0s autopkgtest [18:02:47]: starting date and time: 2025-03-15 18:02:47+0000 0s autopkgtest [18:02:47]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:02:47]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3u34v6t4/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,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade tiddit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.210 lxd-armhf-10.145.243.210:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [18:03:08]: testbed dpkg architecture: armhf 23s autopkgtest [18:03:10]: testbed apt version: 2.9.33 27s autopkgtest [18:03:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [18:03:16]: testbed release detected to be: None 37s autopkgtest [18:03:24]: updating testbed package index (apt update) 39s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 40s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 40s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 40s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 40s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 41s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 62s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 63s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 63s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 64s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 64s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 64s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 79s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 81s Fetched 41.0 MB in 42s (986 kB/s) 82s Reading package lists... 88s autopkgtest [18:04:15]: upgrading testbed (apt dist-upgrade and autopurge) 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 93s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 93s Starting 2 pkgProblemResolver with broken count: 0 93s Done 94s Entering ResolveByKeep 94s 94s Calculating upgrade... 95s The following packages will be upgraded: 95s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 95s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 8683 kB of archives. 95s After this operation, 23.6 kB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 98s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 99s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 102s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 102s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 102s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 103s Preconfiguring packages ... 103s Fetched 8683 kB in 8s (1124 kB/s) 103s (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 ... 64655 files and directories currently installed.) 103s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 103s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 104s Setting up libc6:armhf (2.41-1ubuntu2) ... 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 ... 64655 files and directories currently installed.) 104s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 104s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 104s Setting up libc-bin (2.41-1ubuntu2) ... 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 ... 64655 files and directories currently installed.) 104s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 104s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 105s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 105s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 105s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 105s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 105s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 105s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 105s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 105s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 105s Setting up sos (4.9.0-5) ... 106s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 106s Setting up locales (2.41-1ubuntu2) ... 107s Generating locales (this might take a while)... 108s en_US.UTF-8... done 108s Generation complete. 108s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 109s Setting up strace (6.13+ds-1ubuntu1) ... 109s Processing triggers for man-db (2.13.0-1) ... 110s Processing triggers for systemd (257.3-1ubuntu3) ... 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 113s Solving dependencies... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s autopkgtest [18:04:43]: rebooting testbed after setup commands that affected boot 155s autopkgtest [18:05:22]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 181s autopkgtest [18:05:48]: @@@@@@@@@@@@@@@@@@@@ apt-source tiddit 192s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-2build1 (dsc) [2105 B] 192s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-2build1 (tar) [19.5 kB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tiddit 3.6.1+dfsg-2build1 (diff) [1732 kB] 192s gpgv: Signature made Tue Mar 4 16:30:52 2025 UTC 192s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 192s gpgv: Can't check signature: No public key 192s dpkg-source: warning: cannot verify inline signature for ./tiddit_3.6.1+dfsg-2build1.dsc: no acceptable signature found 193s autopkgtest [18:06:00]: testing package tiddit version 3.6.1+dfsg-2build1 195s autopkgtest [18:06:02]: build not needed 198s autopkgtest [18:06:05]: test run-unit-test: preparing testbed 200s Reading package lists... 200s Building dependency tree... 200s Reading state information... 200s Starting pkgProblemResolver with broken count: 0 200s Starting 2 pkgProblemResolver with broken count: 0 200s Done 201s The following NEW packages will be installed: 201s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 201s python3-joblib python3-numpy python3-numpy-dev python3-pysam samtools tiddit 201s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 201s Need to get 11.6 MB of archives. 201s After this operation, 63.2 MB of additional disk space will be used. 201s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy-dev armhf 1:2.2.3+ds-5 [141 kB] 202s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 202s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 202s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 204s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:2.2.3+ds-5 [3725 kB] 208s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 208s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 208s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB] 209s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.4.2-3 [205 kB] 209s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.23.0+ds-1build1 [3569 kB] 212s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.21-1 [619 kB] 213s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf tiddit armhf 3.6.1+dfsg-2build1 [317 kB] 213s Fetched 11.6 MB in 12s (987 kB/s) 213s Selecting previously unselected package python3-numpy-dev:armhf. 214s (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 ... 64655 files and directories currently installed.) 214s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_armhf.deb ... 214s Unpacking python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 214s Selecting previously unselected package libblas3:armhf. 214s Preparing to unpack .../01-libblas3_3.12.1-2_armhf.deb ... 214s Unpacking libblas3:armhf (3.12.1-2) ... 214s Selecting previously unselected package libgfortran5:armhf. 214s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 214s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 214s Selecting previously unselected package liblapack3:armhf. 214s Preparing to unpack .../03-liblapack3_3.12.1-2_armhf.deb ... 214s Unpacking liblapack3:armhf (3.12.1-2) ... 214s Selecting previously unselected package python3-numpy. 214s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_armhf.deb ... 214s Unpacking python3-numpy (1:2.2.3+ds-5) ... 214s Selecting previously unselected package libdeflate0:armhf. 214s Preparing to unpack .../05-libdeflate0_1.23-1_armhf.deb ... 214s Unpacking libdeflate0:armhf (1.23-1) ... 214s Selecting previously unselected package libhtscodecs2:armhf. 214s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_armhf.deb ... 214s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 214s Selecting previously unselected package libhts3t64:armhf. 214s Preparing to unpack .../07-libhts3t64_1.21+ds-1_armhf.deb ... 214s Unpacking libhts3t64:armhf (1.21+ds-1) ... 214s Selecting previously unselected package python3-joblib. 214s Preparing to unpack .../08-python3-joblib_1.4.2-3_all.deb ... 214s Unpacking python3-joblib (1.4.2-3) ... 214s Selecting previously unselected package python3-pysam. 214s Preparing to unpack .../09-python3-pysam_0.23.0+ds-1build1_armhf.deb ... 214s Unpacking python3-pysam (0.23.0+ds-1build1) ... 214s Selecting previously unselected package samtools. 214s Preparing to unpack .../10-samtools_1.21-1_armhf.deb ... 214s Unpacking samtools (1.21-1) ... 214s Selecting previously unselected package tiddit. 214s Preparing to unpack .../11-tiddit_3.6.1+dfsg-2build1_armhf.deb ... 214s Unpacking tiddit (3.6.1+dfsg-2build1) ... 214s Setting up libhtscodecs2:armhf (1.6.1-2) ... 214s Setting up python3-joblib (1.4.2-3) ... 215s Setting up libdeflate0:armhf (1.23-1) ... 215s Setting up libblas3:armhf (3.12.1-2) ... 215s 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 215s Setting up python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 215s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 215s Setting up libhts3t64:armhf (1.21+ds-1) ... 215s Setting up liblapack3:armhf (3.12.1-2) ... 215s 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 215s Setting up python3-pysam (0.23.0+ds-1build1) ... 215s Setting up samtools (1.21-1) ... 215s Setting up python3-numpy (1:2.2.3+ds-5) ... 217s Setting up tiddit (3.6.1+dfsg-2build1) ... 217s Processing triggers for man-db (2.13.0-1) ... 217s Processing triggers for libc-bin (2.41-1ubuntu2) ... 225s autopkgtest [18:06:32]: test run-unit-test: [----------------------- 227s + echo 'Test 1' 227s + tiddit --cov --bam normal.bam -o test1 227s Test 1 236s + tiddit --cov -w --bam normal.bam -o test1 242s + for f in test1.* 242s + '[' -s test1.bed ']' 242s + cat test1.bed 242s + tail -20 242s + for f in test1.* 242s + '[' -s test1.wig ']' 242s + cat test1.wig 242s + tail -20 242s hs37d5 35468001 35468501 0.0 242s hs37d5 35468501 35469001 0.0 242s hs37d5 35469001 35469501 0.0 242s hs37d5 35469501 35470001 0.0 242s hs37d5 35470001 35470501 0.0 242s hs37d5 35470501 35471001 0.0 242s hs37d5 35471001 35471501 0.0 242s hs37d5 35471501 35472001 0.0 242s hs37d5 35472001 35472501 0.0 242s hs37d5 35472501 35473001 0.0 242s hs37d5 35473001 35473501 0.0 242s hs37d5 35473501 35474001 0.0 242s hs37d5 35474001 35474501 0.0 242s hs37d5 35474501 35475001 0.0 242s hs37d5 35475001 35475501 0.0 242s hs37d5 35475501 35476001 0.0 242s hs37d5 35476001 35476501 0.0 242s hs37d5 35476501 35477001 0.0 242s hs37d5 35477001 35477501 0.0 242s hs37d5 35477501 35477943 0.0 242s + rm -f ./test1.bed ./test1.wig 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 242s 0.0 243s PASS 243s Test 2 243s + echo PASS 243s + echo 'Test 2' 243s + tiddit --cov --bam normal.bam -o test2 252s + tiddit --cov -w --bam tumor.bam -o test2 258s + for f in test2.* 258s + '[' -s test2.bed ']' 258s + cat test2.bed 258s + tail -20 258s + for f in test2.* 258s + '[' -s test2.wig ']' 258s + cat test2.wig 258s + tail -20 258s hs37d5 35468001 35468501 0.0 258s hs37d5 35468501 35469001 0.0 258s hs37d5 35469001 35469501 0.0 258s hs37d5 35469501 35470001 0.0 258s hs37d5 35470001 35470501 0.0 258s hs37d5 35470501 35471001 0.0 258s hs37d5 35471001 35471501 0.0 258s hs37d5 35471501 35472001 0.0 258s hs37d5 35472001 35472501 0.0 258s hs37d5 35472501 35473001 0.0 258s hs37d5 35473001 35473501 0.0 258s hs37d5 35473501 35474001 0.0 258s hs37d5 35474001 35474501 0.0 258s hs37d5 35474501 35475001 0.0 258s hs37d5 35475001 35475501 0.0 258s hs37d5 35475501 35476001 0.0 258s hs37d5 35476001 35476501 0.0 258s hs37d5 35476501 35477001 0.0 258s hs37d5 35477001 35477501 0.0 258s hs37d5 35477501 35477943 0.0 258s + rm -f ./test2.bed ./test2.wig 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s 0.0 258s PASS 258s + echo PASS 259s autopkgtest [18:07:06]: test run-unit-test: -----------------------] 262s autopkgtest [18:07:09]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 262s run-unit-test PASS 266s autopkgtest [18:07:13]: @@@@@@@@@@@@@@@@@@@@ summary 266s run-unit-test PASS