0s autopkgtest [17:11:01]: starting date and time: 2024-03-16 17:11:01+0000 0s autopkgtest [17:11:01]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:11:01]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.91xxhxh4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade fastqtl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build2 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-arm64-19.secgroup --name adt-noble-arm64-fastqtl-20240316-171101-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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://ftpmaster.internal/ubuntu/ 138s autopkgtest [17:13:19]: testbed dpkg architecture: arm64 138s autopkgtest [17:13:19]: testbed apt version: 2.7.12 138s autopkgtest [17:13:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 139s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 141s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 141s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 142s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 142s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 142s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 142s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 142s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 142s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 143s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 143s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 143s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 153s Fetched 9063 kB in 6s (1607 kB/s) 154s Reading package lists... 160s Reading package lists... 161s Building dependency tree... 161s Reading state information... 163s Calculating upgrade... 164s The following packages will be REMOVED: 164s libssl3 164s The following NEW packages will be installed: 164s libssl3t64 164s The following packages have been kept back: 164s curl 164s The following packages will be upgraded: 164s openssl 165s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 165s Need to get 2753 kB of archives. 165s After this operation, 72.7 kB of additional disk space will be used. 165s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 165s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 167s Fetched 2753 kB in 1s (3574 kB/s) 167s (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 ... 75850 files and directories currently installed.) 167s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 167s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 168s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 168s wget depends on libssl3 (>= 3.0.0). 168s u-boot-tools depends on libssl3 (>= 3.0.0). 168s tnftp depends on libssl3 (>= 3.0.0). 168s tcpdump depends on libssl3 (>= 3.0.0). 168s systemd-resolved depends on libssl3 (>= 3.0.0). 168s systemd depends on libssl3 (>= 3.0.0). 168s sudo depends on libssl3 (>= 3.0.0). 168s sbsigntool depends on libssl3 (>= 3.0.0). 168s rsync depends on libssl3 (>= 3.0.0). 168s python3-cryptography depends on libssl3 (>= 3.0.0). 168s openssh-server depends on libssl3 (>= 3.0.10). 168s openssh-client depends on libssl3 (>= 3.0.10). 168s mtd-utils depends on libssl3 (>= 3.0.0). 168s mokutil depends on libssl3 (>= 3.0.0). 168s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 168s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 168s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 168s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 168s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 168s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 168s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 168s libnvme1 depends on libssl3 (>= 3.0.0). 168s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 168s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 168s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 168s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 168s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 168s kmod depends on libssl3 (>= 3.0.0). 168s dhcpcd-base depends on libssl3 (>= 3.0.0). 168s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 168s 168s (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 ... 75850 files and directories currently installed.) 168s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 168s Selecting previously unselected package libssl3t64:arm64. 168s (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 ... 75839 files and directories currently installed.) 168s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 168s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 168s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 168s Setting up openssl (3.0.13-0ubuntu1) ... 168s Processing triggers for man-db (2.12.0-3) ... 170s Processing triggers for libc-bin (2.39-0ubuntu2) ... 171s Reading package lists... 172s Building dependency tree... 172s Reading state information... 174s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 175s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 175s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 175s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 175s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 181s Reading package lists... 182s Reading package lists... 182s Building dependency tree... 182s Reading state information... 184s Calculating upgrade... 185s The following packages have been kept back: 185s curl 185s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 188s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 192s autopkgtest [17:14:13]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 192s autopkgtest [17:14:13]: @@@@@@@@@@@@@@@@@@@@ apt-source fastqtl 197s Get:1 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build1 (dsc) [2280 B] 197s Get:2 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build1 (tar) [17.1 MB] 197s Get:3 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build1 (diff) [21.0 kB] 197s gpgv: Signature made Tue Dec 19 15:01:14 2023 UTC 197s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 197s gpgv: Can't check signature: No public key 197s dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-4build1.dsc: no acceptable signature found 198s autopkgtest [17:14:19]: testing package fastqtl version 2.184+v7+dfsg-4build1 199s autopkgtest [17:14:20]: build not needed 203s autopkgtest [17:14:24]: test run-sample-analysis: preparing testbed 205s Reading package lists... 206s Building dependency tree... 206s Reading state information... 207s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 209s The following additional packages will be installed: 209s fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0 209s libboost-program-options1.83.0 libdeflate0 libgsl27 libgslcblas0 libhts3 209s libhtscodecs2 r-mathlib 209s Suggested packages: 209s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 209s Recommended packages: 209s r-cran-qvalue r-cran-tools r-cran-argparser r-base-core r-base-dev 209s The following NEW packages will be installed: 209s autopkgtest-satdep fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0 209s libboost-program-options1.83.0 libdeflate0 libgsl27 libgslcblas0 libhts3 209s libhtscodecs2 r-mathlib 209s 0 upgraded, 12 newly installed, 0 to remove and 1 not upgraded. 209s Need to get 22.1 MB/22.1 MB of archives. 209s After this operation, 31.0 MB of additional disk space will be used. 209s Get:1 /tmp/autopkgtest.uX09C7/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 209s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 209s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-2ubuntu1 [339 kB] 210s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2ubuntu1 [410 kB] 210s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 210s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 210s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 210s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 210s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhts3 arm64 1.19+ds-1 [429 kB] 210s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 r-mathlib arm64 4.3.2-1build1 [2387 kB] 210s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 fastqtl arm64 2.184+v7+dfsg-4build1 [204 kB] 210s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 fastqtl-doc all 2.184+v7+dfsg-4build1 [17.0 MB] 212s Fetched 22.1 MB in 2s (14.0 MB/s) 212s Selecting previously unselected package libblas3:arm64. 212s (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 ... 75852 files and directories currently installed.) 212s Preparing to unpack .../00-libblas3_3.12.0-3_arm64.deb ... 212s Unpacking libblas3:arm64 (3.12.0-3) ... 212s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 212s Preparing to unpack .../01-libboost-iostreams1.83.0_1.83.0-2ubuntu1_arm64.deb ... 212s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-2ubuntu1) ... 212s Selecting previously unselected package libboost-program-options1.83.0:arm64. 212s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_arm64.deb ... 212s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 212s Selecting previously unselected package libgslcblas0:arm64. 212s Preparing to unpack .../03-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 212s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 212s Selecting previously unselected package libgsl27:arm64. 212s Preparing to unpack .../04-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 212s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 213s Selecting previously unselected package libdeflate0:arm64. 213s Preparing to unpack .../05-libdeflate0_1.19-1_arm64.deb ... 213s Unpacking libdeflate0:arm64 (1.19-1) ... 213s Selecting previously unselected package libhtscodecs2:arm64. 213s Preparing to unpack .../06-libhtscodecs2_1.6.0-1_arm64.deb ... 213s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 213s Selecting previously unselected package libhts3:arm64. 213s Preparing to unpack .../07-libhts3_1.19+ds-1_arm64.deb ... 213s Unpacking libhts3:arm64 (1.19+ds-1) ... 213s Selecting previously unselected package r-mathlib. 213s Preparing to unpack .../08-r-mathlib_4.3.2-1build1_arm64.deb ... 213s Unpacking r-mathlib (4.3.2-1build1) ... 213s Selecting previously unselected package fastqtl. 213s Preparing to unpack .../09-fastqtl_2.184+v7+dfsg-4build1_arm64.deb ... 213s Unpacking fastqtl (2.184+v7+dfsg-4build1) ... 213s Selecting previously unselected package fastqtl-doc. 213s Preparing to unpack .../10-fastqtl-doc_2.184+v7+dfsg-4build1_all.deb ... 213s Unpacking fastqtl-doc (2.184+v7+dfsg-4build1) ... 214s Selecting previously unselected package autopkgtest-satdep. 214s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 214s Unpacking autopkgtest-satdep (0) ... 214s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 214s Setting up libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ... 214s Setting up fastqtl-doc (2.184+v7+dfsg-4build1) ... 214s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 214s Setting up libdeflate0:arm64 (1.19-1) ... 214s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 214s Setting up libblas3:arm64 (3.12.0-3) ... 214s 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 214s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-2ubuntu1) ... 214s Setting up r-mathlib (4.3.2-1build1) ... 214s Setting up libhts3:arm64 (1.19+ds-1) ... 214s Setting up fastqtl (2.184+v7+dfsg-4build1) ... 214s Setting up autopkgtest-satdep (0) ... 214s Processing triggers for man-db (2.12.0-3) ... 215s Processing triggers for libc-bin (2.39-0ubuntu2) ... 223s (Reading database ... 75984 files and directories currently installed.) 223s Removing autopkgtest-satdep (0) ... 224s autopkgtest [17:14:45]: test run-sample-analysis: [----------------------- 224s covariates.txt.gz 224s genotypes.vcf.gz 224s genotypes.vcf.gz.tbi 224s interaction.txt 224s phenotypes.bed.gz 224s phenotypes.bed.gz.tbi 224s 224s Fast QTL 224s * Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS 224s * Contact : olivier.delaneau@gmail.com 224s * Webpage : http://fastqtl.sourceforge.net/ 224s * Version : v2.184_gtex 224s 224s Perform permutation based interaction analysis (used to calculate corrected p-values for MPs) 224s * Perform 100 permutations 224s * Test interaction with term from [interaction.txt] 224s * Random number generator is seeded with 1 224s * Considering variants within 1e+06 bp of the MPs 224s * Using minor allele frequency threshold = 0.0000 224s * Using minor allele sample threshold = 0 224s * Using INFO field AF threshold = 0.0000 224s * Chunk processed 1 / 100 224s 224s Scanning phenotype data in [phenotypes.bed.gz] 224s * 364 phenotypes 224s 224s Reading phenotype data in [phenotypes.bed.gz] 224s * region = 22:17517460-17646177 224s * 373 samples included 224s * 4 phenotypes included 224s 224s Reading genotype data in [genotypes.vcf.gz] in VCF format 224s * region = 22:16517460-18646177 226s * 373 samples included 226s * 8580 sites included 226s 226s Reading covariates in [covariates.txt.gz] 226s * 373 samples included 226s * 4 covariate(s) included 226s 226s Reading interaction term in [interaction.txt] 226s * 373 samples included 226s 226s Imputing missing genotypes 226s 226s Imputing missing phenotypes 226s 226s Initialize covariate 226s 226s Processing gene [ENSG00000237438.1] 226s * Number of variants in cis = 7966 272s * Beta distribution parameters = 1.0382 2287.7101 272s * Progress = 25.0% 272s 272s Processing gene [ENSG00000177663.8] 272s * Number of variants in cis = 8165 319s * Beta distribution parameters = 0.7994 2826.0721 319s * Progress = 50.0% 319s 319s Processing gene [ENSG00000183307.3] 319s * Number of variants in cis = 8279 366s * Beta distribution parameters = 0.9595 9906.5566 366s * Progress = 75.0% 366s 366s Processing gene [ENSG00000069998.8] 366s * Number of variants in cis = 8466 415s * Beta distribution parameters = 0.9606 4564.2130 415s * Progress = 100.0% 415s 415s Running time: 191 seconds 415s autopkgtest [17:17:56]: test run-sample-analysis: -----------------------] 416s run-sample-analysis PASS 416s autopkgtest [17:17:57]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 416s autopkgtest [17:17:57]: @@@@@@@@@@@@@@@@@@@@ summary 416s run-sample-analysis PASS 428s Creating nova instance adt-noble-arm64-fastqtl-20240316-171101-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...