0s autopkgtest [15:18:24]: starting date and time: 2025-03-15 15:18:24+0000 0s autopkgtest [15:18:24]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:18:24]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1btu12pp/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.201 lxd-armhf-10.145.243.201:autopkgtest/ubuntu/plucky/armhf 22s autopkgtest [15:18:46]: testbed dpkg architecture: armhf 24s autopkgtest [15:18:48]: testbed apt version: 2.9.33 27s autopkgtest [15:18:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [15:18:54]: testbed release detected to be: None 38s autopkgtest [15:19:02]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 41s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 41s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 41s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 41s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 41s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 42s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 42s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 42s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 42s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 42s Get:20 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 46s Fetched 40.7 MB in 5s (7588 kB/s) 47s Reading package lists... 53s autopkgtest [15:19:17]: upgrading testbed (apt dist-upgrade and autopurge) 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 56s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 56s Starting 2 pkgProblemResolver with broken count: 0 56s Done 57s Entering ResolveByKeep 57s 57s Calculating upgrade... 58s The following packages will be upgraded: 58s libc-bin libc6 locales sos 58s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 8088 kB of archives. 58s After this operation, 0 B of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 59s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 59s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 59s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 59s Preconfiguring packages ... 59s Fetched 8088 kB in 1s (9756 kB/s) 60s (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 ... 64655 files and directories currently installed.) 60s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 60s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 60s Setting up libc6:armhf (2.41-1ubuntu2) ... 60s (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 ... 64655 files and directories currently installed.) 60s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 60s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 60s Setting up libc-bin (2.41-1ubuntu2) ... 61s (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 ... 64655 files and directories currently installed.) 61s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 61s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 61s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 61s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 61s Setting up sos (4.9.0-5) ... 62s Setting up locales (2.41-1ubuntu2) ... 63s Generating locales (this might take a while)... 65s en_US.UTF-8... done 65s Generation complete. 65s Processing triggers for systemd (257.3-1ubuntu3) ... 65s Processing triggers for man-db (2.13.0-1) ... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Starting pkgProblemResolver with broken count: 0 69s Starting 2 pkgProblemResolver with broken count: 0 69s Done 70s Solving dependencies... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s autopkgtest [15:19:36]: rebooting testbed after setup commands that affected boot 118s autopkgtest [15:20:22]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 146s autopkgtest [15:20:50]: @@@@@@@@@@@@@@@@@@@@ apt-source plink 157s Get:1 http://ftpmaster.internal/ubuntu plucky/universe plink 1.07+dfsg-4 (dsc) [2076 B] 157s Get:2 http://ftpmaster.internal/ubuntu plucky/universe plink 1.07+dfsg-4 (tar) [429 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky/universe plink 1.07+dfsg-4 (diff) [17.4 kB] 157s gpgv: Signature made Sun Oct 31 15:36:45 2021 UTC 157s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 157s gpgv: issuer "nilesh@debian.org" 157s gpgv: Can't check signature: No public key 157s dpkg-source: warning: cannot verify inline signature for ./plink_1.07+dfsg-4.dsc: no acceptable signature found 158s autopkgtest [15:21:02]: testing package plink version 1.07+dfsg-4 160s autopkgtest [15:21:04]: build not needed 162s autopkgtest [15:21:06]: test run-sample-analysis: preparing testbed 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 165s Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 166s The following NEW packages will be installed: 166s plink 166s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 166s Need to get 1188 kB of archives. 166s After this operation, 2372 kB of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf plink armhf 1.07+dfsg-4 [1188 kB] 167s Fetched 1188 kB in 1s (1558 kB/s) 167s Selecting previously unselected package plink. 167s (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 ... 64655 files and directories currently installed.) 167s Preparing to unpack .../plink_1.07+dfsg-4_armhf.deb ... 167s Unpacking plink (1.07+dfsg-4) ... 167s Setting up plink (1.07+dfsg-4) ... 167s Processing triggers for man-db (2.13.0-1) ... 176s autopkgtest [15:21:20]: test run-sample-analysis: [----------------------- 178s 178s @----------------------------------------------------------@ 178s | PLINK! | v1.07 | 10/Aug/2009 | 178s |----------------------------------------------------------| 178s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 178s |----------------------------------------------------------| 178s | For documentation, citation & bug-report instructions: | 178s | http://pngu.mgh.harvard.edu/purcell/plink/ | 178s @----------------------------------------------------------@ 178s 178s Skipping web check... [ --noweb ] 178s Writing this text to log file [ plink.log ] 178s Analysis started: Sat Mar 15 15:21:22 2025 178s 178s Options in effect: 178s --noweb 178s --file test 178s --freq 178s 178s 2 (of 2) markers to be included from [ test.map ] 178s 6 individuals read from [ test.ped ] 178s 6 individuals with nonmissing phenotypes 178s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 178s Missing phenotype value is also -9 178s 3 cases, 3 controls and 0 missing 178s 6 males, 0 females, and 0 of unspecified sex 178s Before frequency and genotyping pruning, there are 2 SNPs 178s 6 founders and 0 non-founders found 178s Writing allele frequencies (founders-only) to [ plink.frq ] 178s 178s Analysis finished: Sat Mar 15 15:21:22 2025 178s 178s 178s @----------------------------------------------------------@ 178s | PLINK! | v1.07 | 10/Aug/2009 | 178s |----------------------------------------------------------| 178s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 178s |----------------------------------------------------------| 178s | For documentation, citation & bug-report instructions: | 178s | http://pngu.mgh.harvard.edu/purcell/plink/ | 178s @----------------------------------------------------------@ 178s 178s Skipping web check... [ --noweb ] 178s Writing this text to log file [ plink.log ] 178s Analysis started: Sat Mar 15 15:21:22 2025 178s 178s Options in effect: 178s --noweb 178s --file test 178s --assoc 178s 178s 2 (of 2) markers to be included from [ test.map ] 178s 6 individuals read from [ test.ped ] 178s 6 individuals with nonmissing phenotypes 178s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 178s Missing phenotype value is also -9 178s 3 cases, 3 controls and 0 missing 178s 6 males, 0 females, and 0 of unspecified sex 178s Before frequency and genotyping pruning, there are 2 SNPs 178s 6 founders and 0 non-founders found 178s Total genotyping rate in remaining individuals is 1 178s 0 SNPs failed missingness test ( GENO > 1 ) 178s 0 SNPs failed frequency test ( MAF < 0 ) 178s After frequency and genotyping pruning, there are 2 SNPs 178s After filtering, 3 cases, 3 controls and 0 missing 178s After filtering, 6 males, 0 females, and 0 of unspecified sex 178s Writing main association results to [ plink.assoc ] 178s 178s Analysis finished: Sat Mar 15 15:21:22 2025 178s 178s autopkgtest [15:21:22]: test run-sample-analysis: -----------------------] 183s autopkgtest [15:21:27]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 183s run-sample-analysis PASS 187s autopkgtest [15:21:31]: @@@@@@@@@@@@@@@@@@@@ summary 187s run-sample-analysis PASS