0s autopkgtest [23:26:47]: starting date and time: 2024-11-14 23:26:47+0000 0s autopkgtest [23:26:47]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [23:26:47]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eru3qrkm/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-23.secgroup --name adt-plucky-amd64-tiddit-20241114-232647-juju-7f2275-prod-proposed-migration-environment-20-59b659d1-2e71-491c-8156-bb2557a93242 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 45s autopkgtest [23:27:32]: testbed dpkg architecture: amd64 45s autopkgtest [23:27:32]: testbed apt version: 2.9.8 45s autopkgtest [23:27:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 46s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 46s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.1 kB] 46s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 46s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1015 kB] 46s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 46s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [141 kB] 46s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [74.2 kB] 46s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 46s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [289 kB] 46s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [793 kB] 46s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 46s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9128 B] 46s Fetched 2550 kB in 1s (3145 kB/s) 46s Reading package lists... 49s Reading package lists... 49s Building dependency tree... 49s Reading state information... 49s Calculating upgrade... 49s The following NEW packages will be installed: 49s python3.13-gdbm 49s The following packages will be upgraded: 49s libcap-ng0 libpython3-stdlib lxd-installer man-db pastebinit python3 49s python3-gdbm python3-minimal python3-systemd 49s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 49s Need to get 1534 kB of archives. 49s After this operation, 327 kB of additional disk space will be used. 49s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 49s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 49s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 49s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 49s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 50s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 50s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 50s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 50s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 50s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 50s Preconfiguring packages ... 50s Fetched 1534 kB in 1s (2573 kB/s) 50s (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 ... 75542 files and directories currently installed.) 50s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 50s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 50s Setting up python3-minimal (3.12.7-1) ... 50s (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 ... 75542 files and directories currently installed.) 50s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 50s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 50s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 50s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 50s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 50s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 50s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 50s (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 ... 75542 files and directories currently installed.) 50s Preparing to unpack .../0-man-db_2.13.0-1_amd64.deb ... 51s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 51s Selecting previously unselected package python3.13-gdbm. 51s Preparing to unpack .../1-python3.13-gdbm_3.13.0-2_amd64.deb ... 51s Unpacking python3.13-gdbm (3.13.0-2) ... 51s Preparing to unpack .../2-python3-gdbm_3.12.7-1_amd64.deb ... 51s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 51s Preparing to unpack .../3-lxd-installer_9_all.deb ... 51s Unpacking lxd-installer (9) over (8) ... 51s Preparing to unpack .../4-pastebinit_1.7.1-1_all.deb ... 51s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 51s Preparing to unpack .../5-python3-systemd_235-1build5_amd64.deb ... 51s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 51s Setting up man-db (2.13.0-1) ... 51s Updating database of manual pages ... 53s man-db.service is a disabled or a static unit not running, not starting it. 53s Setting up lxd-installer (9) ... 53s Setting up python3.13-gdbm (3.13.0-2) ... 53s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 53s Setting up python3 (3.12.7-1) ... 53s Setting up python3-systemd (235-1build5) ... 53s Setting up python3-gdbm:amd64 (3.12.7-1) ... 53s Setting up pastebinit (1.7.1-1) ... 53s Processing triggers for libc-bin (2.40-1ubuntu3) ... 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 54s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 55s Reading package lists... 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 56s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s autopkgtest [23:27:43]: rebooting testbed after setup commands that affected boot 78s autopkgtest [23:28:05]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 81s autopkgtest [23:28:08]: @@@@@@@@@@@@@@@@@@@@ apt-source tiddit 84s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (dsc) [2105 B] 84s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (tar) [19.5 kB] 84s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (diff) [1732 kB] 84s gpgv: Signature made Wed Apr 10 17:41:17 2024 UTC 84s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 84s gpgv: Can't check signature: No public key 84s dpkg-source: warning: cannot verify inline signature for ./tiddit_3.6.1+dfsg-1build1.dsc: no acceptable signature found 84s autopkgtest [23:28:11]: testing package tiddit version 3.6.1+dfsg-1build1 85s autopkgtest [23:28:12]: build not needed 85s autopkgtest [23:28:12]: test run-unit-test: preparing testbed 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Starting pkgProblemResolver with broken count: 0 87s Starting 2 pkgProblemResolver with broken count: 0 87s Done 88s The following additional packages will be installed: 88s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 88s python3-joblib python3-numpy python3-pysam samtools tiddit 88s Suggested packages: 88s python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 88s cwltool 88s Recommended packages: 88s python3-pytest python3-simplejson python3-psutil 88s The following NEW packages will be installed: 88s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 88s libhtscodecs2 liblapack3 python3-joblib python3-numpy python3-pysam samtools 88s tiddit 88s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 13.6 MB/13.6 MB of archives. 88s After this operation, 75.9 MB of additional disk space will be used. 88s Get:1 /tmp/autopkgtest.1FkURP/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [708 B] 88s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 89s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 89s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 90s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 90s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 91s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 91s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 91s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 tiddit amd64 3.6.1+dfsg-1build1 [316 kB] 92s Fetched 13.6 MB in 3s (3959 kB/s) 92s Selecting previously unselected package libblas3:amd64. 92s (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 ... 75555 files and directories currently installed.) 92s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 92s Unpacking libblas3:amd64 (3.12.0-3build2) ... 92s Selecting previously unselected package libdeflate0:amd64. 92s Preparing to unpack .../01-libdeflate0_1.22-1_amd64.deb ... 92s Unpacking libdeflate0:amd64 (1.22-1) ... 92s Selecting previously unselected package libgfortran5:amd64. 92s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 92s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 92s Selecting previously unselected package libhtscodecs2:amd64. 92s Preparing to unpack .../03-libhtscodecs2_1.6.1-1_amd64.deb ... 92s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 92s Selecting previously unselected package libhts3t64:amd64. 92s Preparing to unpack .../04-libhts3t64_1.20+ds-1_amd64.deb ... 92s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 92s Selecting previously unselected package liblapack3:amd64. 92s Preparing to unpack .../05-liblapack3_3.12.0-3build2_amd64.deb ... 92s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 92s Selecting previously unselected package python3-joblib. 92s Preparing to unpack .../06-python3-joblib_1.3.2-5_all.deb ... 92s Unpacking python3-joblib (1.3.2-5) ... 92s Selecting previously unselected package python3-numpy. 92s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 92s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 92s Selecting previously unselected package python3-pysam. 92s Preparing to unpack .../08-python3-pysam_0.22.1+ds-2_amd64.deb ... 92s Unpacking python3-pysam (0.22.1+ds-2) ... 92s Selecting previously unselected package samtools. 92s Preparing to unpack .../09-samtools_1.20-3_amd64.deb ... 92s Unpacking samtools (1.20-3) ... 92s Selecting previously unselected package tiddit. 92s Preparing to unpack .../10-tiddit_3.6.1+dfsg-1build1_amd64.deb ... 92s Unpacking tiddit (3.6.1+dfsg-1build1) ... 93s Selecting previously unselected package autopkgtest-satdep. 93s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 93s Unpacking autopkgtest-satdep (0) ... 93s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 93s Setting up python3-joblib (1.3.2-5) ... 93s Setting up libdeflate0:amd64 (1.22-1) ... 93s Setting up libblas3:amd64 (3.12.0-3build2) ... 93s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 93s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 93s Setting up libhts3t64:amd64 (1.20+ds-1) ... 93s Setting up liblapack3:amd64 (3.12.0-3build2) ... 93s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 93s Setting up python3-pysam (0.22.1+ds-2) ... 93s Setting up samtools (1.20-3) ... 93s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 95s Setting up tiddit (3.6.1+dfsg-1build1) ... 95s Setting up autopkgtest-satdep (0) ... 95s Processing triggers for man-db (2.13.0-1) ... 95s Processing triggers for libc-bin (2.40-1ubuntu3) ... 98s (Reading database ... 77107 files and directories currently installed.) 98s Removing autopkgtest-satdep (0) ... 99s autopkgtest [23:28:26]: test run-unit-test: [----------------------- 99s Test 1 99s + echo 'Test 1' 99s + tiddit --cov --bam normal.bam -o test1 106s + tiddit --cov -w --bam normal.bam -o test1 111s + for f in test1.* 111s + '[' -s test1.bed ']' 111s + cat test1.bed 111s + tail -20 111s hs37d5 35468001 35468501 0.0 111s hs37d5 35468501 35469001 0.0 111s hs37d5 35469001 35469501 0.0 111s hs37d5 35469501 35470001 0.0 111s hs37d5 35470001 35470501 0.0 111s hs37d5 35470501 35471001 0.0 111s hs37d5 35471001 35471501 0.0 111s hs37d5 35471501 35472001 0.0 111s hs37d5 35472001 35472501 0.0 111s hs37d5 35472501 35473001 0.0 111s hs37d5 35473001 35473501 0.0 111s hs37d5 35473501 35474001 0.0 111s hs37d5 35474001 35474501 0.0 111s hs37d5 35474501 35475001 0.0 111s hs37d5 35475001 35475501 0.0 111s hs37d5 35475501 35476001 0.0 111s hs37d5 35476001 35476501 0.0 111s hs37d5 35476501 35477001 0.0 111s hs37d5 35477001 35477501 0.0 111s hs37d5 35477501 35477943 0.0 111s + for f in test1.* 111s + '[' -s test1.wig ']' 111s + cat test1.wig 111s + tail -20 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s 0.0 111s + rm -f ./test1.bed ./test1.wig 111s + echo PASS 111s + echo 'Test 2' 111s + tiddit --cov --bam normal.bam -o test2 111s PASS 111s Test 2 119s + tiddit --cov -w --bam tumor.bam -o test2 123s + for f in test2.* 123s + '[' -s test2.bed ']' 123s + cat test2.bed 123s + tail -20 123s hs37d5 35468001 35468501 0.0 123s hs37d5 35468501 35469001 0.0 123s hs37d5 35469001 35469501 0.0 123s hs37d5 35469501 35470001 0.0 123s hs37d5 35470001 35470501 0.0 123s hs37d5 35470501 35471001 0.0 123s hs37d5 35471001 35471501 0.0 123s hs37d5 35471501 35472001 0.0 123s hs37d5 35472001 35472501 0.0 123s hs37d5 35472501 35473001 0.0 123s hs37d5 35473001 35473501 0.0 123s hs37d5 35473501 35474001 0.0 123s hs37d5 35474001 35474501 0.0 123s hs37d5 35474501 35475001 0.0 123s hs37d5 35475001 35475501 0.0 123s hs37d5 35475501 35476001 0.0 123s hs37d5 35476001 35476501 0.0 123s hs37d5 35476501 35477001 0.0 123s hs37d5 35477001 35477501 0.0 123s hs37d5 35477501 35477943 0.0 123s + for f in test2.* 123s + '[' -s test2.wig ']' 123s + cat test2.wig 123s + tail -20 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s 0.0 123s + rm -f ./test2.bed ./test2.wig 123s + echo PASS 123s PASS 124s autopkgtest [23:28:51]: test run-unit-test: -----------------------] 124s run-unit-test PASS 124s autopkgtest [23:28:51]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 124s autopkgtest [23:28:51]: @@@@@@@@@@@@@@@@@@@@ summary 124s run-unit-test PASS 136s nova [W] Skipping flock for amd64 136s Creating nova instance adt-plucky-amd64-tiddit-20241114-232647-juju-7f2275-prod-proposed-migration-environment-20-59b659d1-2e71-491c-8156-bb2557a93242 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...