0s autopkgtest [11:17:29]: starting date and time: 2024-11-13 11:17:29+0000 0s autopkgtest [11:17:29]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [11:17:29]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mkiyrcrn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade tiddit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-43.secgroup --name adt-plucky-arm64-tiddit-20241113-111729-juju-7f2275-prod-proposed-migration-environment-2-f245290e-7ffa-42e6-b2ad-243ba63dc5e1 --image adt/ubuntu-plucky-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,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/ 85s autopkgtest [11:18:54]: testbed dpkg architecture: arm64 85s autopkgtest [11:18:54]: testbed apt version: 2.9.8 85s autopkgtest [11:18:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 86s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 87s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 87s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 87s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 87s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 87s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 87s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 87s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 87s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 87s Fetched 1794 kB in 1s (2278 kB/s) 87s Reading package lists... 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 91s Calculating upgrade... 92s The following NEW packages will be installed: 92s python3.13-gdbm 92s The following packages will be upgraded: 92s libpython3-stdlib python3 python3-gdbm python3-minimal 92s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 92s Need to get 101 kB of archives. 92s After this operation, 141 kB of additional disk space will be used. 92s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 92s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 92s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 92s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 93s Fetched 101 kB in 0s (287 kB/s) 93s (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 ... 79924 files and directories currently installed.) 93s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 93s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 93s Setting up python3-minimal (3.12.7-1) ... 93s (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 ... 79924 files and directories currently installed.) 93s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 93s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 94s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 94s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 94s Selecting previously unselected package python3.13-gdbm. 94s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 94s Unpacking python3.13-gdbm (3.13.0-2) ... 94s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 94s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 94s Setting up python3.13-gdbm (3.13.0-2) ... 94s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 94s Setting up python3 (3.12.7-1) ... 94s Setting up python3-gdbm:arm64 (3.12.7-1) ... 94s Processing triggers for man-db (2.12.1-3) ... 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 97s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 97s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 97s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 98s Reading package lists... 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 99s Calculating upgrade... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s autopkgtest [11:19:14]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 105s autopkgtest [11:19:14]: @@@@@@@@@@@@@@@@@@@@ apt-source tiddit 107s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (dsc) [2105 B] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (tar) [19.5 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (diff) [1732 kB] 108s gpgv: Signature made Wed Apr 10 17:41:17 2024 UTC 108s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 108s gpgv: Can't check signature: No public key 108s dpkg-source: warning: cannot verify inline signature for ./tiddit_3.6.1+dfsg-1build1.dsc: no acceptable signature found 108s autopkgtest [11:19:17]: testing package tiddit version 3.6.1+dfsg-1build1 109s autopkgtest [11:19:18]: build not needed 110s autopkgtest [11:19:19]: test run-unit-test: preparing testbed 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 114s The following additional packages will be installed: 114s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 114s python3-joblib python3-numpy python3-pysam samtools tiddit 114s Suggested packages: 114s python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 114s cwltool 114s Recommended packages: 114s python3-pytest python3-simplejson python3-psutil 114s The following NEW packages will be installed: 114s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 114s libhtscodecs2 liblapack3 python3-joblib python3-numpy python3-pysam samtools 114s tiddit 114s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 11.6 MB/11.6 MB of archives. 114s After this operation, 67.8 MB of additional disk space will be used. 114s Get:1 /tmp/autopkgtest.hnLtz8/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 114s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 114s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 114s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 114s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 114s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 115s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 115s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 115s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 115s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.20-3 [590 kB] 115s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 tiddit arm64 3.6.1+dfsg-1build1 [284 kB] 115s Fetched 11.6 MB in 1s (11.5 MB/s) 115s Selecting previously unselected package libblas3:arm64. 115s (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 ... 79931 files and directories currently installed.) 115s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 115s Unpacking libblas3:arm64 (3.12.0-3build2) ... 115s Selecting previously unselected package libdeflate0:arm64. 115s Preparing to unpack .../01-libdeflate0_1.22-1_arm64.deb ... 115s Unpacking libdeflate0:arm64 (1.22-1) ... 115s Selecting previously unselected package libgfortran5:arm64. 115s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 115s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 115s Selecting previously unselected package libhtscodecs2:arm64. 115s Preparing to unpack .../03-libhtscodecs2_1.6.1-1_arm64.deb ... 115s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 115s Selecting previously unselected package libhts3t64:arm64. 115s Preparing to unpack .../04-libhts3t64_1.20+ds-1_arm64.deb ... 115s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 115s Selecting previously unselected package liblapack3:arm64. 115s Preparing to unpack .../05-liblapack3_3.12.0-3build2_arm64.deb ... 115s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 116s Selecting previously unselected package python3-joblib. 116s Preparing to unpack .../06-python3-joblib_1.3.2-5_all.deb ... 116s Unpacking python3-joblib (1.3.2-5) ... 116s Selecting previously unselected package python3-numpy. 116s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 116s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 116s Selecting previously unselected package python3-pysam. 116s Preparing to unpack .../08-python3-pysam_0.22.1+ds-2_arm64.deb ... 116s Unpacking python3-pysam (0.22.1+ds-2) ... 116s Selecting previously unselected package samtools. 116s Preparing to unpack .../09-samtools_1.20-3_arm64.deb ... 116s Unpacking samtools (1.20-3) ... 116s Selecting previously unselected package tiddit. 116s Preparing to unpack .../10-tiddit_3.6.1+dfsg-1build1_arm64.deb ... 116s Unpacking tiddit (3.6.1+dfsg-1build1) ... 116s Selecting previously unselected package autopkgtest-satdep. 116s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 116s Unpacking autopkgtest-satdep (0) ... 116s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 116s Setting up python3-joblib (1.3.2-5) ... 116s Setting up libdeflate0:arm64 (1.22-1) ... 116s Setting up libblas3:arm64 (3.12.0-3build2) ... 116s 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 116s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 117s Setting up libhts3t64:arm64 (1.20+ds-1) ... 117s Setting up liblapack3:arm64 (3.12.0-3build2) ... 117s 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 117s Setting up python3-pysam (0.22.1+ds-2) ... 117s Setting up samtools (1.20-3) ... 117s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 119s Setting up tiddit (3.6.1+dfsg-1build1) ... 119s Setting up autopkgtest-satdep (0) ... 119s Processing triggers for man-db (2.12.1-3) ... 119s Processing triggers for libc-bin (2.40-1ubuntu3) ... 123s (Reading database ... 81483 files and directories currently installed.) 123s Removing autopkgtest-satdep (0) ... 124s autopkgtest [11:19:33]: test run-unit-test: [----------------------- 124s Test 1 124s + echo 'Test 1' 124s + tiddit --cov --bam normal.bam -o test1 135s + tiddit --cov -w --bam normal.bam -o test1 142s + for f in test1.* 142s + '[' -s test1.bed ']' 142s + cat test1.bed 142s + tail -20 142s hs37d5 35468001 35468501 0.0 142s hs37d5 35468501 35469001 0.0 142s hs37d5 35469001 35469501 0.0 142s hs37d5 35469501 35470001 0.0 142s hs37d5 35470001 35470501 0.0 142s hs37d5 35470501 35471001 0.0 142s hs37d5 35471001 35471501 0.0 142s hs37d5 35471501 35472001 0.0 142s hs37d5 35472001 35472501 0.0 142s hs37d5 35472501 35473001 0.0 142s hs37d5 35473001 35473501 0.0 142s hs37d5 35473501 35474001 0.0 142s hs37d5 35474001 35474501 0.0 142s hs37d5 35474501 35475001 0.0 142s hs37d5 35475001 35475501 0.0 142s hs37d5 35475501 35476001 0.0 142s hs37d5 35476001 35476501 0.0 142s hs37d5 35476501 35477001 0.0 142s hs37d5 35477001 35477501 0.0 142s hs37d5 35477501 35477943 0.0 142s + for f in test1.* 142s + '[' -s test1.wig ']' 142s + cat test1.wig 142s + tail -20 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s 0.0 142s + rm -f ./test1.bed ./test1.wig 142s PASS 142s Test 2 142s + echo PASS 142s + echo 'Test 2' 142s + tiddit --cov --bam normal.bam -o test2 152s + tiddit --cov -w --bam tumor.bam -o test2 160s + for f in test2.* 160s + '[' -s test2.bed ']' 160s + cat test2.bed 160s + tail -20 160s hs37d5 35468001 35468501 0.0 160s hs37d5 35468501 35469001 0.0 160s hs37d5 35469001 35469501 0.0 160s hs37d5 35469501 35470001 0.0 160s hs37d5 35470001 35470501 0.0 160s hs37d5 35470501 35471001 0.0 160s hs37d5 35471001 35471501 0.0 160s hs37d5 35471501 35472001 0.0 160s hs37d5 35472001 35472501 0.0 160s hs37d5 35472501 35473001 0.0 160s hs37d5 35473001 35473501 0.0 160s hs37d5 35473501 35474001 0.0 160s hs37d5 35474001 35474501 0.0 160s hs37d5 35474501 35475001 0.0 160s hs37d5 35475001 35475501 0.0 160s hs37d5 35475501 35476001 0.0 160s hs37d5 35476001 35476501 0.0 160s hs37d5 35476501 35477001 0.0 160s hs37d5 35477001 35477501 0.0 160s hs37d5 35477501 35477943 0.0 160s + for f in test2.* 160s + '[' -s test2.wig ']' 160s + cat test2.wig 160s + tail -20 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s 0.0 160s + rm -f ./test2.bed ./test2.wig 160s PASS 160s + echo PASS 160s autopkgtest [11:20:09]: test run-unit-test: -----------------------] 161s autopkgtest [11:20:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 161s run-unit-test PASS 161s autopkgtest [11:20:10]: @@@@@@@@@@@@@@@@@@@@ summary 161s run-unit-test PASS 176s virt: nova [W] Skipping flock in bos03-arm64 176s virt: Creating nova instance adt-plucky-arm64-tiddit-20241113-111729-juju-7f2275-prod-proposed-migration-environment-2-f245290e-7ffa-42e6-b2ad-243ba63dc5e1 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...