0s autopkgtest [02:52:16]: starting date and time: 2026-02-05 02:52:16+0000 0s autopkgtest [02:52:16]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [02:52:16]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.p1dgvplu/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade fastqtl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- lxd -r lxd-armhf-10.145.243.39 lxd-armhf-10.145.243.39:autopkgtest/ubuntu/resolute/armhf 23s autopkgtest [02:52:39]: testbed dpkg architecture: armhf 25s autopkgtest [02:52:41]: testbed apt version: 3.1.14 28s autopkgtest [02:52:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [02:52:46]: testbed release detected to be: None 38s autopkgtest [02:52:54]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 40s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 40s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 41s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 41s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 41s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 41s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 41s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 41s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [250 kB] 41s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1364 kB] 41s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [9664 B] 41s Fetched 3735 kB in 1s (2989 kB/s) 42s Reading package lists... 48s autopkgtest [02:53:04]: upgrading testbed (apt dist-upgrade and autopurge) 50s Reading package lists... 50s Building dependency tree... 50s Reading state information... 51s Calculating upgrade... 51s The following packages will be upgraded: 51s libc-bin libc-gconv-modules-extra libc6 locales 51s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s Need to get 7850 kB of archives. 51s After this operation, 0 B of additional disk space will be used. 51s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-gconv-modules-extra armhf 2.42-2ubuntu5 [1417 kB] 52s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc6 armhf 2.42-2ubuntu5 [1632 kB] 52s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-bin armhf 2.42-2ubuntu5 [545 kB] 52s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf locales all 2.42-2ubuntu5 [4255 kB] 53s Preconfiguring packages ... 53s Fetched 7850 kB in 1s (7601 kB/s) 53s (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 ... 68395 files and directories currently installed.) 53s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_armhf.deb ... 53s Unpacking libc-gconv-modules-extra:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 53s Setting up libc-gconv-modules-extra:armhf (2.42-2ubuntu5) ... 53s (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 ... 68395 files and directories currently installed.) 53s Preparing to unpack .../libc6_2.42-2ubuntu5_armhf.deb ... 53s readlink: /usr/lib/libeatmydata: No such file or directory 53s Unpacking libc6:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 53s Setting up libc6:armhf (2.42-2ubuntu5) ... 54s (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 ... 68395 files and directories currently installed.) 54s Preparing to unpack .../libc-bin_2.42-2ubuntu5_armhf.deb ... 54s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 54s Setting up libc-bin (2.42-2ubuntu5) ... 54s (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 ... 68395 files and directories currently installed.) 54s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 54s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 55s Setting up locales (2.42-2ubuntu5) ... 55s Generating locales (this might take a while)... 58s en_US.UTF-8... done 58s Generation complete. 58s Processing triggers for systemd (259-1ubuntu3) ... 58s Processing triggers for man-db (2.13.1-1) ... 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 62s Solving dependencies... 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s autopkgtest [02:53:20]: rebooting testbed after setup commands that affected boot 106s autopkgtest [02:54:02]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 132s autopkgtest [02:54:28]: @@@@@@@@@@@@@@@@@@@@ apt-source fastqtl 148s Get:1 http://ftpmaster.internal/ubuntu resolute/universe fastqtl 2.184+v7+dfsg-5 (dsc) [2406 B] 148s Get:2 http://ftpmaster.internal/ubuntu resolute/universe fastqtl 2.184+v7+dfsg-5 (tar) [17.1 MB] 148s Get:3 http://ftpmaster.internal/ubuntu resolute/universe fastqtl 2.184+v7+dfsg-5 (diff) [21.0 kB] 148s gpgv: Signature made Mon Nov 17 21:53:57 2025 UTC 148s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 148s gpgv: issuer "emollier@debian.org" 148s gpgv: Can't check signature: No public key 148s dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-5.dsc: no acceptable signature found 149s autopkgtest [02:54:45]: testing package fastqtl version 2.184+v7+dfsg-5 151s autopkgtest [02:54:47]: build not needed 154s autopkgtest [02:54:50]: test run-sample-analysis: preparing testbed 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Solving dependencies... 157s The following NEW packages will be installed: 157s fastqtl fastqtl-doc libblas3 libboost-iostreams1.88.0 157s libboost-program-options1.88.0 libdeflate0 libgsl28 libgslcblas0 libhts3t64 157s libhtscodecs2 r-mathlib 157s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 22.1 MB of archives. 157s After this operation, 29.6 MB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 158s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libboost-iostreams1.88.0 armhf 1.88.0-1.4ubuntu3 [260 kB] 158s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libboost-program-options1.88.0 armhf 1.88.0-1.4ubuntu3 [345 kB] 158s Get:4 http://ftpmaster.internal/ubuntu resolute/universe armhf libgslcblas0 armhf 2.8+dfsg-6 [85.2 kB] 158s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf libgsl28 armhf 2.8+dfsg-6 [889 kB] 158s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 158s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2build1 [67.0 kB] 158s Get:8 http://ftpmaster.internal/ubuntu resolute/universe armhf libhts3t64 armhf 1.22.1+ds2-1 [408 kB] 158s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf r-mathlib armhf 4.5.2-1ubuntu2 [2586 kB] 158s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf fastqtl armhf 2.184+v7+dfsg-5 [212 kB] 158s Get:11 http://ftpmaster.internal/ubuntu resolute/universe armhf fastqtl-doc all 2.184+v7+dfsg-5 [17.1 MB] 160s Fetched 22.1 MB in 2s (9254 kB/s) 160s Selecting previously unselected package libblas3:armhf. 160s (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 ... 68395 files and directories currently installed.) 160s Preparing to unpack .../00-libblas3_3.12.1-7ubuntu1_armhf.deb ... 160s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 160s Selecting previously unselected package libboost-iostreams1.88.0:armhf. 160s Preparing to unpack .../01-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_armhf.deb ... 160s Unpacking libboost-iostreams1.88.0:armhf (1.88.0-1.4ubuntu3) ... 160s Selecting previously unselected package libboost-program-options1.88.0:armhf. 160s Preparing to unpack .../02-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_armhf.deb ... 160s Unpacking libboost-program-options1.88.0:armhf (1.88.0-1.4ubuntu3) ... 160s Selecting previously unselected package libgslcblas0:armhf. 160s Preparing to unpack .../03-libgslcblas0_2.8+dfsg-6_armhf.deb ... 160s Unpacking libgslcblas0:armhf (2.8+dfsg-6) ... 160s Selecting previously unselected package libgsl28:armhf. 160s Preparing to unpack .../04-libgsl28_2.8+dfsg-6_armhf.deb ... 160s Unpacking libgsl28:armhf (2.8+dfsg-6) ... 160s Selecting previously unselected package libdeflate0:armhf. 160s Preparing to unpack .../05-libdeflate0_1.23-2_armhf.deb ... 160s Unpacking libdeflate0:armhf (1.23-2) ... 160s Selecting previously unselected package libhtscodecs2:armhf. 160s Preparing to unpack .../06-libhtscodecs2_1.6.1-2build1_armhf.deb ... 160s Unpacking libhtscodecs2:armhf (1.6.1-2build1) ... 160s Selecting previously unselected package libhts3t64:armhf. 160s Preparing to unpack .../07-libhts3t64_1.22.1+ds2-1_armhf.deb ... 160s Unpacking libhts3t64:armhf (1.22.1+ds2-1) ... 160s Selecting previously unselected package r-mathlib. 160s Preparing to unpack .../08-r-mathlib_4.5.2-1ubuntu2_armhf.deb ... 160s Unpacking r-mathlib (4.5.2-1ubuntu2) ... 160s Selecting previously unselected package fastqtl. 160s Preparing to unpack .../09-fastqtl_2.184+v7+dfsg-5_armhf.deb ... 160s Unpacking fastqtl (2.184+v7+dfsg-5) ... 160s Selecting previously unselected package fastqtl-doc. 160s Preparing to unpack .../10-fastqtl-doc_2.184+v7+dfsg-5_all.deb ... 160s Unpacking fastqtl-doc (2.184+v7+dfsg-5) ... 161s Setting up libhtscodecs2:armhf (1.6.1-2build1) ... 161s Setting up libboost-program-options1.88.0:armhf (1.88.0-1.4ubuntu3) ... 161s Setting up fastqtl-doc (2.184+v7+dfsg-5) ... 161s Setting up libgslcblas0:armhf (2.8+dfsg-6) ... 161s Setting up libdeflate0:armhf (1.23-2) ... 161s Setting up libboost-iostreams1.88.0:armhf (1.88.0-1.4ubuntu3) ... 161s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 161s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 161s Setting up r-mathlib (4.5.2-1ubuntu2) ... 161s Setting up libhts3t64:armhf (1.22.1+ds2-1) ... 161s Setting up libgsl28:armhf (2.8+dfsg-6) ... 161s Setting up fastqtl (2.184+v7+dfsg-5) ... 161s Processing triggers for man-db (2.13.1-1) ... 161s Processing triggers for libc-bin (2.42-2ubuntu5) ... 171s autopkgtest [02:55:07]: test run-sample-analysis: [----------------------- 173s covariates.txt.gz 173s genotypes.vcf.gz 173s genotypes.vcf.gz.tbi 173s interaction.txt 173s phenotypes.bed.gz 173s phenotypes.bed.gz.tbi 173s 173s Fast QTL 173s * Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS 173s * Contact : olivier.delaneau@gmail.com 173s * Webpage : http://fastqtl.sourceforge.net/ 173s * Version : v2.184_gtex 173s 173s Perform permutation based interaction analysis (used to calculate corrected p-values for MPs) 173s * Perform 100 permutations 173s * Test interaction with term from [interaction.txt] 173s * Random number generator is seeded with 1 173s * Considering variants within 1e+06 bp of the MPs 173s * Using minor allele frequency threshold = 0.0000 173s * Using minor allele sample threshold = 0 173s * Using INFO field AF threshold = 0.0000 173s * Chunk processed 1 / 100 173s 173s Scanning phenotype data in [phenotypes.bed.gz] 173s * 364 phenotypes 173s 173s Reading phenotype data in [phenotypes.bed.gz] 173s * region = 22:17517460-17646177 173s * 373 samples included 173s * 4 phenotypes included 173s 173s Reading genotype data in [genotypes.vcf.gz] in VCF format 173s * region = 22:16517460-18646177 174s * 373 samples included 174s * 8580 sites included 174s 174s Reading covariates in [covariates.txt.gz] 174s * 373 samples included 174s * 4 covariate(s) included 174s 174s Reading interaction term in [interaction.txt] 174s * 373 samples included 174s 174s Imputing missing genotypes 174s 174s Imputing missing phenotypes 174s 174s Initialize covariate 174s 174s Processing gene [ENSG00000237438.1] 174s * Number of variants in cis = 7966 196s * Beta distribution parameters = 1.0382 2287.7101 196s * Progress = 25.0% 196s 196s Processing gene [ENSG00000177663.8] 196s * Number of variants in cis = 8165 217s * Beta distribution parameters = 0.7994 2826.0721 217s * Progress = 50.0% 217s 217s Processing gene [ENSG00000183307.3] 217s * Number of variants in cis = 8279 240s * Beta distribution parameters = 0.9595 9906.5566 240s * Progress = 75.0% 240s 240s Processing gene [ENSG00000069998.8] 240s * Number of variants in cis = 8466 263s * Beta distribution parameters = 0.9606 4564.2130 263s * Progress = 100.0% 263s 263s Running time: 90 seconds 263s autopkgtest [02:56:39]: test run-sample-analysis: -----------------------] 267s autopkgtest [02:56:43]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 267s run-sample-analysis PASS 271s autopkgtest [02:56:47]: @@@@@@@@@@@@@@@@@@@@ summary 271s run-sample-analysis PASS