0s autopkgtest [19:35:26]: starting date and time: 2024-11-14 19:35:26+0000 0s autopkgtest [19:35:26]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [19:35:26]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._gre3uld/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,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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.232 lxd-armhf-10.145.243.232:autopkgtest/ubuntu/plucky/armhf 52s autopkgtest [19:36:18]: testbed dpkg architecture: armhf 54s autopkgtest [19:36:20]: testbed apt version: 2.9.8 54s autopkgtest [19:36:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 62s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 62s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [937 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [110 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [674 kB] 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4136 B] 63s Fetched 1926 kB in 1s (2035 kB/s) 63s Reading package lists... 80s tee: /proc/self/fd/2: Permission denied 102s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 102s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 102s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 102s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 103s Reading package lists... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s Calculating upgrade... 105s The following packages will be upgraded: 105s libcap-ng0 pastebinit python3-systemd 105s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Need to get 72.8 kB of archives. 105s After this operation, 89.1 kB of additional disk space will be used. 105s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libcap-ng0 armhf 0.8.5-3build1 [13.8 kB] 105s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf pastebinit all 1.7.1-1 [14.9 kB] 105s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-systemd armhf 235-1build5 [44.0 kB] 105s Fetched 72.8 kB in 0s (213 kB/s) 105s (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 ... 59560 files and directories currently installed.) 105s Preparing to unpack .../libcap-ng0_0.8.5-3build1_armhf.deb ... 105s Unpacking libcap-ng0:armhf (0.8.5-3build1) over (0.8.5-1) ... 106s Setting up libcap-ng0:armhf (0.8.5-3build1) ... 106s (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 ... 59560 files and directories currently installed.) 106s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 106s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 106s Preparing to unpack .../python3-systemd_235-1build5_armhf.deb ... 106s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 106s Setting up pastebinit (1.7.1-1) ... 106s Setting up python3-systemd (235-1build5) ... 106s Processing triggers for man-db (2.12.1-3) ... 106s Processing triggers for libc-bin (2.40-1ubuntu3) ... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s autopkgtest [19:37:16]: rebooting testbed after setup commands that affected boot 176s autopkgtest [19:38:22]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 203s autopkgtest [19:38:49]: @@@@@@@@@@@@@@@@@@@@ apt-source tiddit 213s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (dsc) [2105 B] 213s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (tar) [19.5 kB] 213s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-1build1 (diff) [1732 kB] 213s gpgv: Signature made Wed Apr 10 17:41:17 2024 UTC 213s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 213s gpgv: Can't check signature: No public key 213s dpkg-source: warning: cannot verify inline signature for ./tiddit_3.6.1+dfsg-1build1.dsc: no acceptable signature found 213s autopkgtest [19:38:59]: testing package tiddit version 3.6.1+dfsg-1build1 216s autopkgtest [19:39:02]: build not needed 219s autopkgtest [19:39:05]: test run-unit-test: preparing testbed 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 229s Starting pkgProblemResolver with broken count: 0 229s Starting 2 pkgProblemResolver with broken count: 0 229s Done 231s The following additional packages will be installed: 231s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 231s python3-joblib python3-numpy python3-pysam samtools tiddit 231s Suggested packages: 231s python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 231s cwltool 231s Recommended packages: 231s python3-pytest python3-simplejson python3-psutil 231s The following NEW packages will be installed: 231s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 231s libhtscodecs2 liblapack3 python3-joblib python3-numpy python3-pysam samtools 231s tiddit 231s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 231s Need to get 11.5 MB/11.5 MB of archives. 231s After this operation, 64.0 MB of additional disk space will be used. 231s Get:1 /tmp/autopkgtest.q4moyS/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [712 B] 231s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 231s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 231s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 231s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-1 [67.9 kB] 231s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 231s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 231s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.3.2-5 [206 kB] 231s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 231s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.22.1+ds-2 [3383 kB] 231s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.20-3 [607 kB] 231s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf tiddit armhf 3.6.1+dfsg-1build1 [293 kB] 232s Fetched 11.5 MB in 1s (10.7 MB/s) 232s Selecting previously unselected package libblas3:armhf. 232s (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 ... 59565 files and directories currently installed.) 232s Preparing to unpack .../00-libblas3_3.12.0-3build2_armhf.deb ... 232s Unpacking libblas3:armhf (3.12.0-3build2) ... 232s Selecting previously unselected package libdeflate0:armhf. 232s Preparing to unpack .../01-libdeflate0_1.22-1_armhf.deb ... 232s Unpacking libdeflate0:armhf (1.22-1) ... 232s Selecting previously unselected package libgfortran5:armhf. 232s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 232s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 232s Selecting previously unselected package libhtscodecs2:armhf. 232s Preparing to unpack .../03-libhtscodecs2_1.6.1-1_armhf.deb ... 232s Unpacking libhtscodecs2:armhf (1.6.1-1) ... 232s Selecting previously unselected package libhts3t64:armhf. 232s Preparing to unpack .../04-libhts3t64_1.20+ds-1_armhf.deb ... 232s Unpacking libhts3t64:armhf (1.20+ds-1) ... 232s Selecting previously unselected package liblapack3:armhf. 232s Preparing to unpack .../05-liblapack3_3.12.0-3build2_armhf.deb ... 232s Unpacking liblapack3:armhf (3.12.0-3build2) ... 232s Selecting previously unselected package python3-joblib. 232s Preparing to unpack .../06-python3-joblib_1.3.2-5_all.deb ... 232s Unpacking python3-joblib (1.3.2-5) ... 232s Selecting previously unselected package python3-numpy. 232s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 232s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 233s Selecting previously unselected package python3-pysam. 233s Preparing to unpack .../08-python3-pysam_0.22.1+ds-2_armhf.deb ... 233s Unpacking python3-pysam (0.22.1+ds-2) ... 233s Selecting previously unselected package samtools. 233s Preparing to unpack .../09-samtools_1.20-3_armhf.deb ... 233s Unpacking samtools (1.20-3) ... 233s Selecting previously unselected package tiddit. 233s Preparing to unpack .../10-tiddit_3.6.1+dfsg-1build1_armhf.deb ... 233s Unpacking tiddit (3.6.1+dfsg-1build1) ... 233s Selecting previously unselected package autopkgtest-satdep. 233s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 233s Unpacking autopkgtest-satdep (0) ... 233s Setting up libhtscodecs2:armhf (1.6.1-1) ... 233s Setting up python3-joblib (1.3.2-5) ... 234s Setting up libdeflate0:armhf (1.22-1) ... 234s Setting up libblas3:armhf (3.12.0-3build2) ... 234s 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 234s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 234s Setting up libhts3t64:armhf (1.20+ds-1) ... 234s Setting up liblapack3:armhf (3.12.0-3build2) ... 234s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 234s Setting up python3-pysam (0.22.1+ds-2) ... 234s Setting up samtools (1.20-3) ... 234s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 236s Setting up tiddit (3.6.1+dfsg-1build1) ... 236s Setting up autopkgtest-satdep (0) ... 236s Processing triggers for man-db (2.12.1-3) ... 237s Processing triggers for libc-bin (2.40-1ubuntu3) ... 248s (Reading database ... 61138 files and directories currently installed.) 248s Removing autopkgtest-satdep (0) ... 254s autopkgtest [19:39:40]: test run-unit-test: [----------------------- 256s Test 1 256s + echo 'Test 1' 256s + tiddit --cov --bam normal.bam -o test1 266s + tiddit --cov -w --bam normal.bam -o test1 273s + for f in test1.* 273s + '[' -s test1.bed ']' 273s + cat test1.bed 273s + tail -20 273s + for f in test1.* 273s + '[' -s test1.wig ']' 273s hs37d5 35468001 35468501 0.0 273s hs37d5 35468501 35469001 0.0 273s hs37d5 35469001 35469501 0.0 273s hs37d5 35469501 35470001 0.0 273s hs37d5 35470001 35470501 0.0 273s hs37d5 35470501 35471001 0.0 273s hs37d5 35471001 35471501 0.0 273s hs37d5 35471501 35472001 0.0 273s hs37d5 35472001 35472501 0.0 273s hs37d5 35472501 35473001 0.0 273s hs37d5 35473001 35473501 0.0 273s hs37d5 35473501 35474001 0.0 273s hs37d5 35474001 35474501 0.0 273s hs37d5 35474501 35475001 0.0 273s hs37d5 35475001 35475501 0.0 273s hs37d5 35475501 35476001 0.0 273s hs37d5 35476001 35476501 0.0 273s hs37d5 35476501 35477001 0.0 273s hs37d5 35477001 35477501 0.0 273s hs37d5 35477501 35477943 0.0 273s + cat test1.wig 273s + tail -20 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s 0.0 273s + rm -f ./test1.bed ./test1.wig 273s PASS 273s Test 2 273s + echo PASS 273s + echo 'Test 2' 273s + tiddit --cov --bam normal.bam -o test2 284s + tiddit --cov -w --bam tumor.bam -o test2 291s + for f in test2.* 291s + '[' -s test2.bed ']' 291s + cat test2.bed 291s + tail -20 291s hs37d5 35468001 35468501 0.0 291s hs37d5 35468501 35469001 0.0 291s hs37d5 35469001 35469501 0.0 291s hs37d5 35469501 35470001 0.0 291s hs37d5 35470001 35470501 0.0 291s hs37d5 35470501 35471001 0.0 291s hs37d5 35471001 35471501 0.0 291s hs37d5 35471501 35472001 0.0 291s hs37d5 35472001 35472501 0.0 291s hs37d5 35472501 35473001 0.0 291s hs37d5 35473001 35473501 0.0 291s hs37d5 35473501 35474001 0.0 291s hs37d5 35474001 35474501 0.0 291s hs37d5 35474501 35475001 0.0 291s hs37d5 35475001 35475501 0.0 291s hs37d5 35475501 35476001 0.0 291s hs37d5 35476001 35476501 0.0 291s hs37d5 35476501 35477001 0.0 291s hs37d5 35477001 35477501 0.0 291s hs37d5 35477501 35477943 0.0 291s + for f in test2.* 291s + '[' -s test2.wig ']' 291s + cat test2.wig 291s + tail -20 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s 0.0 291s + rm -f ./test2.bed ./test2.wig 291s PASS 291s + echo PASS 291s autopkgtest [19:40:17]: test run-unit-test: -----------------------] 295s run-unit-test PASS 295s autopkgtest [19:40:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 299s autopkgtest [19:40:25]: @@@@@@@@@@@@@@@@@@@@ summary 299s run-unit-test PASS