0s autopkgtest [02:10:44]: starting date and time: 2024-04-19 02:10:44+0000 0s autopkgtest [02:10:44]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [02:10:44]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pxzvi7iv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:gsl --apt-upgrade gemma --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=gsl/2.7.1+dfsg-6ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-arm64-21.secgroup --name adt-noble-arm64-gemma-20240419-012605-juju-7f2275-prod-proposed-migration-environment-3-b9efec6b-ad80-490b-a057-81f849ad30a8 --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/ 121s autopkgtest [02:12:45]: testbed dpkg architecture: arm64 121s autopkgtest [02:12:45]: testbed apt version: 2.7.14build2 121s autopkgtest [02:12:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 122s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 123s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 123s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 123s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [338 kB] 124s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [53.4 kB] 124s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [129 kB] 124s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 124s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [92.9 kB] 124s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 124s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [464 kB] 124s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 124s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 130s Fetched 1221 kB in 2s (580 kB/s) 131s Reading package lists... 133s sh: 4: dhclient: not found 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 138s Calculating upgrade... 139s The following packages will be upgraded: 139s apport apport-core-dump-handler libkeyutils1 libnetplan1 libnuma1 libunwind8 139s make man-db netcat-openbsd netplan-generator netplan.io numactl 139s python3-apport python3-netplan python3-problem-report 139s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 2062 kB of archives. 139s After this operation, 1024 B of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB] 139s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3-apport all 2.28.1-0ubuntu1 [92.1 kB] 139s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB] 139s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 apport all 2.28.1-0ubuntu1 [83.5 kB] 139s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3build1 [9654 B] 139s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 netplan-generator arm64 1.0-2ubuntu1 [58.9 kB] 139s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 python3-netplan arm64 1.0-2ubuntu1 [21.5 kB] 139s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 netplan.io arm64 1.0-2ubuntu1 [65.8 kB] 139s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libnetplan1 arm64 1.0-2ubuntu1 [119 kB] 139s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 netcat-openbsd arm64 1.226-1ubuntu2 [43.8 kB] 139s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1build1 [23.6 kB] 139s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 man-db arm64 2.12.0-4build2 [1232 kB] 140s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libunwind8 arm64 1.6.2-3build1 [53.5 kB] 140s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build2 [178 kB] 140s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 numactl arm64 2.0.18-1build1 [39.5 kB] 140s Preconfiguring packages ... 141s Fetched 2062 kB in 1s (2471 kB/s) 141s (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 ... 77740 files and directories currently installed.) 141s Preparing to unpack .../00-python3-problem-report_2.28.1-0ubuntu1_all.deb ... 141s Unpacking python3-problem-report (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 141s Preparing to unpack .../01-python3-apport_2.28.1-0ubuntu1_all.deb ... 142s Unpacking python3-apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 142s Preparing to unpack .../02-apport-core-dump-handler_2.28.1-0ubuntu1_all.deb ... 142s Unpacking apport-core-dump-handler (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 142s Preparing to unpack .../03-apport_2.28.1-0ubuntu1_all.deb ... 142s Unpacking apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 142s Preparing to unpack .../04-libkeyutils1_1.6.3-3build1_arm64.deb ... 142s Unpacking libkeyutils1:arm64 (1.6.3-3build1) over (1.6.3-3) ... 143s Preparing to unpack .../05-netplan-generator_1.0-2ubuntu1_arm64.deb ... 143s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 143s Unpacking netplan-generator (1.0-2ubuntu1) over (1.0-2build1) ... 143s Preparing to unpack .../06-python3-netplan_1.0-2ubuntu1_arm64.deb ... 143s Unpacking python3-netplan (1.0-2ubuntu1) over (1.0-2build1) ... 143s Preparing to unpack .../07-netplan.io_1.0-2ubuntu1_arm64.deb ... 143s Unpacking netplan.io (1.0-2ubuntu1) over (1.0-2build1) ... 143s Preparing to unpack .../08-libnetplan1_1.0-2ubuntu1_arm64.deb ... 143s Unpacking libnetplan1:arm64 (1.0-2ubuntu1) over (1.0-2build1) ... 143s Preparing to unpack .../09-netcat-openbsd_1.226-1ubuntu2_arm64.deb ... 143s Unpacking netcat-openbsd (1.226-1ubuntu2) over (1.226-1ubuntu1) ... 143s Preparing to unpack .../10-libnuma1_2.0.18-1build1_arm64.deb ... 143s Unpacking libnuma1:arm64 (2.0.18-1build1) over (2.0.18-1) ... 143s Preparing to unpack .../11-man-db_2.12.0-4build2_arm64.deb ... 143s Unpacking man-db (2.12.0-4build2) over (2.12.0-4build1) ... 144s Preparing to unpack .../12-libunwind8_1.6.2-3build1_arm64.deb ... 144s Unpacking libunwind8:arm64 (1.6.2-3build1) over (1.6.2-3) ... 144s Preparing to unpack .../13-make_4.3-4.1build2_arm64.deb ... 144s Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... 144s Preparing to unpack .../14-numactl_2.0.18-1build1_arm64.deb ... 144s Unpacking numactl (2.0.18-1build1) over (2.0.18-1) ... 144s Setting up libkeyutils1:arm64 (1.6.3-3build1) ... 144s Setting up python3-problem-report (2.28.1-0ubuntu1) ... 145s Setting up netcat-openbsd (1.226-1ubuntu2) ... 145s Setting up libnetplan1:arm64 (1.0-2ubuntu1) ... 145s Setting up man-db (2.12.0-4build2) ... 145s Updating database of manual pages ... 150s man-db.service is a disabled or a static unit not running, not starting it. 151s Setting up libunwind8:arm64 (1.6.2-3build1) ... 151s Setting up python3-apport (2.28.1-0ubuntu1) ... 151s Setting up make (4.3-4.1build2) ... 151s Setting up libnuma1:arm64 (2.0.18-1build1) ... 151s Setting up python3-netplan (1.0-2ubuntu1) ... 151s Setting up netplan-generator (1.0-2ubuntu1) ... 152s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 152s Setting up numactl (2.0.18-1build1) ... 152s Setting up netplan.io (1.0-2ubuntu1) ... 152s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ... 156s Setting up apport (2.28.1-0ubuntu1) ... 156s Installing new version of config file /etc/apport/crashdb.conf ... 159s apport-autoreport.service is a disabled or a static unit not running, not starting it. 159s Processing triggers for dbus (1.14.10-4ubuntu4) ... 159s Processing triggers for libc-bin (2.39-0ubuntu8) ... 160s Reading package lists... 161s Building dependency tree... 161s Reading state information... 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 163s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 163s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 163s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 169s Reading package lists... 169s Reading package lists... 170s Building dependency tree... 170s Reading state information... 171s Calculating upgrade... 172s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Reading package lists... 173s Building dependency tree... 173s Reading state information... 175s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s autopkgtest [02:13:39]: rebooting testbed after setup commands that affected boot 336s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 344s autopkgtest [02:16:28]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP PREEMPT_DYNAMIC Fri Apr 5 02:52:09 UTC 2024 348s autopkgtest [02:16:32]: @@@@@@@@@@@@@@@@@@@@ apt-source gemma 354s Get:1 http://ftpmaster.internal/ubuntu noble/universe gemma 0.98.5+dfsg-2 (dsc) [2130 B] 354s Get:2 http://ftpmaster.internal/ubuntu noble/universe gemma 0.98.5+dfsg-2 (tar) [44.2 MB] 354s Get:3 http://ftpmaster.internal/ubuntu noble/universe gemma 0.98.5+dfsg-2 (diff) [6636 B] 355s gpgv: Signature made Fri Nov 18 11:18:27 2022 UTC 355s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 355s gpgv: issuer "tille@debian.org" 355s gpgv: Can't check signature: No public key 355s dpkg-source: warning: cannot verify inline signature for ./gemma_0.98.5+dfsg-2.dsc: no acceptable signature found 364s autopkgtest [02:16:48]: testing package gemma version 0.98.5+dfsg-2 364s autopkgtest [02:16:48]: build not needed 377s autopkgtest [02:17:01]: test run-unit-test: preparing testbed 379s Reading package lists... 379s Building dependency tree... 379s Reading state information... 380s Starting pkgProblemResolver with broken count: 0 380s Starting 2 pkgProblemResolver with broken count: 0 380s Done 382s The following additional packages will be installed: 382s gemma gemma-doc libgfortran5 libgsl27 libgslcblas0 libopenblas0 382s libopenblas0-pthread 382s Suggested packages: 382s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 382s The following NEW packages will be installed: 382s autopkgtest-satdep gemma gemma-doc libgfortran5 libgsl27 libgslcblas0 382s libopenblas0 libopenblas0-pthread 382s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 382s Need to get 40.6 MB/40.6 MB of archives. 382s After this operation, 63.5 MB of additional disk space will be used. 382s Get:1 /tmp/autopkgtest.24A4of/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 382s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu2 [72.8 kB] 383s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu2 [918 kB] 383s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240412-0ubuntu1 [444 kB] 384s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenblas0-pthread arm64 0.3.26+ds-1 [5464 kB] 393s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenblas0 arm64 0.3.26+ds-1 [6170 B] 393s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 gemma arm64 0.98.5+dfsg-2 [335 kB] 393s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 gemma-doc all 0.98.5+dfsg-2 [33.4 MB] 425s Fetched 40.6 MB in 42s (970 kB/s) 425s Selecting previously unselected package libgslcblas0:arm64. 426s (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 ... 77739 files and directories currently installed.) 426s Preparing to unpack .../0-libgslcblas0_2.7.1+dfsg-6ubuntu2_arm64.deb ... 426s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 426s Selecting previously unselected package libgsl27:arm64. 426s Preparing to unpack .../1-libgsl27_2.7.1+dfsg-6ubuntu2_arm64.deb ... 426s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 426s Selecting previously unselected package libgfortran5:arm64. 426s Preparing to unpack .../2-libgfortran5_14-20240412-0ubuntu1_arm64.deb ... 426s Unpacking libgfortran5:arm64 (14-20240412-0ubuntu1) ... 426s Selecting previously unselected package libopenblas0-pthread:arm64. 426s Preparing to unpack .../3-libopenblas0-pthread_0.3.26+ds-1_arm64.deb ... 426s Unpacking libopenblas0-pthread:arm64 (0.3.26+ds-1) ... 427s Selecting previously unselected package libopenblas0:arm64. 427s Preparing to unpack .../4-libopenblas0_0.3.26+ds-1_arm64.deb ... 427s Unpacking libopenblas0:arm64 (0.3.26+ds-1) ... 427s Selecting previously unselected package gemma. 427s Preparing to unpack .../5-gemma_0.98.5+dfsg-2_arm64.deb ... 427s Unpacking gemma (0.98.5+dfsg-2) ... 427s Selecting previously unselected package gemma-doc. 427s Preparing to unpack .../6-gemma-doc_0.98.5+dfsg-2_all.deb ... 427s Unpacking gemma-doc (0.98.5+dfsg-2) ... 428s Selecting previously unselected package autopkgtest-satdep. 428s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 428s Unpacking autopkgtest-satdep (0) ... 428s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 428s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 428s Setting up libgfortran5:arm64 (14-20240412-0ubuntu1) ... 428s Setting up gemma-doc (0.98.5+dfsg-2) ... 428s Setting up libopenblas0-pthread:arm64 (0.3.26+ds-1) ... 428s update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 428s update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 428s update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/aarch64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-aarch64-linux-gnu) in auto mode 428s Setting up libopenblas0:arm64 (0.3.26+ds-1) ... 428s Setting up gemma (0.98.5+dfsg-2) ... 428s Setting up autopkgtest-satdep (0) ... 428s Processing triggers for libc-bin (2.39-0ubuntu8) ... 435s (Reading database ... 77801 files and directories currently installed.) 435s Removing autopkgtest-satdep (0) ... 436s autopkgtest [02:18:00]: test run-unit-test: [----------------------- 438s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 438s Reading Files ... 442s ## number of total individuals = 1940 442s ## number of analyzed individuals = 1410 442s ## number of covariates = 1 442s ## number of phenotypes = 1 442s ## number of total SNPs/var = 12226 442s ## number of analyzed SNPs = 10768 442s Calculating Relatedness Matrix ... 495s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 499s **** INFO: Done. 500s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 500s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 500s Reading Files ... 504s ## number of total individuals = 1940 504s ## number of analyzed individuals = 1410 504s ## number of covariates = 1 504s ## number of phenotypes = 1 504s ## number of total SNPs/var = 12226 504s ## number of analyzed SNPs = 10768 506s Start Eigen-Decomposition... 511s pve estimate =0.608801 511s se(pve) =0.032774 562s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% 563s **** INFO: Done. 563s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 563s Reading Files ... 567s ## number of total individuals = 1940 567s ## number of analyzed individuals = 1197 567s ## number of covariates = 1 567s ## number of phenotypes = 2 567s ## number of total SNPs/var = 12226 567s ## number of analyzed SNPs = 10758 568s Start Eigen-Decomposition... 571s REMLE estimate for Vg in the null model: 571s 1.3940 571s -0.2267 2.0817 571s se(Vg): 571s 0.1567 571s 0.1363 0.2359 571s REMLE estimate for Ve in the null model: 571s 0.3489 571s 0.0491 0.4144 571s se(Ve): 571s 0.0206 571s 0.0166 0.0267 571s REMLE likelihood = -2855.1664 571s MLE estimate for Vg in the null model: 571s 1.3959 571s -0.2267 2.0854 571s se(Vg): 571s 0.1568 571s 0.1365 0.2361 571s MLE estimate for Ve in the null model: 571s 0.3483 571s 0.0490 0.4136 571s se(Ve): 571s 0.0206 571s 0.0166 0.0266 571s MLE likelihood = -2856.0280 668s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 668s **** INFO: Done. 668s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 668s Reading Files ... 672s ## number of total individuals = 1940 672s ## number of analyzed individuals = 1940 672s ## number of individuals with full phenotypes = 1197 672s ## number of covariates = 1 672s ## number of phenotypes = 2 672s ## number of observed data = 2990 672s ## number of missing data = 890 675s Start Eigen-Decomposition... 678s REMLE estimate for Vg in the null model: 678s 1.39398 678s -0.226714 2.08168 678s REMLE estimate for Ve in the null model: 678s 0.348882 678s 0.0490525 0.414433 679s Predicting Missing Phentypes ... 686s **** INFO: Done. 686s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 686s Reading Files ... 691s ## number of total individuals = 1940 691s ## number of analyzed individuals = 1940 691s ## number of covariates = 1 691s ## number of phenotypes = 2 691s ## number of total SNPs/var = 12226 691s ## number of analyzed SNPs = 10783 693s Start Eigen-Decomposition... 707s REMLE estimate for Vg in the null model: 707s 1.3918 707s -0.1223 2.0525 707s se(Vg): 707s 0.1163 707s 0.1015 0.1769 707s REMLE estimate for Ve in the null model: 707s 0.2245 707s 0.0365 0.3270 707s se(Ve): 707s 0.0101 707s 0.0088 0.0150 707s REMLE likelihood = -4007.1527 707s MLE estimate for Vg in the null model: 707s 1.3928 707s -0.1222 2.0542 707s se(Vg): 707s 0.1163 707s 0.1015 0.1768 707s MLE estimate for Ve in the null model: 707s 0.2243 707s 0.0365 0.3266 707s se(Ve): 707s 0.0101 707s 0.0088 0.0150 707s MLE likelihood = -4007.6750 831s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 831s **** INFO: Done. 831s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 831s Reading Files ... 834s ## number of total individuals = 1940 834s ## number of analyzed individuals = 757 834s ## number of covariates = 1 834s ## number of phenotypes = 1 834s ## number of total SNPs/var = 12226 834s ## number of analyzed SNPs = 10775 846s Start Eigen-Decomposition... 846s pve estimate =0.372151 846s se(pve) =0.0522377 846s Calculating UtX... 860s initial value of h = 0.372151 860s initial value of rho = 0.393216 860s initial value of pi = 0.00194896 860s initial value of |gamma| = 21 874s 0% 0.00 ==== 9% 0.26 ========= 18% 0.25 ============= 27% 0.24 ================== 36% 0.23 ====================== 45% 0.23 =========================== 55% 0.23 =============================== 64% 0.23 ==================================== 73% 0.23 ======================================== 82% 0.22 ============================================= 91% 0.22 ================================================== 100% 0.22 874s **** INFO: Done. 874s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 874s Reading Files ... 878s ## number of total individuals = 1940 878s ## number of analyzed individuals = 757 878s ## number of covariates = 1 878s ## number of phenotypes = 1 878s ## number of total SNPs/var = 12226 878s ## number of analyzed SNPs = 10775 878s ## number of cases = 409 878s ## number of controls = 348 889s Start Eigen-Decomposition... 890s pve estimate =0.372151 890s se(pve) =0.0522377 890s Calculating UtX... 904s initial value of h = 0.372151 904s initial value of rho = 0.393216 904s initial value of pi = 0.00194896 904s initial value of |gamma| = 21 2248s 0% 0.00 ==== 9% 0.12 ========= 18% 0.11 ============= 27% 0.10 ================== 36% 0.10 ====================== 45% 0.11 =========================== 55% 0.11 =============================== 64% 0.11 ==================================== 73% 0.11 ======================================== 82% 0.11 ============================================= 91% 0.11 ================================================== 100% 0.11 2248s **** INFO: Done. 2248s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 2248s Reading Files ... 2254s ## number of total individuals = 1940 2254s ## number of analyzed individuals = 757 2254s ## number of covariates = 1 2254s ## number of phenotypes = 1 2254s ## number of total SNPs/var = 12226 2254s ## number of analyzed SNPs = 10775 2254s Calculating Relatedness Matrix ... 2305s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 2310s **** INFO: Done. 2310s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 2310s Reading Files ... 2310s ## number of total individuals = 1940 2310s ## number of analyzed individuals = 757 2310s ## number of covariates = 1 2310s ## number of phenotypes = 1 2310s Adding Breeding Values ... 2312s Start Eigen-Decomposition... 2318s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 2318s **** INFO: Done. 2318s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 2318s Reading Files ... 2318s ## number of total individuals = 1940 2318s ## number of analyzed individuals = 757 2318s ## number of covariates = 1 2318s ## number of phenotypes = 1 2323s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 2323s **** INFO: Done. 2323s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 2323s Reading Files ... 2323s ## number of total individuals = 1940 2323s ## number of analyzed individuals = 757 2323s ## number of covariates = 1 2323s ## number of phenotypes = 1 2328s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 2328s **** INFO: Done. 2328s GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 2328s Reading Files ... 2328s ## number of total individuals = 1940 2328s ## number of analyzed individuals = 757 2328s ## number of covariates = 1 2328s ## number of phenotypes = 1 2333s 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% 2333s **** INFO: Done. 2333s autopkgtest [02:49:37]: test run-unit-test: -----------------------] 2334s run-unit-test PASS 2334s autopkgtest [02:49:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 2335s autopkgtest [02:49:39]: @@@@@@@@@@@@@@@@@@@@ summary 2335s run-unit-test PASS 2345s Creating nova instance adt-noble-arm64-gemma-20240419-012605-juju-7f2275-prod-proposed-migration-environment-3-b9efec6b-ad80-490b-a057-81f849ad30a8 from image adt/ubuntu-noble-arm64-server-20240418.img (UUID 6f8e97a7-9a55-4e99-9797-31213b709dd4)...