0s autopkgtest [02:46:33]: starting date and time: 2026-02-05 02:46:33+0000 0s autopkgtest [02:46:33]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [02:46:33]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7sbinbqw/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,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade emmax --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- lxd -r lxd-armhf-10.145.243.227 lxd-armhf-10.145.243.227:autopkgtest/ubuntu/resolute/armhf 25s autopkgtest [02:46:58]: testbed dpkg architecture: armhf 27s autopkgtest [02:47:00]: testbed apt version: 3.1.14 31s autopkgtest [02:47:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s autopkgtest [02:47:06]: testbed release detected to be: None 40s autopkgtest [02:47:13]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 43s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 43s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 43s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 43s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 43s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 43s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 43s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 43s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [250 kB] 43s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1364 kB] 43s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [9664 B] 44s Fetched 3735 kB in 1s (2604 kB/s) 45s Reading package lists... 50s autopkgtest [02:47:23]: upgrading testbed (apt dist-upgrade and autopurge) 52s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s Calculating upgrade... 53s The following packages will be upgraded: 53s libc-bin libc-gconv-modules-extra libc6 locales 54s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 7850 kB of archives. 54s After this operation, 0 B of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-gconv-modules-extra armhf 2.42-2ubuntu5 [1417 kB] 54s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc6 armhf 2.42-2ubuntu5 [1632 kB] 54s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-bin armhf 2.42-2ubuntu5 [545 kB] 54s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf locales all 2.42-2ubuntu5 [4255 kB] 55s Preconfiguring packages ... 55s Fetched 7850 kB in 1s (5324 kB/s) 56s (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 ... 68395 files and directories currently installed.) 56s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_armhf.deb ... 56s Unpacking libc-gconv-modules-extra:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 56s Setting up libc-gconv-modules-extra:armhf (2.42-2ubuntu5) ... 56s (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 ... 68395 files and directories currently installed.) 56s Preparing to unpack .../libc6_2.42-2ubuntu5_armhf.deb ... 56s readlink: /usr/lib/libeatmydata: No such file or directory 56s Unpacking libc6:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 56s Setting up libc6:armhf (2.42-2ubuntu5) ... 56s (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 ... 68395 files and directories currently installed.) 56s Preparing to unpack .../libc-bin_2.42-2ubuntu5_armhf.deb ... 56s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 56s Setting up libc-bin (2.42-2ubuntu5) ... 57s (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 ... 68395 files and directories currently installed.) 57s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 57s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 57s Setting up locales (2.42-2ubuntu5) ... 58s Generating locales (this might take a while)... 60s en_US.UTF-8... done 60s Generation complete. 60s Processing triggers for systemd (259-1ubuntu3) ... 60s Processing triggers for man-db (2.13.1-1) ... 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s Solving dependencies... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s autopkgtest [02:47:40]: rebooting testbed after setup commands that affected boot 109s autopkgtest [02:48:22]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 135s autopkgtest [02:48:48]: @@@@@@@@@@@@@@@@@@@@ apt-source emmax 145s Get:1 http://ftpmaster.internal/ubuntu resolute/universe emmax 0~beta.20100307-6 (dsc) [2258 B] 145s Get:2 http://ftpmaster.internal/ubuntu resolute/universe emmax 0~beta.20100307-6 (tar) [18.6 kB] 145s Get:3 http://ftpmaster.internal/ubuntu resolute/universe emmax 0~beta.20100307-6 (diff) [9100 B] 145s gpgv: Signature made Sun Jul 13 11:52:30 2025 UTC 145s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 145s gpgv: issuer "emollier@debian.org" 145s gpgv: Can't check signature: No public key 145s dpkg-source: warning: cannot verify inline signature for ./emmax_0~beta.20100307-6.dsc: no acceptable signature found 145s autopkgtest [02:48:58]: testing package emmax version 0~beta.20100307-6 147s autopkgtest [02:49:00]: build not needed 150s autopkgtest [02:49:03]: test run-unit-test: preparing testbed 151s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Solving dependencies... 153s The following NEW packages will be installed: 153s emmax libblas3 libgfortran5 liblapack3 liblapacke libtmglib3 plink 153s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 4313 kB of archives. 153s After this operation, 9751 kB of additional disk space will be used. 153s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 153s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 153s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 154s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libtmglib3 armhf 3.12.1-7ubuntu1 [102 kB] 154s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf liblapacke armhf 3.12.1-7ubuntu1 [372 kB] 154s Get:6 http://ftpmaster.internal/ubuntu resolute/universe armhf emmax armhf 0~beta.20100307-6 [26.1 kB] 154s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf plink armhf 1.07+dfsg-5 [1256 kB] 155s Fetched 4313 kB in 2s (2527 kB/s) 155s Selecting previously unselected package libblas3:armhf. 155s (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 ... 68395 files and directories currently installed.) 155s Preparing to unpack .../0-libblas3_3.12.1-7ubuntu1_armhf.deb ... 155s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 155s Selecting previously unselected package libgfortran5:armhf. 155s Preparing to unpack .../1-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 155s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 155s Selecting previously unselected package liblapack3:armhf. 155s Preparing to unpack .../2-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 155s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 155s Selecting previously unselected package libtmglib3:armhf. 155s Preparing to unpack .../3-libtmglib3_3.12.1-7ubuntu1_armhf.deb ... 155s Unpacking libtmglib3:armhf (3.12.1-7ubuntu1) ... 155s Selecting previously unselected package liblapacke:armhf. 155s Preparing to unpack .../4-liblapacke_3.12.1-7ubuntu1_armhf.deb ... 155s Unpacking liblapacke:armhf (3.12.1-7ubuntu1) ... 155s Selecting previously unselected package emmax. 155s Preparing to unpack .../5-emmax_0~beta.20100307-6_armhf.deb ... 155s Unpacking emmax (0~beta.20100307-6) ... 155s Selecting previously unselected package plink. 155s Preparing to unpack .../6-plink_1.07+dfsg-5_armhf.deb ... 155s Unpacking plink (1.07+dfsg-5) ... 155s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 155s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 155s Setting up libgfortran5:armhf (15.2.0-12ubuntu1) ... 155s Setting up plink (1.07+dfsg-5) ... 155s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 155s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 155s Setting up libtmglib3:armhf (3.12.1-7ubuntu1) ... 155s Setting up liblapacke:armhf (3.12.1-7ubuntu1) ... 155s Setting up emmax (0~beta.20100307-6) ... 155s Processing triggers for man-db (2.13.1-1) ... 156s Processing triggers for libc-bin (2.42-2ubuntu5) ... 165s autopkgtest [02:49:17]: test run-unit-test: [----------------------- 166s 166s @----------------------------------------------------------@ 166s | PLINK! | v1.07 | 10/Aug/2009 | 166s |----------------------------------------------------------| 166s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 166s |----------------------------------------------------------| 166s | For documentation, citation & bug-report instructions: | 166s | http://pngu.mgh.harvard.edu/purcell/plink/ | 166s @----------------------------------------------------------@ 166s 166s Skipping web check... [ --noweb ] 166s Writing this text to log file [ test.log ] 166s Analysis started: Thu Feb 5 02:49:19 2026 166s 166s Options in effect: 166s --noweb 166s --file test 166s --recode12 166s --output-missing-genotype 0 166s --transpose 166s --out test 166s 166s 2 (of 2) markers to be included from [ test.map ] 166s 6 individuals read from [ test.ped ] 166s 6 individuals with nonmissing phenotypes 166s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 166s Missing phenotype value is also -9 166s 3 cases, 3 controls and 0 missing 166s 6 males, 0 females, and 0 of unspecified sex 166s Before frequency and genotyping pruning, there are 2 SNPs 166s 6 founders and 0 non-founders found 166s Total genotyping rate in remaining individuals is 1 166s 0 SNPs failed missingness test ( GENO > 1 ) 166s 0 SNPs failed frequency test ( MAF < 0 ) 166s After frequency and genotyping pruning, there are 2 SNPs 166s After filtering, 3 cases, 3 controls and 0 missing 166s After filtering, 6 males, 0 females, and 0 of unspecified sex 166s 166s Reading TFAM file test.tfam .... 166s 166s Reading TPED file test.tped .... 166s Reading 0 SNPs 166s Printing the kinship matrix to file 166s 166s Reading TFAM file test.tfam .... 166s 166s 166s Reading kinship file test.BN.kinf... 166s 166s 6 rows and 6 columns were observed with 0 missing values. 166s 166s 166s Reading the phenotype file test.emmax_phenotypes... 166s 166s 6 rows and 1 columns were observed with 0 missing values 166s 166s nmiss = 0 , mphenoflag = 0 166s 166s No covariates were found... using intercept only 166s 166s File reading - elapsed CPU time is 0.000953 166s 166s evals[0] = -0.000000, evals[1] = 1.000000, evals[n-1] = 2.941379 166s k = 5, n-q = 5 166s eRvals[0] = 0.000000, eRvals[n-q-1] = 1.941379, eRvals[n-q] = 0.000000 166s eigen_R - elapsed CPU time is 0.002960 166s etas[0] = -0.138011, lambdas[0] = 0.000000 166s etas[1] = 0.044521, lambdas[1] = 0.000000 166s etas[2] = -0.514476, lambdas[2] = 0.000000 166s etas[3] = -1.076217, lambdas[3] = 1.390764 166s etas[4] = -0.236732, lambdas[4] = 1.941379 166s 0 22018.257738 18025.554634 -10.436184 166s 166s 1 18025.554634 14756.603366 -10.236267 166s 166s 2 14756.603366 12080.210867 -10.036367 166s 166s 3 12080.210867 9888.965064 -9.836490 166s 166s 4 9888.965064 8094.924207 -9.636639 166s 166s 5 8094.924207 6626.087568 -9.436822 166s 166s 6 6626.087568 5423.505863 -9.237045 166s 166s 7 5423.505863 4438.915457 -9.037317 166s 166s 8 4438.915457 3632.801410 -8.837649 166s 166s 9 3632.801410 2972.811620 -8.638055 166s 166s 10 2972.811620 2432.458439 -8.438550 166s 166s 11 2432.458439 1990.055632 -8.239155 166s 166s 12 1990.055632 1627.848047 -8.039894 166s 166s 13 1627.848047 1331.299038 -7.840796 166s 166s 14 1331.299038 1088.507059 -7.641896 166s 166s 15 1088.507059 889.728021 -7.443240 166s 166s 16 889.728021 726.984222 -7.244880 166s 166s 17 726.984222 593.744175 -7.046881 166s 166s 18 593.744175 484.660477 -6.849323 166s 166s 19 484.660477 395.355199 -6.652300 166s 166s Writing transposed ped file to [ test.tped ] 166s Writing family information to [ test.tfam ] 166s 166s Analysis finished: Thu Feb 5 02:49:19 2026 166s 166s Running Tests 166s Test 1 166s Test 2 166s test.emmax.ps: OK 166s PASS 166s 20 395.355199 322.244175 -6.455931 166s 166s 21 322.244175 262.393159 -6.260357 166s 166s 22 262.393159 213.400052 -6.065749 166s 166s 23 213.400052 173.298491 -5.872315 166s 166s 24 173.298491 140.478912 -5.680305 166s 166s 25 140.478912 113.623936 -5.490020 166s 166s 26 113.623936 91.655465 -5.301821 166s 166s 27 91.655465 73.691370 -5.116138 166s 166s 28 73.691370 59.010027 -4.933484 166s 166s 29 59.010027 47.021271 -4.754462 166s 166s 30 47.021271 37.242592 -4.579783 166s 166s 31 37.242592 29.279612 -4.410267 166s 166s 32 29.279612 22.810053 -4.246860 166s 166s 33 22.810053 17.570543 -4.090633 166s 166s 34 17.570543 13.345722 -3.942779 166s 166s 35 13.345722 9.959235 -3.804597 166s 166s 36 9.959235 7.266243 -3.677472 166s 166s 37 7.266243 5.147220 -3.562823 166s 166s 38 5.147220 3.502813 -3.462051 166s 166s 39 3.502813 2.249657 -3.376452 166s 166s 40 2.249657 1.317042 -3.307126 166s 166s 41 1.317042 0.644369 -3.254875 166s 166s 42 0.644369 0.179318 -3.220102 166s 166s 43 0.179318 -0.123364 -3.202722 166s 166s 44 -0.123364 -0.302600 -3.202114 166s 166s 45 -0.302600 -0.391402 -3.217103 166s 166s 46 -0.391402 -0.417145 -3.246000 166s 166s 47 -0.417145 -0.401842 -3.286683 166s 166s 48 -0.401842 -0.362510 -3.336729 166s 166s 49 -0.362510 -0.311679 -3.393560 166s 166s 50 -0.311679 -0.258015 -3.454610 166s 166s 51 -0.258015 -0.207024 -3.517470 166s 166s 52 -0.207024 -0.161777 -3.580015 166s 166s 53 -0.161777 -0.123578 -3.640489 166s 166s 54 -0.123578 -0.092560 -3.697547 166s 166s 55 -0.092560 -0.068157 -3.750255 166s 166s 56 -0.068157 -0.049454 -3.798063 166s 166s 57 -0.049454 -0.035431 -3.840743 166s 166s 58 -0.035431 -0.025110 -3.878327 166s 166s 59 -0.025110 -0.017632 -3.911038 166s 166s 60 -0.017632 -0.012285 -3.939222 166s 166s 61 -0.012285 -0.008503 -3.963300 166s 166s 62 -0.008503 -0.005853 -3.983722 166s 166s 63 -0.005853 -0.004010 -4.000940 166s 166s 64 -0.004010 -0.002737 -4.015382 166s 166s 65 -0.002737 -0.001862 -4.027444 166s 166s 66 -0.001862 -0.001264 -4.037485 166s 166s 67 -0.001264 -0.000856 -4.045817 166s 166s 68 -0.000856 -0.000578 -4.052716 166s 166s 69 -0.000578 -0.000390 -4.058416 166s 166s 70 -0.000390 -0.000263 -4.063118 166s 166s 71 -0.000263 -0.000177 -4.066992 166s 166s 72 -0.000177 -0.000119 -4.070180 166s 166s 73 -0.000119 -0.000080 -4.072800 166s 166s 74 -0.000080 -0.000054 -4.074953 166s 166s 75 -0.000054 -0.000036 -4.076721 166s 166s 76 -0.000036 -0.000024 -4.078172 166s 166s 77 -0.000024 -0.000016 -4.079361 166s 166s 78 -0.000016 -0.000011 -4.080337 166s 166s 79 -0.000011 -0.000007 -4.081137 166s 166s 80 -0.000007 -0.000005 -4.081792 166s 166s 81 -0.000005 -0.000003 -4.082330 166s 166s 82 -0.000003 -0.000002 -4.082770 166s 166s 83 -0.000002 -0.000001 -4.083130 166s 166s 84 -0.000001 -0.000001 -4.083425 166s 166s 85 -0.000001 -0.000001 -4.083667 166s 166s 86 -0.000001 -0.000000 -4.083865 166s 166s 87 -0.000000 -0.000000 -4.084028 166s 166s 88 -0.000000 -0.000000 -4.084160 166s 166s 89 -0.000000 -0.000000 -4.084269 166s 166s 90 -0.000000 -0.000000 -4.084358 166s 166s 91 -0.000000 -0.000000 -4.084431 166s 166s 92 -0.000000 -0.000000 -4.084491 166s 166s 93 -0.000000 -0.000000 -4.084540 166s 166s 94 -0.000000 -0.000000 -4.084580 166s 166s 95 -0.000000 -0.000000 -4.084613 166s 166s 96 -0.000000 -0.000000 -4.084639 166s 166s 97 -0.000000 -0.000000 -4.084661 166s 166s 98 -0.000000 -0.000000 -4.084679 166s 166s 99 -0.000000 -0.000000 -4.084694 166s 166s REMLE (delta=0.274428, REML=-3.200372, REML0=-4.084761)- elapsed CPU time is 0.000356 166s eigen_L - elapsed CPU time is 0.000010 166s 166s 166s Reading TPED file test... 166s 166s Reading 0-th SNP and testing association.... 166s 166s GLS association - elapsed CPU time is 0.000251 166s 166s Breakdown for input file parsing : 0.000025 166s 166s matrix computation : 0.000002 166s 166s p-value computation : 0.000002 166s 166s autopkgtest [02:49:19]: test run-unit-test: -----------------------] 173s autopkgtest [02:49:23]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 173s run-unit-test PASS 178s autopkgtest [02:49:30]: @@@@@@@@@@@@@@@@@@@@ summary 178s run-unit-test PASS