0s autopkgtest [00:47:19]: starting date and time: 2024-04-19 00:47:19+0000 0s autopkgtest [00:47:19]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [00:47:19]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.luyoqswr/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@bos01-s390x-13.secgroup --name adt-noble-s390x-fastqtl-20240419-004719-juju-7f2275-prod-proposed-migration-environment-3-64bff402-04e3-4077-b2f2-45201276fb8c --image adt/ubuntu-noble-s390x-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://us.ports.ubuntu.com/ubuntu-ports/ 128s autopkgtest [00:49:27]: testbed dpkg architecture: s390x 128s autopkgtest [00:49:27]: testbed apt version: 2.7.14build2 128s autopkgtest [00:49:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 128s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 129s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 129s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 129s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [376 kB] 129s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [54.2 kB] 129s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [95.6 kB] 129s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 129s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [976 B] 129s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 129s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [497 kB] 129s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 129s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 130s Fetched 1166 kB in 1s (1192 kB/s) 130s Reading package lists... 132s sh: 4: dhclient: not found 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s Calculating upgrade... 133s The following packages will be upgraded: 133s apport apport-core-dump-handler libkeyutils1 libnuma1 make man-db 133s netcat-openbsd numactl python3-apport python3-problem-report 134s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Need to get 1783 kB of archives. 134s After this operation, 3072 B disk space will be freed. 134s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x python3-problem-report all 2.28.1-0ubuntu1 [23.8 kB] 134s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x python3-apport all 2.28.1-0ubuntu1 [92.1 kB] 134s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x apport-core-dump-handler all 2.28.1-0ubuntu1 [16.8 kB] 134s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x apport all 2.28.1-0ubuntu1 [83.5 kB] 134s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libkeyutils1 s390x 1.6.3-3build1 [9556 B] 134s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x netcat-openbsd s390x 1.226-1ubuntu2 [44.0 kB] 134s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libnuma1 s390x 2.0.18-1build1 [25.1 kB] 134s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x man-db s390x 2.12.0-4build2 [1253 kB] 134s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x make s390x 4.3-4.1build2 [196 kB] 134s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x numactl s390x 2.0.18-1build1 [40.0 kB] 134s Preconfiguring packages ... 135s Fetched 1783 kB in 1s (2476 kB/s) 135s (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 ... 78323 files and directories currently installed.) 135s Preparing to unpack .../0-python3-problem-report_2.28.1-0ubuntu1_all.deb ... 135s Unpacking python3-problem-report (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 135s Preparing to unpack .../1-python3-apport_2.28.1-0ubuntu1_all.deb ... 135s Unpacking python3-apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 135s Preparing to unpack .../2-apport-core-dump-handler_2.28.1-0ubuntu1_all.deb ... 135s Unpacking apport-core-dump-handler (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 135s Preparing to unpack .../3-apport_2.28.1-0ubuntu1_all.deb ... 135s Unpacking apport (2.28.1-0ubuntu1) over (2.28.0-0ubuntu1) ... 135s Preparing to unpack .../4-libkeyutils1_1.6.3-3build1_s390x.deb ... 135s Unpacking libkeyutils1:s390x (1.6.3-3build1) over (1.6.3-3) ... 135s Preparing to unpack .../5-netcat-openbsd_1.226-1ubuntu2_s390x.deb ... 135s Unpacking netcat-openbsd (1.226-1ubuntu2) over (1.226-1ubuntu1) ... 135s Preparing to unpack .../6-libnuma1_2.0.18-1build1_s390x.deb ... 135s Unpacking libnuma1:s390x (2.0.18-1build1) over (2.0.18-1) ... 135s Preparing to unpack .../7-man-db_2.12.0-4build2_s390x.deb ... 135s Unpacking man-db (2.12.0-4build2) over (2.12.0-4build1) ... 135s Preparing to unpack .../8-make_4.3-4.1build2_s390x.deb ... 135s Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... 135s Preparing to unpack .../9-numactl_2.0.18-1build1_s390x.deb ... 135s Unpacking numactl (2.0.18-1build1) over (2.0.18-1) ... 135s Setting up libkeyutils1:s390x (1.6.3-3build1) ... 135s Setting up python3-problem-report (2.28.1-0ubuntu1) ... 136s Setting up netcat-openbsd (1.226-1ubuntu2) ... 136s Setting up man-db (2.12.0-4build2) ... 136s Updating database of manual pages ... 137s man-db.service is a disabled or a static unit not running, not starting it. 137s Setting up python3-apport (2.28.1-0ubuntu1) ... 138s Setting up make (4.3-4.1build2) ... 138s Setting up libnuma1:s390x (2.0.18-1build1) ... 138s Setting up numactl (2.0.18-1build1) ... 138s Setting up apport-core-dump-handler (2.28.1-0ubuntu1) ... 139s Setting up apport (2.28.1-0ubuntu1) ... 139s Installing new version of config file /etc/apport/crashdb.conf ... 139s apport-autoreport.service is a disabled or a static unit not running, not starting it. 139s Processing triggers for libc-bin (2.39-0ubuntu8) ... 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 141s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 141s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 142s Reading package lists... 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s Calculating upgrade... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s autopkgtest [00:49:42]: rebooting testbed after setup commands that affected boot 185s autopkgtest [00:50:24]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP Thu Apr 4 21:54:17 UTC 2024 188s autopkgtest [00:50:27]: @@@@@@@@@@@@@@@@@@@@ apt-source fastqtl 207s Get:1 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build3 (dsc) [2359 B] 207s Get:2 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build3 (tar) [17.1 MB] 207s Get:3 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build3 (diff) [21.2 kB] 207s gpgv: Signature made Mon Apr 1 05:47:14 2024 UTC 207s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 207s gpgv: Can't check signature: No public key 207s dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-4build3.dsc: no acceptable signature found 208s autopkgtest [00:50:47]: testing package fastqtl version 2.184+v7+dfsg-4build3 208s autopkgtest [00:50:47]: build not needed 215s autopkgtest [00:50:54]: test run-sample-analysis: preparing testbed 217s Reading package lists... 217s Building dependency tree... 217s Reading state information... 217s Starting pkgProblemResolver with broken count: 0 217s Starting 2 pkgProblemResolver with broken count: 0 217s Done 217s The following additional packages will be installed: 217s fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0 217s libboost-program-options1.83.0 libgsl27 libgslcblas0 libhts3t64 217s libhtscodecs2 r-mathlib 217s Suggested packages: 217s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 217s Recommended packages: 217s r-cran-qvalue r-cran-tools r-cran-argparser r-base-core r-base-dev 217s The following NEW packages will be installed: 217s autopkgtest-satdep fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0 217s libboost-program-options1.83.0 libgsl27 libgslcblas0 libhts3t64 217s libhtscodecs2 r-mathlib 217s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 217s Need to get 22.3 MB/22.3 MB of archives. 217s After this operation, 31.5 MB of additional disk space will be used. 217s Get:1 /tmp/autopkgtest.2TfKC7/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 217s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3build1 [245 kB] 218s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libboost-iostreams1.83.0 s390x 1.83.0-2.1ubuntu3 [259 kB] 218s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libboost-program-options1.83.0 s390x 1.83.0-2.1ubuntu3 [325 kB] 218s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libgslcblas0 s390x 2.7.1+dfsg-6ubuntu2 [150 kB] 219s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libgsl27 s390x 2.7.1+dfsg-6ubuntu2 [1084 kB] 219s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 219s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3t64 s390x 1.19+ds-1.1build3 [474 kB] 220s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x r-mathlib s390x 4.3.3-2build2 [2383 kB] 220s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x fastqtl s390x 2.184+v7+dfsg-4build3 [228 kB] 220s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x fastqtl-doc all 2.184+v7+dfsg-4build3 [17.0 MB] 223s Fetched 22.3 MB in 5s (4393 kB/s) 223s Selecting previously unselected package libblas3:s390x. 223s (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 ... 78322 files and directories currently installed.) 223s Preparing to unpack .../00-libblas3_3.12.0-3build1_s390x.deb ... 223s Unpacking libblas3:s390x (3.12.0-3build1) ... 223s Selecting previously unselected package libboost-iostreams1.83.0:s390x. 223s Preparing to unpack .../01-libboost-iostreams1.83.0_1.83.0-2.1ubuntu3_s390x.deb ... 223s Unpacking libboost-iostreams1.83.0:s390x (1.83.0-2.1ubuntu3) ... 223s Selecting previously unselected package libboost-program-options1.83.0:s390x. 223s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2.1ubuntu3_s390x.deb ... 223s Unpacking libboost-program-options1.83.0:s390x (1.83.0-2.1ubuntu3) ... 223s Selecting previously unselected package libgslcblas0:s390x. 223s Preparing to unpack .../03-libgslcblas0_2.7.1+dfsg-6ubuntu2_s390x.deb ... 223s Unpacking libgslcblas0:s390x (2.7.1+dfsg-6ubuntu2) ... 223s Selecting previously unselected package libgsl27:s390x. 223s Preparing to unpack .../04-libgsl27_2.7.1+dfsg-6ubuntu2_s390x.deb ... 223s Unpacking libgsl27:s390x (2.7.1+dfsg-6ubuntu2) ... 223s Selecting previously unselected package libhtscodecs2:s390x. 223s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_s390x.deb ... 223s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 223s Selecting previously unselected package libhts3t64:s390x. 223s Preparing to unpack .../06-libhts3t64_1.19+ds-1.1build3_s390x.deb ... 223s Unpacking libhts3t64:s390x (1.19+ds-1.1build3) ... 223s Selecting previously unselected package r-mathlib. 223s Preparing to unpack .../07-r-mathlib_4.3.3-2build2_s390x.deb ... 223s Unpacking r-mathlib (4.3.3-2build2) ... 223s Selecting previously unselected package fastqtl. 223s Preparing to unpack .../08-fastqtl_2.184+v7+dfsg-4build3_s390x.deb ... 223s Unpacking fastqtl (2.184+v7+dfsg-4build3) ... 223s Selecting previously unselected package fastqtl-doc. 223s Preparing to unpack .../09-fastqtl-doc_2.184+v7+dfsg-4build3_all.deb ... 223s Unpacking fastqtl-doc (2.184+v7+dfsg-4build3) ... 223s Selecting previously unselected package autopkgtest-satdep. 223s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 223s Unpacking autopkgtest-satdep (0) ... 223s Setting up libhtscodecs2:s390x (1.6.0-1) ... 223s Setting up libboost-program-options1.83.0:s390x (1.83.0-2.1ubuntu3) ... 223s Setting up fastqtl-doc (2.184+v7+dfsg-4build3) ... 223s Setting up libgslcblas0:s390x (2.7.1+dfsg-6ubuntu2) ... 223s Setting up libgsl27:s390x (2.7.1+dfsg-6ubuntu2) ... 223s Setting up libblas3:s390x (3.12.0-3build1) ... 223s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 223s Setting up libboost-iostreams1.83.0:s390x (1.83.0-2.1ubuntu3) ... 223s Setting up r-mathlib (4.3.3-2build2) ... 223s Setting up libhts3t64:s390x (1.19+ds-1.1build3) ... 223s Setting up fastqtl (2.184+v7+dfsg-4build3) ... 223s Setting up autopkgtest-satdep (0) ... 223s Processing triggers for man-db (2.12.0-4build2) ... 224s Processing triggers for libc-bin (2.39-0ubuntu8) ... 227s (Reading database ... 78451 files and directories currently installed.) 227s Removing autopkgtest-satdep (0) ... 228s autopkgtest [00:51:07]: test run-sample-analysis: [----------------------- 228s covariates.txt.gz 228s genotypes.vcf.gz 228s genotypes.vcf.gz.tbi 228s interaction.txt 228s phenotypes.bed.gz 228s phenotypes.bed.gz.tbi 228s 228s Fast QTL 228s * Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS 228s * Contact : olivier.delaneau@gmail.com 228s * Webpage : http://fastqtl.sourceforge.net/ 228s * Version : v2.184_gtex 228s 228s Perform permutation based interaction analysis (used to calculate corrected p-values for MPs) 228s * Perform 100 permutations 228s * Test interaction with term from [interaction.txt] 228s * Random number generator is seeded with 1 228s * Considering variants within 1e+06 bp of the MPs 228s * Using minor allele frequency threshold = 0.0000 228s * Using minor allele sample threshold = 0 228s * Using INFO field AF threshold = 0.0000 228s * Chunk processed 1 / 100 228s 228s Scanning phenotype data in [phenotypes.bed.gz] 228s * 364 phenotypes 228s 228s Reading phenotype data in [phenotypes.bed.gz] 228s * region = 22:17517460-17646177 228s * 373 samples included 228s * 4 phenotypes included 228s 228s Reading genotype data in [genotypes.vcf.gz] in VCF format 228s * region = 22:16517460-18646177 228s * 373 samples included 228s * 8580 sites included 228s 228s Reading covariates in [covariates.txt.gz] 228s * 373 samples included 228s * 4 covariate(s) included 228s 228s Reading interaction term in [interaction.txt] 228s * 373 samples included 228s 228s Imputing missing genotypes 229s 229s Imputing missing phenotypes 229s 229s Initialize covariate 229s 229s Processing gene [ENSG00000237438.1] 229s * Number of variants in cis = 7966 243s * Beta distribution parameters = 1.0382 2287.7101 243s * Progress = 25.0% 243s 243s Processing gene [ENSG00000177663.8] 243s * Number of variants in cis = 8165 258s * Beta distribution parameters = 0.7994 2826.0721 258s * Progress = 50.0% 258s 258s Processing gene [ENSG00000183307.3] 258s * Number of variants in cis = 8279 274s * Beta distribution parameters = 0.9595 9906.5566 274s * Progress = 75.0% 274s 274s Processing gene [ENSG00000069998.8] 274s * Number of variants in cis = 8466 289s * Beta distribution parameters = 0.9606 4564.2130 289s * Progress = 100.0% 289s 289s Running time: 61 seconds 289s autopkgtest [00:52:08]: test run-sample-analysis: -----------------------] 290s run-sample-analysis PASS 290s autopkgtest [00:52:09]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 290s autopkgtest [00:52:09]: @@@@@@@@@@@@@@@@@@@@ summary 290s run-sample-analysis PASS 308s Creating nova instance adt-noble-s390x-fastqtl-20240419-004719-juju-7f2275-prod-proposed-migration-environment-3-64bff402-04e3-4077-b2f2-45201276fb8c from image adt/ubuntu-noble-s390x-server-20240418.img (UUID 85e53509-ea4e-4742-afdb-a30c7e328507)...