0s autopkgtest [16:47:36]: starting date and time: 2024-11-14 16:47:36+0000 0s autopkgtest [16:47:36]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:47:36]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u81h1f0n/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade tiddit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-42.secgroup --name adt-plucky-arm64-tiddit-20241114-164736-juju-7f2275-prod-proposed-migration-environment-20-3b98dc24-4eb0-46a1-afcf-527b8ecb3e52 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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,keyserver.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/ 70s autopkgtest [16:48:46]: testbed dpkg architecture: arm64 71s autopkgtest [16:48:47]: testbed apt version: 2.9.8 71s autopkgtest [16:48:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 72s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 72s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 72s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 72s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [951 kB] 72s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 72s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [136 kB] 72s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 72s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [711 kB] 72s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [5488 B] 73s Fetched 2054 kB in 1s (2138 kB/s) 73s Reading package lists... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 77s Calculating upgrade... 78s The following packages will be upgraded: 78s libcap-ng0 pastebinit python3-systemd 78s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 76.6 kB of archives. 78s After this operation, 349 kB of additional disk space will be used. 78s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libcap-ng0 arm64 0.8.5-3build1 [15.0 kB] 78s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 78s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 79s Fetched 76.6 kB in 0s (217 kB/s) 79s (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 ... 79925 files and directories currently installed.) 79s Preparing to unpack .../libcap-ng0_0.8.5-3build1_arm64.deb ... 79s Unpacking libcap-ng0:arm64 (0.8.5-3build1) over (0.8.5-1) ... 80s Setting up libcap-ng0:arm64 (0.8.5-3build1) ... 80s (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 ... 79925 files and directories currently installed.) 80s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 80s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 80s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 80s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 80s Setting up pastebinit (1.7.1-1) ... 80s Setting up python3-systemd (235-1build5) ... 80s Processing triggers for man-db (2.12.1-3) ... 81s Processing triggers for libc-bin (2.40-1ubuntu3) ... 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 84s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 84s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 84s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 85s Reading package lists... 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s Calculating upgrade... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s autopkgtest [16:49:10]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 95s autopkgtest [16:49:11]: @@@@@@@@@@@@@@@@@@@@ apt-source tiddit 97s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (dsc) [2105 B] 97s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (tar) [19.5 kB] 97s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (diff) [1732 kB] 97s gpgv: Signature made Wed Apr 10 17:41:17 2024 UTC 97s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 97s gpgv: Can't check signature: No public key 97s dpkg-source: warning: cannot verify inline signature for ./tiddit_3.6.1+dfsg-1build1.dsc: no acceptable signature found 97s autopkgtest [16:49:13]: testing package tiddit version 3.6.1+dfsg-1build1 98s autopkgtest [16:49:14]: build not needed 99s autopkgtest [16:49:15]: test run-unit-test: preparing testbed 100s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Starting pkgProblemResolver with broken count: 0 102s Starting 2 pkgProblemResolver with broken count: 0 102s Done 103s The following additional packages will be installed: 103s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 103s python3-joblib python3-numpy python3-pysam samtools tiddit 103s Suggested packages: 103s python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 103s cwltool 103s Recommended packages: 103s python3-pytest python3-simplejson python3-psutil 103s The following NEW packages will be installed: 103s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 103s libhtscodecs2 liblapack3 python3-joblib python3-numpy python3-pysam samtools 103s tiddit 103s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 12.1 MB/12.1 MB of archives. 103s After this operation, 75.7 MB of additional disk space will be used. 103s Get:1 /tmp/autopkgtest.b9SMNp/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 103s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 103s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 103s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 103s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 103s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 104s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 104s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 104s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 104s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.20-3 [590 kB] 104s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 tiddit arm64 3.6.1+dfsg-1build1 [284 kB] 104s Fetched 12.1 MB in 1s (12.3 MB/s) 104s Selecting previously unselected package libblas3:arm64. 104s (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 ... 79930 files and directories currently installed.) 104s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 104s Unpacking libblas3:arm64 (3.12.0-3build2) ... 104s Selecting previously unselected package libdeflate0:arm64. 104s Preparing to unpack .../01-libdeflate0_1.22-1_arm64.deb ... 104s Unpacking libdeflate0:arm64 (1.22-1) ... 104s Selecting previously unselected package libgfortran5:arm64. 105s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 105s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 105s Selecting previously unselected package libhtscodecs2:arm64. 105s Preparing to unpack .../03-libhtscodecs2_1.6.1-1_arm64.deb ... 105s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 105s Selecting previously unselected package libhts3t64:arm64. 105s Preparing to unpack .../04-libhts3t64_1.20+ds-1_arm64.deb ... 105s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 105s Selecting previously unselected package liblapack3:arm64. 105s Preparing to unpack .../05-liblapack3_3.12.0-3build2_arm64.deb ... 105s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 105s Selecting previously unselected package python3-joblib. 105s Preparing to unpack .../06-python3-joblib_1.3.2-5_all.deb ... 105s Unpacking python3-joblib (1.3.2-5) ... 105s Selecting previously unselected package python3-numpy. 105s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 105s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 105s Selecting previously unselected package python3-pysam. 105s Preparing to unpack .../08-python3-pysam_0.22.1+ds-2_arm64.deb ... 105s Unpacking python3-pysam (0.22.1+ds-2) ... 105s Selecting previously unselected package samtools. 105s Preparing to unpack .../09-samtools_1.20-3_arm64.deb ... 105s Unpacking samtools (1.20-3) ... 105s Selecting previously unselected package tiddit. 105s Preparing to unpack .../10-tiddit_3.6.1+dfsg-1build1_arm64.deb ... 105s Unpacking tiddit (3.6.1+dfsg-1build1) ... 106s Selecting previously unselected package autopkgtest-satdep. 106s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 106s Unpacking autopkgtest-satdep (0) ... 106s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 106s Setting up python3-joblib (1.3.2-5) ... 106s Setting up libdeflate0:arm64 (1.22-1) ... 106s Setting up libblas3:arm64 (3.12.0-3build2) ... 106s 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 106s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 106s Setting up libhts3t64:arm64 (1.20+ds-1) ... 106s Setting up liblapack3:arm64 (3.12.0-3build2) ... 106s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 106s Setting up python3-pysam (0.22.1+ds-2) ... 106s Setting up samtools (1.20-3) ... 106s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 109s Setting up tiddit (3.6.1+dfsg-1build1) ... 109s Setting up autopkgtest-satdep (0) ... 109s Processing triggers for man-db (2.12.1-3) ... 110s Processing triggers for libc-bin (2.40-1ubuntu3) ... 116s (Reading database ... 81502 files and directories currently installed.) 116s Removing autopkgtest-satdep (0) ... 116s autopkgtest [16:49:32]: test run-unit-test: [----------------------- 117s + echo 'Test 1' 117s + tiddit --cov --bam normal.bam -o test1 117s Test 1 128s + tiddit --cov -w --bam normal.bam -o test1 135s + for f in test1.* 135s + '[' -s test1.bed ']' 135s + cat test1.bed 135s + tail -20 135s hs37d5 35468001 35468501 0.0 135s hs37d5 35468501 35469001 0.0 135s hs37d5 35469001 35469501 0.0 135s hs37d5 35469501 35470001 0.0 135s hs37d5 35470001 35470501 0.0 135s hs37d5 35470501 35471001 0.0 135s hs37d5 35471001 35471501 0.0 135s hs37d5 35471501 35472001 0.0 135s hs37d5 35472001 35472501 0.0 135s hs37d5 35472501 35473001 0.0 135s hs37d5 35473001 35473501 0.0 135s hs37d5 35473501 35474001 0.0 135s hs37d5 35474001 35474501 0.0 135s hs37d5 35474501 35475001 0.0 135s hs37d5 35475001 35475501 0.0 135s hs37d5 35475501 35476001 0.0 135s hs37d5 35476001 35476501 0.0 135s hs37d5 35476501 35477001 0.0 135s hs37d5 35477001 35477501 0.0 135s hs37d5 35477501 35477943 0.0 135s + for f in test1.* 135s + '[' -s test1.wig ']' 135s + cat test1.wig 135s + tail -20 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s 0.0 135s + rm -f ./test1.bed ./test1.wig 135s PASS 135s Test 2 135s + echo PASS 135s + echo 'Test 2' 135s + tiddit --cov --bam normal.bam -o test2 146s + tiddit --cov -w --bam tumor.bam -o test2 154s + for f in test2.* 154s + '[' -s test2.bed ']' 154s + cat test2.bed 154s + tail -20 154s hs37d5 35468001 35468501 0.0 154s hs37d5 35468501 35469001 0.0 154s hs37d5 35469001 35469501 0.0 154s hs37d5 35469501 35470001 0.0 154s hs37d5 35470001 35470501 0.0 154s hs37d5 35470501 35471001 0.0 154s hs37d5 35471001 35471501 0.0 154s hs37d5 35471501 35472001 0.0 154s hs37d5 35472001 35472501 0.0 154s hs37d5 35472501 35473001 0.0 154s hs37d5 35473001 35473501 0.0 154s hs37d5 35473501 35474001 0.0 154s hs37d5 35474001 35474501 0.0 154s hs37d5 35474501 35475001 0.0 154s hs37d5 35475001 35475501 0.0 154s hs37d5 35475501 35476001 0.0 154s hs37d5 35476001 35476501 0.0 154s hs37d5 35476501 35477001 0.0 154s hs37d5 35477001 35477501 0.0 154s hs37d5 35477501 35477943 0.0 154s + for f in test2.* 154s + '[' -s test2.wig ']' 154s + cat test2.wig 154s + tail -20 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s 0.0 154s + rm -f ./test2.bed ./test2.wig 154s PASS 154s + echo PASS 154s autopkgtest [16:50:10]: test run-unit-test: -----------------------] 155s autopkgtest [16:50:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 155s run-unit-test PASS 155s autopkgtest [16:50:11]: @@@@@@@@@@@@@@@@@@@@ summary 155s run-unit-test PASS 168s nova [W] Skipping flock in bos03-arm64 168s Creating nova instance adt-plucky-arm64-tiddit-20241114-164736-juju-7f2275-prod-proposed-migration-environment-20-3b98dc24-4eb0-46a1-afcf-527b8ecb3e52 from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...