0s autopkgtest [23:46:55]: starting date and time: 2024-04-18 23:46:55+0000 0s autopkgtest [23:46:55]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [23:46:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._wsl5vtb/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-2@bos01-ppc64el-10.secgroup --name adt-noble-ppc64el-fastqtl-20240418-234655-juju-7f2275-prod-proposed-migration-environment-2-b4573988-debf-4896-896f-13e1fd78e046 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 550s autopkgtest [23:56:05]: testbed dpkg architecture: ppc64el 550s autopkgtest [23:56:05]: testbed apt version: 2.7.14build2 550s autopkgtest [23:56:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 551s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 551s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [2340 B] 551s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [12.2 kB] 551s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [381 kB] 552s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [57.5 kB] 552s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [112 kB] 553s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 553s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [976 B] 553s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 553s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [587 kB] 554s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 554s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [1004 B] 554s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 556s Fetched 1282 kB in 4s (360 kB/s) 556s Reading package lists... 557s sh: 4: dhclient: not found 558s Reading package lists... 558s Building dependency tree... 558s Reading state information... 559s Calculating upgrade... 559s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 559s Reading package lists... 559s Building dependency tree... 559s Reading state information... 559s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 560s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 560s Get:2 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 560s Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] 561s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 561s Get:5 http://ftpmaster.internal/ubuntu noble/main Sources [1383 kB] 562s Get:6 http://ftpmaster.internal/ubuntu noble/universe Sources [20.0 MB] 568s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el Packages [1337 kB] 569s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el Packages [15.1 MB] 575s Fetched 38.1 MB in 16s (2414 kB/s) 576s Reading package lists... 576s Reading package lists... 576s Building dependency tree... 576s Reading state information... 576s Calculating upgrade... 577s The following packages will be upgraded: 577s libnuma1 make netcat-openbsd numactl 577s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 577s Need to get 332 kB of archives. 577s After this operation, 16.4 kB disk space will be freed. 577s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el netcat-openbsd ppc64el 1.226-1ubuntu2 [46.2 kB] 577s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libnuma1 ppc64el 2.0.18-1build1 [28.2 kB] 577s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el make ppc64el 4.3-4.1build2 [214 kB] 577s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el numactl ppc64el 2.0.18-1build1 [43.9 kB] 577s Fetched 332 kB in 1s (631 kB/s) 578s (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 ... 71981 files and directories currently installed.) 578s Preparing to unpack .../netcat-openbsd_1.226-1ubuntu2_ppc64el.deb ... 578s Unpacking netcat-openbsd (1.226-1ubuntu2) over (1.226-1ubuntu1) ... 578s Preparing to unpack .../libnuma1_2.0.18-1build1_ppc64el.deb ... 578s Unpacking libnuma1:ppc64el (2.0.18-1build1) over (2.0.18-1) ... 578s Preparing to unpack .../make_4.3-4.1build2_ppc64el.deb ... 578s Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... 578s Preparing to unpack .../numactl_2.0.18-1build1_ppc64el.deb ... 578s Unpacking numactl (2.0.18-1build1) over (2.0.18-1) ... 578s Setting up netcat-openbsd (1.226-1ubuntu2) ... 578s Setting up make (4.3-4.1build2) ... 578s Setting up libnuma1:ppc64el (2.0.18-1build1) ... 578s Setting up numactl (2.0.18-1build1) ... 578s Processing triggers for man-db (2.12.0-4build1) ... 579s Processing triggers for libc-bin (2.39-0ubuntu8) ... 579s Reading package lists... 579s Building dependency tree... 579s Reading state information... 579s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 582s autopkgtest [23:56:37]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP Thu Apr 4 22:47:57 UTC 2024 582s autopkgtest [23:56:37]: @@@@@@@@@@@@@@@@@@@@ apt-source fastqtl 587s Get:1 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build3 (dsc) [2359 B] 587s Get:2 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build3 (tar) [17.1 MB] 587s Get:3 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build3 (diff) [21.2 kB] 587s gpgv: Signature made Mon Apr 1 05:47:14 2024 UTC 587s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 587s gpgv: Can't check signature: No public key 587s dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-4build3.dsc: no acceptable signature found 587s autopkgtest [23:56:42]: testing package fastqtl version 2.184+v7+dfsg-4build3 588s autopkgtest [23:56:43]: build not needed 606s autopkgtest [23:57:01]: test run-sample-analysis: preparing testbed 607s Reading package lists... 607s Building dependency tree... 607s Reading state information... 608s Starting pkgProblemResolver with broken count: 0 608s Starting 2 pkgProblemResolver with broken count: 0 608s Done 608s The following additional packages will be installed: 608s fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0 608s libboost-program-options1.83.0 libgsl27 libgslcblas0 libhts3t64 608s libhtscodecs2 r-mathlib 608s Suggested packages: 608s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 608s Recommended packages: 608s r-cran-qvalue r-cran-tools r-cran-argparser r-base-core r-base-dev 608s The following NEW packages will be installed: 608s autopkgtest-satdep fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0 608s libboost-program-options1.83.0 libgsl27 libgslcblas0 libhts3t64 608s libhtscodecs2 r-mathlib 608s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 608s Need to get 22.4 MB/22.4 MB of archives. 608s After this operation, 33.1 MB of additional disk space will be used. 608s Get:1 /tmp/autopkgtest.6qqetG/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 608s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 608s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2.1ubuntu3 [260 kB] 609s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2.1ubuntu3 [329 kB] 609s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu2 [86.6 kB] 609s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu2 [1090 kB] 609s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 609s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3t64 ppc64el 1.19+ds-1.1build3 [569 kB] 609s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-mathlib ppc64el 4.3.3-2build2 [2440 kB] 609s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el fastqtl ppc64el 2.184+v7+dfsg-4build3 [243 kB] 610s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el fastqtl-doc all 2.184+v7+dfsg-4build3 [17.0 MB] 612s Fetched 22.4 MB in 3s (6531 kB/s) 612s Selecting previously unselected package libblas3:ppc64el. 612s (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 ... 71981 files and directories currently installed.) 612s Preparing to unpack .../00-libblas3_3.12.0-3build1_ppc64el.deb ... 612s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 612s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 612s Preparing to unpack .../01-libboost-iostreams1.83.0_1.83.0-2.1ubuntu3_ppc64el.deb ... 612s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 612s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 612s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2.1ubuntu3_ppc64el.deb ... 612s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 612s Selecting previously unselected package libgslcblas0:ppc64el. 612s Preparing to unpack .../03-libgslcblas0_2.7.1+dfsg-6ubuntu2_ppc64el.deb ... 612s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu2) ... 612s Selecting previously unselected package libgsl27:ppc64el. 612s Preparing to unpack .../04-libgsl27_2.7.1+dfsg-6ubuntu2_ppc64el.deb ... 612s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu2) ... 612s Selecting previously unselected package libhtscodecs2:ppc64el. 612s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_ppc64el.deb ... 612s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 612s Selecting previously unselected package libhts3t64:ppc64el. 612s Preparing to unpack .../06-libhts3t64_1.19+ds-1.1build3_ppc64el.deb ... 612s Unpacking libhts3t64:ppc64el (1.19+ds-1.1build3) ... 612s Selecting previously unselected package r-mathlib. 612s Preparing to unpack .../07-r-mathlib_4.3.3-2build2_ppc64el.deb ... 612s Unpacking r-mathlib (4.3.3-2build2) ... 612s Selecting previously unselected package fastqtl. 612s Preparing to unpack .../08-fastqtl_2.184+v7+dfsg-4build3_ppc64el.deb ... 612s Unpacking fastqtl (2.184+v7+dfsg-4build3) ... 612s Selecting previously unselected package fastqtl-doc. 612s Preparing to unpack .../09-fastqtl-doc_2.184+v7+dfsg-4build3_all.deb ... 612s Unpacking fastqtl-doc (2.184+v7+dfsg-4build3) ... 612s Selecting previously unselected package autopkgtest-satdep. 612s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 612s Unpacking autopkgtest-satdep (0) ... 612s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 612s Setting up libboost-program-options1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 612s Setting up fastqtl-doc (2.184+v7+dfsg-4build3) ... 612s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu2) ... 612s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu2) ... 612s Setting up libblas3:ppc64el (3.12.0-3build1) ... 612s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 612s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2.1ubuntu3) ... 612s Setting up r-mathlib (4.3.3-2build2) ... 612s Setting up libhts3t64:ppc64el (1.19+ds-1.1build3) ... 612s Setting up fastqtl (2.184+v7+dfsg-4build3) ... 612s Setting up autopkgtest-satdep (0) ... 612s Processing triggers for man-db (2.12.0-4build1) ... 613s Processing triggers for libc-bin (2.39-0ubuntu8) ... 615s (Reading database ... 72110 files and directories currently installed.) 615s Removing autopkgtest-satdep (0) ... 616s autopkgtest [23:57:11]: test run-sample-analysis: [----------------------- 616s covariates.txt.gz 616s genotypes.vcf.gz 616s genotypes.vcf.gz.tbi 616s interaction.txt 616s phenotypes.bed.gz 616s phenotypes.bed.gz.tbi 616s 616s Fast QTL 616s * Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS 616s * Contact : olivier.delaneau@gmail.com 616s * Webpage : http://fastqtl.sourceforge.net/ 616s * Version : v2.184_gtex 616s 616s Perform permutation based interaction analysis (used to calculate corrected p-values for MPs) 616s * Perform 100 permutations 616s * Test interaction with term from [interaction.txt] 616s * Random number generator is seeded with 1 616s * Considering variants within 1e+06 bp of the MPs 616s * Using minor allele frequency threshold = 0.0000 616s * Using minor allele sample threshold = 0 616s * Using INFO field AF threshold = 0.0000 616s * Chunk processed 1 / 100 616s 616s Scanning phenotype data in [phenotypes.bed.gz] 616s * 364 phenotypes 616s 616s Reading phenotype data in [phenotypes.bed.gz] 616s * region = 22:17517460-17646177 616s * 373 samples included 616s * 4 phenotypes included 616s 616s Reading genotype data in [genotypes.vcf.gz] in VCF format 616s * region = 22:16517460-18646177 616s * 373 samples included 616s * 8580 sites included 616s 616s Reading covariates in [covariates.txt.gz] 616s * 373 samples included 616s * 4 covariate(s) included 616s 616s Reading interaction term in [interaction.txt] 616s * 373 samples included 616s 616s Imputing missing genotypes 616s 616s Imputing missing phenotypes 616s 616s Initialize covariate 616s 616s Processing gene [ENSG00000237438.1] 617s * Number of variants in cis = 7966 641s * Beta distribution parameters = 1.0382 2287.7101 641s * Progress = 25.0% 641s 641s Processing gene [ENSG00000177663.8] 641s * Number of variants in cis = 8165 666s * Beta distribution parameters = 0.7994 2826.0721 666s * Progress = 50.0% 666s 666s Processing gene [ENSG00000183307.3] 666s * Number of variants in cis = 8279 692s * Beta distribution parameters = 0.9595 9906.5566 692s * Progress = 75.0% 692s 692s Processing gene [ENSG00000069998.8] 692s * Number of variants in cis = 8466 719s * Beta distribution parameters = 0.9606 4564.2130 719s * Progress = 100.0% 719s 719s Running time: 103 seconds 719s autopkgtest [23:58:54]: test run-sample-analysis: -----------------------] 720s run-sample-analysis PASS 720s autopkgtest [23:58:55]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 720s autopkgtest [23:58:55]: @@@@@@@@@@@@@@@@@@@@ summary 720s run-sample-analysis PASS 736s Creating nova instance adt-noble-ppc64el-fastqtl-20240418-234655-juju-7f2275-prod-proposed-migration-environment-2-b4573988-debf-4896-896f-13e1fd78e046 from image adt/ubuntu-noble-ppc64el-server-20240418.img (UUID af0116ce-26c5-4050-9dd9-30d9ab0ee27b)...