0s autopkgtest [01:01:43]: starting date and time: 2024-04-19 01:01:43+0000 0s autopkgtest [01:01:43]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [01:01:43]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.megcuonj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:gsl --apt-upgrade fastqtl --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-arm64-9.secgroup --name adt-noble-arm64-fastqtl-20240419-010143-juju-7f2275-prod-proposed-migration-environment-3-22733d05-12b9-413d-b43f-8bcdfa86c6f3 --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/ 93s autopkgtest [01:03:16]: testbed dpkg architecture: arm64 94s autopkgtest [01:03:17]: testbed apt version: 2.7.14build2 94s autopkgtest [01:03:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 95s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 96s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [376 kB] 97s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 97s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [54.2 kB] 97s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [130 kB] 98s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 98s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [92.9 kB] 98s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 98s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [563 kB] 101s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 101s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 104s Fetched 1360 kB in 7s (205 kB/s) 104s Reading package lists... 106s sh: 4: dhclient: not found 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Calculating upgrade... 110s The following packages will be upgraded: 110s apport apport-core-dump-handler libkeyutils1 libnuma1 libunwind8 make man-db 110s netcat-openbsd numactl python3-apport python3-problem-report 110s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Need to get 1797 kB of archives. 110s After this operation, 1024 B of additional disk space will be used. 110s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB] 110s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3-apport all 2.28.1-0ubuntu1 [92.1 kB] 111s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB] 111s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 apport all 2.28.1-0ubuntu1 [83.5 kB] 111s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3build1 [9654 B] 111s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 netcat-openbsd arm64 1.226-1ubuntu2 [43.8 kB] 111s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1build1 [23.6 kB] 111s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 man-db arm64 2.12.0-4build2 [1232 kB] 113s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libunwind8 arm64 1.6.2-3build1 [53.5 kB] 113s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build2 [178 kB] 113s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 numactl arm64 2.0.18-1build1 [39.5 kB] 114s Preconfiguring packages ... 114s Fetched 1797 kB in 3s (561 kB/s) 114s (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.) 114s Preparing to unpack .../00-python3-problem-report_2.28.1-0ubuntu1_all.deb ... 114s Unpacking python3-problem-report (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 114s Preparing to unpack .../01-python3-apport_2.28.1-0ubuntu1_all.deb ... 115s Unpacking python3-apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 115s Preparing to unpack .../02-apport-core-dump-handler_2.28.1-0ubuntu1_all.deb ... 115s Unpacking apport-core-dump-handler (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 115s Preparing to unpack .../03-apport_2.28.1-0ubuntu1_all.deb ... 115s Unpacking apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 115s Preparing to unpack .../04-libkeyutils1_1.6.3-3build1_arm64.deb ... 115s Unpacking libkeyutils1:arm64 (1.6.3-3build1) over (1.6.3-3) ... 115s Preparing to unpack .../05-netcat-openbsd_1.226-1ubuntu2_arm64.deb ... 115s Unpacking netcat-openbsd (1.226-1ubuntu2) over (1.226-1ubuntu1) ... 115s Preparing to unpack .../06-libnuma1_2.0.18-1build1_arm64.deb ... 115s Unpacking libnuma1:arm64 (2.0.18-1build1) over (2.0.18-1) ... 115s Preparing to unpack .../07-man-db_2.12.0-4build2_arm64.deb ... 115s Unpacking man-db (2.12.0-4build2) over (2.12.0-4build1) ... 115s Preparing to unpack .../08-libunwind8_1.6.2-3build1_arm64.deb ... 115s Unpacking libunwind8:arm64 (1.6.2-3build1) over (1.6.2-3) ... 116s Preparing to unpack .../09-make_4.3-4.1build2_arm64.deb ... 116s Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... 116s Preparing to unpack .../10-numactl_2.0.18-1build1_arm64.deb ... 116s Unpacking numactl (2.0.18-1build1) over (2.0.18-1) ... 116s Setting up libkeyutils1:arm64 (1.6.3-3build1) ... 116s Setting up python3-problem-report (2.28.1-0ubuntu1) ... 116s Setting up netcat-openbsd (1.226-1ubuntu2) ... 116s Setting up man-db (2.12.0-4build2) ... 116s Updating database of manual pages ... 120s man-db.service is a disabled or a static unit not running, not starting it. 120s Setting up libunwind8:arm64 (1.6.2-3build1) ... 120s Setting up python3-apport (2.28.1-0ubuntu1) ... 120s Setting up make (4.3-4.1build2) ... 120s Setting up libnuma1:arm64 (2.0.18-1build1) ... 120s Setting up numactl (2.0.18-1build1) ... 120s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ... 123s Setting up apport (2.28.1-0ubuntu1) ... 123s Installing new version of config file /etc/apport/crashdb.conf ... 125s apport-autoreport.service is a disabled or a static unit not running, not starting it. 125s Processing triggers for libc-bin (2.39-0ubuntu8) ... 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 127s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 127s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 127s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 130s Reading package lists... 130s Reading package lists... 131s Building dependency tree... 131s Reading state information... 132s Calculating upgrade... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s autopkgtest [01:03:57]: rebooting testbed after setup commands that affected boot 285s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 293s autopkgtest [01:06:36]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP PREEMPT_DYNAMIC Fri Apr 5 02:52:09 UTC 2024 296s autopkgtest [01:06:39]: @@@@@@@@@@@@@@@@@@@@ apt-source fastqtl 303s Get:1 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build3 (dsc) [2359 B] 303s Get:2 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build3 (tar) [17.1 MB] 303s Get:3 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build3 (diff) [21.2 kB] 304s gpgv: Signature made Mon Apr 1 05:47:14 2024 UTC 304s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 304s gpgv: Can't check signature: No public key 304s dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-4build3.dsc: no acceptable signature found 304s autopkgtest [01:06:47]: testing package fastqtl version 2.184+v7+dfsg-4build3 305s autopkgtest [01:06:48]: build not needed 332s autopkgtest [01:07:15]: test run-sample-analysis: preparing testbed 333s Reading package lists... 334s Building dependency tree... 334s Reading state information... 334s Starting pkgProblemResolver with broken count: 0 334s Starting 2 pkgProblemResolver with broken count: 0 334s Done 335s The following additional packages will be installed: 335s fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0 335s libboost-program-options1.83.0 libgsl27 libgslcblas0 libhts3t64 335s libhtscodecs2 r-mathlib 335s Suggested packages: 335s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 335s Recommended packages: 335s r-cran-qvalue r-cran-tools r-cran-argparser r-base-core r-base-dev 335s The following NEW packages will be installed: 335s autopkgtest-satdep fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0 335s libboost-program-options1.83.0 libgsl27 libgslcblas0 libhts3t64 335s libhtscodecs2 r-mathlib 335s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 335s Need to get 21.9 MB/21.9 MB of archives. 335s After this operation, 30.9 MB of additional disk space will be used. 335s Get:1 /tmp/autopkgtest.smYAZA/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 335s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 336s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-2.1ubuntu3 [258 kB] 336s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2.1ubuntu3 [317 kB] 336s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu2 [72.8 kB] 336s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu2 [918 kB] 337s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 337s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3t64 arm64 1.19+ds-1.1build3 [429 kB] 337s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 r-mathlib arm64 4.3.3-2build2 [2400 kB] 338s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 fastqtl arm64 2.184+v7+dfsg-4build3 [204 kB] 338s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 fastqtl-doc all 2.184+v7+dfsg-4build3 [17.0 MB] 340s Fetched 21.9 MB in 4s (5011 kB/s) 340s Selecting previously unselected package libblas3:arm64. 341s (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.) 341s Preparing to unpack .../00-libblas3_3.12.0-3build1_arm64.deb ... 341s Unpacking libblas3:arm64 (3.12.0-3build1) ... 341s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 341s Preparing to unpack .../01-libboost-iostreams1.83.0_1.83.0-2.1ubuntu3_arm64.deb ... 341s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-2.1ubuntu3) ... 341s Selecting previously unselected package libboost-program-options1.83.0:arm64. 341s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2.1ubuntu3_arm64.deb ... 341s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-2.1ubuntu3) ... 341s Selecting previously unselected package libgslcblas0:arm64. 341s Preparing to unpack .../03-libgslcblas0_2.7.1+dfsg-6ubuntu2_arm64.deb ... 341s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 341s Selecting previously unselected package libgsl27:arm64. 341s Preparing to unpack .../04-libgsl27_2.7.1+dfsg-6ubuntu2_arm64.deb ... 341s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 341s Selecting previously unselected package libhtscodecs2:arm64. 341s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_arm64.deb ... 341s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 341s Selecting previously unselected package libhts3t64:arm64. 341s Preparing to unpack .../06-libhts3t64_1.19+ds-1.1build3_arm64.deb ... 341s Unpacking libhts3t64:arm64 (1.19+ds-1.1build3) ... 341s Selecting previously unselected package r-mathlib. 341s Preparing to unpack .../07-r-mathlib_4.3.3-2build2_arm64.deb ... 341s Unpacking r-mathlib (4.3.3-2build2) ... 341s Selecting previously unselected package fastqtl. 341s Preparing to unpack .../08-fastqtl_2.184+v7+dfsg-4build3_arm64.deb ... 341s Unpacking fastqtl (2.184+v7+dfsg-4build3) ... 341s Selecting previously unselected package fastqtl-doc. 341s Preparing to unpack .../09-fastqtl-doc_2.184+v7+dfsg-4build3_all.deb ... 341s Unpacking fastqtl-doc (2.184+v7+dfsg-4build3) ... 342s Selecting previously unselected package autopkgtest-satdep. 342s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 342s Unpacking autopkgtest-satdep (0) ... 342s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 342s Setting up libboost-program-options1.83.0:arm64 (1.83.0-2.1ubuntu3) ... 342s Setting up fastqtl-doc (2.184+v7+dfsg-4build3) ... 342s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu2) ... 342s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu2) ... 342s Setting up libblas3:arm64 (3.12.0-3build1) ... 342s 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 342s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-2.1ubuntu3) ... 342s Setting up r-mathlib (4.3.3-2build2) ... 342s Setting up libhts3t64:arm64 (1.19+ds-1.1build3) ... 342s Setting up fastqtl (2.184+v7+dfsg-4build3) ... 342s Setting up autopkgtest-satdep (0) ... 342s Processing triggers for man-db (2.12.0-4build2) ... 343s Processing triggers for libc-bin (2.39-0ubuntu8) ... 348s (Reading database ... 77868 files and directories currently installed.) 348s Removing autopkgtest-satdep (0) ... 349s autopkgtest [01:07:32]: test run-sample-analysis: [----------------------- 349s covariates.txt.gz 349s genotypes.vcf.gz 349s genotypes.vcf.gz.tbi 349s interaction.txt 349s phenotypes.bed.gz 349s phenotypes.bed.gz.tbi 349s 349s Fast QTL 349s * Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS 349s * Contact : olivier.delaneau@gmail.com 349s * Webpage : http://fastqtl.sourceforge.net/ 349s * Version : v2.184_gtex 349s 349s Perform permutation based interaction analysis (used to calculate corrected p-values for MPs) 349s * Perform 100 permutations 349s * Test interaction with term from [interaction.txt] 349s * Random number generator is seeded with 1 349s * Considering variants within 1e+06 bp of the MPs 349s * Using minor allele frequency threshold = 0.0000 349s * Using minor allele sample threshold = 0 349s * Using INFO field AF threshold = 0.0000 349s * Chunk processed 1 / 100 349s 349s Scanning phenotype data in [phenotypes.bed.gz] 349s * 364 phenotypes 349s 349s Reading phenotype data in [phenotypes.bed.gz] 349s * region = 22:17517460-17646177 349s * 373 samples included 349s * 4 phenotypes included 349s 349s Reading genotype data in [genotypes.vcf.gz] in VCF format 349s * region = 22:16517460-18646177 350s * 373 samples included 350s * 8580 sites included 350s 350s Reading covariates in [covariates.txt.gz] 350s * 373 samples included 350s * 4 covariate(s) included 350s 350s Reading interaction term in [interaction.txt] 350s * 373 samples included 350s 350s Imputing missing genotypes 350s 350s Imputing missing phenotypes 350s 350s Initialize covariate 350s 350s Processing gene [ENSG00000237438.1] 350s * Number of variants in cis = 7966 382s * Beta distribution parameters = 1.0382 2287.7101 382s * Progress = 25.0% 382s 382s Processing gene [ENSG00000177663.8] 382s * Number of variants in cis = 8165 415s * Beta distribution parameters = 0.7994 2826.0721 415s * Progress = 50.0% 415s 415s Processing gene [ENSG00000183307.3] 415s * Number of variants in cis = 8279 449s * Beta distribution parameters = 0.9595 9906.5566 449s * Progress = 75.0% 449s 449s Processing gene [ENSG00000069998.8] 449s * Number of variants in cis = 8466 483s * Beta distribution parameters = 0.9606 4564.2130 483s * Progress = 100.0% 483s 483s Running time: 134 seconds 483s autopkgtest [01:09:46]: test run-sample-analysis: -----------------------] 484s autopkgtest [01:09:47]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 484s run-sample-analysis PASS 484s autopkgtest [01:09:47]: @@@@@@@@@@@@@@@@@@@@ summary 484s run-sample-analysis PASS 496s Creating nova instance adt-noble-arm64-fastqtl-20240419-010143-juju-7f2275-prod-proposed-migration-environment-3-22733d05-12b9-413d-b43f-8bcdfa86c6f3 from image adt/ubuntu-noble-arm64-server-20240418.img (UUID 6f8e97a7-9a55-4e99-9797-31213b709dd4)...