0s autopkgtest [14:22:56]: starting date and time: 2025-03-15 14:22:56+0000 0s autopkgtest [14:22:56]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:22:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._q01glea/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade plink --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-arm64-7.secgroup --name adt-plucky-arm64-plink-20250315-142256-juju-7f2275-prod-proposed-migration-environment-2-bc80231e-f03f-4678-9f7e-a495d81ea4d1 --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/ 157s autopkgtest [14:25:33]: testbed dpkg architecture: arm64 157s autopkgtest [14:25:33]: testbed apt version: 2.9.33 157s autopkgtest [14:25:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 158s autopkgtest [14:25:34]: testbed release detected to be: None 158s autopkgtest [14:25:34]: updating testbed package index (apt update) 159s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 159s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 159s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 159s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 159s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 160s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 160s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 160s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 160s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 160s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 160s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 160s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 160s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 160s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 161s Fetched 1094 kB in 2s (712 kB/s) 161s Reading package lists... 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 163s Calculating upgrade... 163s Calculating upgrade... 163s The following packages will be upgraded: 163s python3-jinja2 strace 164s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Need to get 608 kB of archives. 164s After this operation, 11.3 kB of additional disk space will be used. 164s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 164s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 165s Fetched 608 kB in 1s (662 kB/s) 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 ... 117701 files and directories currently installed.) 165s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 165s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 165s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 165s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 165s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 166s Setting up strace (6.13+ds-1ubuntu1) ... 166s Processing triggers for man-db (2.13.0-1) ... 166s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s Solving dependencies... 168s The following packages will be REMOVED: 168s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 168s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 168s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 168s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 168s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 168s After this operation, 267 MB disk space will be freed. 168s (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 ... 117701 files and directories currently installed.) 168s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 168s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 168s Removing libpython3.12t64:arm64 (3.12.9-1) ... 168s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 168s Removing libnsl2:arm64 (1.3.0-3build3) ... 168s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 168s Removing libunwind8:arm64 (1.6.2-3.1) ... 168s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 169s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 171s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 171s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 171s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 171s /etc/kernel/postrm.d/initramfs-tools: 171s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 171s /etc/kernel/postrm.d/zz-flash-kernel: 171s flash-kernel: Kernel 6.11.0-8-generic has been removed. 171s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 171s /etc/kernel/postrm.d/zz-update-grub: 171s Sourcing file `/etc/default/grub' 171s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 171s Generating grub configuration file ... 171s Found linux image: /boot/vmlinuz-6.14.0-10-generic 171s Found initrd image: /boot/initrd.img-6.14.0-10-generic 172s Warning: os-prober will not be executed to detect other bootable partitions. 172s Systems on them will not be added to the GRUB boot configuration. 172s Check GRUB_DISABLE_OS_PROBER documentation entry. 172s Adding boot menu entry for UEFI Firmware Settings ... 172s done 172s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 172s Processing triggers for libc-bin (2.41-1ubuntu1) ... 172s (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 ... 81650 files and directories currently installed.) 172s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 172s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 172s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 173s autopkgtest [14:25:49]: upgrading testbed (apt dist-upgrade and autopurge) 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 175s Entering ResolveByKeep 175s 175s Calculating upgrade... 175s The following packages will be upgraded: 175s libc-bin libc-dev-bin libc6 libc6-dev locales 176s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 9530 kB of archives. 176s After this operation, 0 B of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 178s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 178s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 180s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 181s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 185s Preconfiguring packages ... 185s Fetched 9530 kB in 9s (1011 kB/s) 185s (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 ... 81647 files and directories currently installed.) 185s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 185s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 186s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 186s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 186s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 186s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 186s Setting up libc6:arm64 (2.41-1ubuntu2) ... 186s (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 ... 81647 files and directories currently installed.) 186s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 186s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up libc-bin (2.41-1ubuntu2) ... 187s (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 ... 81647 files and directories currently installed.) 187s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 187s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up locales (2.41-1ubuntu2) ... 187s Generating locales (this might take a while)... 189s en_US.UTF-8... done 189s Generation complete. 189s Setting up libc-dev-bin (2.41-1ubuntu2) ... 189s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 189s Processing triggers for man-db (2.13.0-1) ... 191s Processing triggers for systemd (257.3-1ubuntu3) ... 191s Reading package lists... 192s Building dependency tree... 192s Reading state information... 192s Starting pkgProblemResolver with broken count: 0 192s Starting 2 pkgProblemResolver with broken count: 0 192s Done 193s Solving dependencies... 193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s autopkgtest [14:26:09]: rebooting testbed after setup commands that affected boot 217s autopkgtest [14:26:33]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 220s autopkgtest [14:26:36]: @@@@@@@@@@@@@@@@@@@@ apt-source plink 222s Get:1 http://ftpmaster.internal/ubuntu plucky/universe plink 1.07+dfsg-4 (dsc) [2076 B] 222s Get:2 http://ftpmaster.internal/ubuntu plucky/universe plink 1.07+dfsg-4 (tar) [429 kB] 222s Get:3 http://ftpmaster.internal/ubuntu plucky/universe plink 1.07+dfsg-4 (diff) [17.4 kB] 223s gpgv: Signature made Sun Oct 31 15:36:45 2021 UTC 223s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 223s gpgv: issuer "nilesh@debian.org" 223s gpgv: Can't check signature: No public key 223s dpkg-source: warning: cannot verify inline signature for ./plink_1.07+dfsg-4.dsc: no acceptable signature found 223s autopkgtest [14:26:39]: testing package plink version 1.07+dfsg-4 223s autopkgtest [14:26:39]: build not needed 224s autopkgtest [14:26:40]: test run-sample-analysis: preparing testbed 224s Reading package lists... 225s Building dependency tree... 225s Reading state information... 225s Starting pkgProblemResolver with broken count: 0 225s Starting 2 pkgProblemResolver with broken count: 0 225s Done 226s The following NEW packages will be installed: 226s plink 226s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 1005 kB of archives. 226s After this operation, 2458 kB of additional disk space will be used. 226s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 plink arm64 1.07+dfsg-4 [1005 kB] 228s Fetched 1005 kB in 1s (756 kB/s) 228s Selecting previously unselected package plink. 228s (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 ... 81647 files and directories currently installed.) 228s Preparing to unpack .../plink_1.07+dfsg-4_arm64.deb ... 228s Unpacking plink (1.07+dfsg-4) ... 228s Setting up plink (1.07+dfsg-4) ... 228s Processing triggers for man-db (2.13.0-1) ... 230s autopkgtest [14:26:46]: test run-sample-analysis: [----------------------- 230s 230s @----------------------------------------------------------@ 230s | PLINK! | v1.07 | 10/Aug/2009 | 230s |----------------------------------------------------------| 230s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 230s |----------------------------------------------------------| 230s | For documentation, citation & bug-report instructions: | 230s | http://pngu.mgh.harvard.edu/purcell/plink/ | 230s @----------------------------------------------------------@ 230s 230s Skipping web check... [ --noweb ] 230s Writing this text to log file [ plink.log ] 230s Analysis started: Sat Mar 15 14:26:46 2025 230s 230s Options in effect: 230s --noweb 230s --file test 230s --freq 230s 230s 2 (of 2) markers to be included from [ test.map ] 230s 6 individuals read from [ test.ped ] 230s 6 individuals with nonmissing phenotypes 230s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 230s Missing phenotype value is also -9 230s 3 cases, 3 controls and 0 missing 230s 6 males, 0 females, and 0 of unspecified sex 230s Before frequency and genotyping pruning, there are 2 SNPs 230s 6 founders and 0 non-founders found 230s Writing allele frequencies (founders-only) to [ plink.frq ] 230s 230s Analysis finished: Sat Mar 15 14:26:46 2025 230s 230s 230s @----------------------------------------------------------@ 230s | PLINK! | v1.07 | 10/Aug/2009 | 230s |----------------------------------------------------------| 230s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 230s |----------------------------------------------------------| 230s | For documentation, citation & bug-report instructions: | 230s | http://pngu.mgh.harvard.edu/purcell/plink/ | 230s @----------------------------------------------------------@ 230s 230s Skipping web check... [ --noweb ] 230s Writing this text to log file [ plink.log ] 230s Analysis started: Sat Mar 15 14:26:46 2025 230s 230s Options in effect: 230s --noweb 230s --file test 230s --assoc 230s 230s 2 (of 2) markers to be included from [ test.map ] 230s 6 individuals read from [ test.ped ] 230s 6 individuals with nonmissing phenotypes 230s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 230s Missing phenotype value is also -9 230s 3 cases, 3 controls and 0 missing 230s 6 males, 0 females, and 0 of unspecified sex 230s Before frequency and genotyping pruning, there are 2 SNPs 230s 6 founders and 0 non-founders found 230s Total genotyping rate in remaining individuals is 1 230s 0 SNPs failed missingness test ( GENO > 1 ) 230s 0 SNPs failed frequency test ( MAF < 0 ) 230s After frequency and genotyping pruning, there are 2 SNPs 230s After filtering, 3 cases, 3 controls and 0 missing 230s After filtering, 6 males, 0 females, and 0 of unspecified sex 230s Writing main association results to [ plink.assoc ] 230s 230s Analysis finished: Sat Mar 15 14:26:46 2025 230s 230s autopkgtest [14:26:46]: test run-sample-analysis: -----------------------] 231s run-sample-analysis PASS 231s autopkgtest [14:26:47]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 231s autopkgtest [14:26:47]: @@@@@@@@@@@@@@@@@@@@ summary 231s run-sample-analysis PASS 250s nova [W] Using flock in prodstack6-arm64 250s flock: timeout while waiting to get lock 250s Creating nova instance adt-plucky-arm64-plink-20250315-142256-juju-7f2275-prod-proposed-migration-environment-2-bc80231e-f03f-4678-9f7e-a495d81ea4d1 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 250s nova [W] Timed out waiting for 414b2d2a-fa3e-4991-8072-49ebb56aae50 to get deleted.