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
211s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ...
212s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
212s Setting up libc6:arm64 (2.41-1ubuntu2) ...
212s (Reading database ... 
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(Reading database ... 81647 files and directories currently installed.)
212s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ...
212s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
212s Setting up libc-bin (2.41-1ubuntu2) ...
212s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81647 files and directories currently installed.)
212s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
212s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
212s Setting up locales (2.41-1ubuntu2) ...
213s Generating locales (this might take a while)...
215s   en_US.UTF-8... done
215s Generation complete.
215s Setting up libc-dev-bin (2.41-1ubuntu2) ...
215s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ...
215s Processing triggers for man-db (2.13.0-1) ...
216s Processing triggers for systemd (257.3-1ubuntu3) ...
217s Reading package lists...
217s Building dependency tree...
217s Reading state information...
218s Starting pkgProblemResolver with broken count: 0
218s Starting 2 pkgProblemResolver with broken count: 0
218s Done
218s Solving dependencies...
219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
219s autopkgtest [17:13:20]: rebooting testbed after setup commands that affected boot
242s autopkgtest [17:13:43]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025
245s autopkgtest [17:13:46]: @@@@@@@@@@@@@@@@@@@@ apt-source trinculo
247s Get:1 http://ftpmaster.internal/ubuntu plucky/universe trinculo 0.96+dfsg-4 (dsc) [2076 B]
247s Get:2 http://ftpmaster.internal/ubuntu plucky/universe trinculo 0.96+dfsg-4 (tar) [61.4 kB]
247s Get:3 http://ftpmaster.internal/ubuntu plucky/universe trinculo 0.96+dfsg-4 (diff) [13.5 kB]
247s gpgv: Signature made Sun Oct 31 19:18:58 2021 UTC
247s gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
247s gpgv:                issuer "nilesh@debian.org"
247s gpgv: Can't check signature: No public key
247s dpkg-source: warning: cannot verify inline signature for ./trinculo_0.96+dfsg-4.dsc: no acceptable signature found
247s autopkgtest [17:13:48]: testing package trinculo version 0.96+dfsg-4
248s autopkgtest [17:13:49]: build not needed
248s autopkgtest [17:13:49]: test run-unit-test: preparing testbed
249s Reading package lists...
249s Building dependency tree...
249s Reading state information...
249s Starting pkgProblemResolver with broken count: 0
249s Starting 2 pkgProblemResolver with broken count: 0
249s Done
250s The following NEW packages will be installed:
250s   libblas3 libgfortran5 liblapack3 trinculo
250s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
250s Need to get 3001 kB of archives.
250s After this operation, 8729 kB of additional disk space will be used.
250s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB]
251s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB]
251s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB]
254s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 trinculo arm64 0.96+dfsg-4 [89.5 kB]
254s Fetched 3001 kB in 4s (792 kB/s)
254s Selecting previously unselected package libblas3:arm64.
255s (Reading database ... 
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(Reading database ... 95%
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(Reading database ... 81647 files and directories currently installed.)
255s Preparing to unpack .../libblas3_3.12.1-2_arm64.deb ...
255s Unpacking libblas3:arm64 (3.12.1-2) ...
255s Selecting previously unselected package libgfortran5:arm64.
255s Preparing to unpack .../libgfortran5_15-20250222-0ubuntu1_arm64.deb ...
255s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ...
255s Selecting previously unselected package liblapack3:arm64.
255s Preparing to unpack .../liblapack3_3.12.1-2_arm64.deb ...
255s Unpacking liblapack3:arm64 (3.12.1-2) ...
255s Selecting previously unselected package trinculo.
255s Preparing to unpack .../trinculo_0.96+dfsg-4_arm64.deb ...
255s Unpacking trinculo (0.96+dfsg-4) ...
255s Setting up libblas3:arm64 (3.12.1-2) ...
255s 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
255s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ...
255s Setting up liblapack3:arm64 (3.12.1-2) ...
255s 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
255s Setting up trinculo (0.96+dfsg-4) ...
255s Processing triggers for man-db (2.13.0-1) ...
255s Processing triggers for libc-bin (2.41-1ubuntu2) ...
257s autopkgtest [17:13:58]: test run-unit-test: [-----------------------
257s 1. Testing frequentist association (plink)...
257s Running a multinomial logistic analysis
257s Reading FAM file
257s Reading BIM file
257s Reading BED file
257s BED in SNP-Major format
257s Reading phenotypes file
257s Carrying out association testing on 5 SNPs.
257s Analyses finished.
257s PASSED
257s 2. Testing frequentist association (dosage)...
257s Running a multinomial logistic analysis
257s Reading dosage file
257s Read 0
257s Read 1000
257s Reading phenotypes file
257s Carrying out association testing on 5 SNPs.
257s Analyses finished.
257s PASSED
257s 3. Testing frequentist association (covariates)...
257s Running a multinomial logistic analysis
257s Reading FAM file
257s Reading BIM file
257s Reading BED file
257s BED in SNP-Major format
257s Reading covariants file
257s Reading phenotypes file
257s Carrying out association testing on 5 SNPs.
257s Analyses finished.
257s PASSED
257s 4. Testing frequentist association (conditioning)...
257s Running a multinomial logistic analysis
257s Reading FAM file
257s Reading BIM file
257s Reading BED file
257s BED in SNP-Major format
257s Conditioning on 1 SNPs.
257s Reading covariants file
257s Reading phenotypes file
257s Carrying out association testing on 5 SNPs.
257s Analyses finished.
257s PASSED
257s 5. Testing Bayesian association...
257s Running a multinomial logistic analysis
257s Reading FAM file
257s Reading BIM file
257s Reading BED file
257s BED in SNP-Major format
257s Reading covariants file
257s Reading phenotypes file
257s Carrying out association testing on 5 SNPs.
257s Analyses finished.
257s PASSED
257s 6. Testing Bayesian association (prior file)...
257s Running a multinomial logistic analysis
257s Reading FAM file
257s Reading BIM file
257s Reading BED file
257s BED in SNP-Major format
257s Reading covariants file
257s Reading phenotypes file
257s Carrying out association testing on 5 SNPs.
257s Analyses finished.
257s PASSED
257s 7. Testing Bayesian model selection...
257s Running a multinomial logistic analysis
257s Reading FAM file
257s Reading BIM file
257s Reading BED file
257s BED in SNP-Major format
257s Reading covariants file
257s Reading phenotypes file
257s Carrying out association testing on 5 SNPs.
257s Analyses finished.
257s PASSED
257s 8. Testing Bayesian model selection (empirical prior)...
257s Running a multinomial logistic analysis
257s Reading FAM file
257s Reading BIM file
257s Reading BED file
257s BED in SNP-Major format
257s Reading covariants file
257s Reading phenotypes file
257s Inferred phenotype covariance matrix:
257s  0.493951 0.365634
257s  0.365634 0.424441
257s Carrying out association testing on 5 SNPs.
257s Analyses finished.
257s PASSED
257s 9. Testing ordinal regression...
257s Running a ordinal (proportional odds) logistic analysis
257s Reading FAM file
257s Reading BIM file
257s Reading BED file
257s BED in SNP-Major format
257s Reading covariants file
257s Reading phenotypes file
257s Carrying out association testing on 5 SNPs.
257s Warning: Null model did not coverge for SNP SNP1
257s Warning: Alt model did not coverge for SNP SNP1
257s Warning: Null model did not coverge for SNP SNP2
257s Warning: Alt model did not coverge for SNP SNP2
257s Warning: Null model did not coverge for SNP SNP3
257s Warning: Alt model did not coverge for SNP SNP3
257s Warning: Null model did not coverge for SNP SNP4
257s Warning: Alt model did not coverge for SNP SNP4
257s Warning: Null model did not coverge for SNP SNP5
257s Warning: Alt model did not coverge for SNP SNP5
257s Analyses finished.
257s PASSED
257s autopkgtest [17:13:58]: test run-unit-test: -----------------------]
258s autopkgtest [17:13:59]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
258s run-unit-test        PASS
258s autopkgtest [17:13:59]: test run-upstream-test: preparing testbed
259s Reading package lists...
259s Building dependency tree...
259s Reading state information...
259s Starting pkgProblemResolver with broken count: 0
259s Starting 2 pkgProblemResolver with broken count: 0
259s Done
260s The following NEW packages will be installed:
260s   python3-all
260s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
260s Need to get 886 B of archives.
260s After this operation, 6144 B of additional disk space will be used.
260s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B]
261s Fetched 886 B in 0s (4337 B/s)
261s Selecting previously unselected package python3-all.
261s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81687 files and directories currently installed.)
261s Preparing to unpack .../python3-all_3.13.2-2_arm64.deb ...
261s Unpacking python3-all (3.13.2-2) ...
261s Setting up python3-all (3.13.2-2) ...
262s autopkgtest [17:14:03]: test run-upstream-test: [-----------------------
262s Testing with python3.13 in /tmp/autopkgtest.OOlbLd/autopkgtest_tmp:
262s Testing trinculo (v0.95)
262s Test files are written to: /tmp/tmpvjhvpa6a
262s 1. Testing frequentist association (plink)... PASSED
262s 2. Testing frequentist association (dosage)... PASSED
262s 3. Testing frequentist association (covariates)... PASSED
262s 4. Testing frequentist association (conditioning)... PASSED
262s 5. Testing Bayesian association... PASSED
262s 6. Testing Bayesian association (prior file)... PASSED
262s 7. Testing Bayesian model selection... PASSED
262s 8. Testing Bayesian model selection (empirical prior)... PASSED
262s 9. Testing ordinal regression... PASSED
262s PASSED
263s autopkgtest [17:14:04]: test run-upstream-test: -----------------------]
263s run-upstream-test    PASS
263s autopkgtest [17:14:04]: test run-upstream-test:  - - - - - - - - - - results - - - - - - - - - -
264s autopkgtest [17:14:05]: @@@@@@@@@@@@@@@@@@@@ summary
264s run-unit-test        PASS
264s run-upstream-test    PASS
282s nova [W] Using flock in prodstack6-arm64
282s Creating nova instance adt-plucky-arm64-trinculo-20250315-170941-juju-7f2275-prod-proposed-migration-environment-2-493ac98f-66fb-4c06-847e-c77bbfed6a91 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)...
282s nova [W] Timed out waiting for 90d4d801-c3e3-473e-96e8-c0954c637fe0 to get deleted.