0s autopkgtest [17:04:20]: starting date and time: 2025-03-15 17:04:20+0000 0s autopkgtest [17:04:20]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:04:20]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sjh66d8h/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 wham-align --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.242 lxd-armhf-10.145.243.242:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [17:04:41]: testbed dpkg architecture: armhf 23s autopkgtest [17:04:43]: testbed apt version: 2.9.33 27s autopkgtest [17:04:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [17:04:48]: testbed release detected to be: None 36s autopkgtest [17:04:56]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 39s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 40s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 40s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 63s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 63s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 65s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 66s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 66s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 66s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 82s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 84s Fetched 41.0 MB in 46s (886 kB/s) 85s Reading package lists... 91s autopkgtest [17:05:51]: upgrading testbed (apt dist-upgrade and autopurge) 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 94s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 94s Starting 2 pkgProblemResolver with broken count: 0 94s Done 95s Entering ResolveByKeep 95s 97s Calculating upgrade... 97s The following packages will be upgraded: 97s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 97s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 8683 kB of archives. 97s After this operation, 23.6 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 100s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 106s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 106s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 106s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 106s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 107s Preconfiguring packages ... 107s Fetched 8683 kB in 10s (846 kB/s) 107s (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.) 107s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 108s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 108s Setting up libc6:armhf (2.41-1ubuntu2) ... 108s (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.) 108s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 108s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 108s Setting up libc-bin (2.41-1ubuntu2) ... 109s (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.) 109s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 109s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 109s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 109s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 109s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 109s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 109s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 109s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 110s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 110s Setting up sos (4.9.0-5) ... 110s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 110s Setting up locales (2.41-1ubuntu2) ... 112s Generating locales (this might take a while)... 115s en_US.UTF-8... done 115s Generation complete. 115s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 116s Setting up strace (6.13+ds-1ubuntu1) ... 116s Processing triggers for man-db (2.13.0-1) ... 117s Processing triggers for systemd (257.3-1ubuntu3) ... 119s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 122s Solving dependencies... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s autopkgtest [17:06:25]: rebooting testbed after setup commands that affected boot 165s autopkgtest [17:07:05]: 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 202s autopkgtest [17:07:42]: @@@@@@@@@@@@@@@@@@@@ apt-source wham-align 214s Get:1 http://ftpmaster.internal/ubuntu plucky/universe wham-align 0.1.5-8 (dsc) [1987 B] 214s Get:2 http://ftpmaster.internal/ubuntu plucky/universe wham-align 0.1.5-8 (tar) [120 kB] 214s Get:3 http://ftpmaster.internal/ubuntu plucky/universe wham-align 0.1.5-8 (diff) [7760 B] 214s gpgv: Signature made Fri Feb 19 07:13:34 2021 UTC 214s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 214s gpgv: issuer "npatra974@gmail.com" 214s gpgv: Can't check signature: No public key 214s dpkg-source: warning: cannot verify inline signature for ./wham-align_0.1.5-8.dsc: no acceptable signature found 214s autopkgtest [17:07:54]: testing package wham-align version 0.1.5-8 216s autopkgtest [17:07:56]: build not needed 218s autopkgtest [17:07:58]: test run-unit-test: preparing testbed 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 222s Starting pkgProblemResolver with broken count: 0 222s Starting 2 pkgProblemResolver with broken count: 0 222s Done 224s The following NEW packages will be installed: 224s wham-align 224s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 224s Need to get 196 kB of archives. 224s After this operation, 608 kB of additional disk space will be used. 224s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf wham-align armhf 0.1.5-8 [196 kB] 225s Fetched 196 kB in 1s (392 kB/s) 225s Selecting previously unselected package wham-align. 225s (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.) 225s Preparing to unpack .../wham-align_0.1.5-8_armhf.deb ... 225s Unpacking wham-align (0.1.5-8) ... 225s Setting up wham-align (0.1.5-8) ... 225s Processing triggers for man-db (2.13.0-1) ... 234s autopkgtest [17:08:14]: test run-unit-test: [----------------------- 236s .: 236s reads 236s ref 236s sequences 236s 236s ./reads: 236s sample.fq 236s sample_pair_1.fq 236s sample_pair_2.fq 236s 236s ./ref: 236s README.test_data 236s output1 236s output2 236s output3 236s output4 236s output5 236s output6 236s output7 236s 236s ./sequences: 236s chr1_100k.fa 236s Test 1 236s length: 60, #mismatch: 2, #partition: 0 236s loading reference sequences... 236s Preprocessing reference sequences... 236s preprocessing sequences/chr1_100k.fa... 236s 236s loading reference sequences... 236s [ ] 0% ] 1% ] 2%# ] 3%# ] 4%## ] 5%## ] 6%## ] 7%### ] 8%### ] 9%#### ] 10%#### ] 11%#### ] 12%##### ] 13%##### ] 14%###### ] 15%###### ] 16%###### ] 17%####### ] 18%####### ] 19%######## ] 20%######## ] 21%######## ] 22%######### ] 23%######### ] 24%########## ] 25%########## ] 26%########## ] 27%########### ] 28%########### ] 29%############ ] 30%############ ] 31%############ ] 32%############# ] 33%############# ] 34%############## ] 35%############## ] 36%############## ] 37%############### ] 38%############### ] 39%################ ] 40%################ ] 41%################ ] 42%################# ] 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the reference sequences... 236s optimizer chooses 3 fragments 236s building WHAM index... 236s preprocessing... 236s [ ] 0% ] 1% ] 2%# ] 3%# ] 4%## ] 5%## ] 6%## ] 7%### ] 8%### ] 9%#### ] 10%#### ] 11%#### ] 12%##### ] 13%##### ] 14%###### ] 15%###### ] 16%###### ] 17%####### ] 18%####### ] 19%######## ] 20%######## ] 21%######## ] 22%######### ] 23%######### ] 24%########## ] 25%########## ] 26%########## ] 27%########### ] 28%########### ] 29%############ ] 30%############ ] 31%############ ] 32%############# ] 33%############# ] 34%############## ] 35%############## ] 36%############## ] 37%############### ] 38%############### ] 39%################ ] 40%################ ] 41%################ ] 42%################# ] 43%################# ] 44%################## ] 45%################## ] 46%################## ] 47%################### ] 48%################### ] 49%#################### ] 50%#################### ] 51%#################### ] 52%##################### ] 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92%##################################### ] 93%##################################### ] 94%###################################### ] 95%###################################### ] 96%###################################### ] 97%####################################### ] 98%####################################### ] 99%########################################] 100% 236s saving... 236s building time: 0.069429 sec 236s Complete. 236s Passed 236s 236s Test 2 236s loading short reads... 236s loading WHAM indexes... 236s loading time: 0 sec 236s align reads using indexes... 236s [ ] 0%########## ] 25%#################### ] 50%############################## ] 75%########################################] 100% 236s 236s *************************** 236s Total Align Time: 0.000231 sec 236s Valid Reads: 3/5=60.00% 236s Valid Alignments: 3 236s *************************** 236s 236s see output1 for all valid alignments. 236s Passed 236s 236s Test 3 236s loading short reads... 236s loading WHAM indexes... 236s loading time: 0 sec 236s align reads using indexes... 236s [ ] 0%########## ] 25%#################### ] 50%############################## ] 75%########################################] 100% 236s 236s *************************** 236s Total Align Time: 0.000302 sec 236s Valid Reads: 3/5=60.00% 236s Valid Alignments: 9 236s *************************** 236s 236s see output2 for all valid alignments. 236s Passed 236s 236s Test 4 236s loading short reads... 236s loading WHAM indexes... 236s loading time: 0 sec 236s align reads using indexes... 236s [ ] 0%########## ] 25%#################### ] 50%############################## ] 75%########################################] 100% 236s 236s *************************** 236s Total Align Time: 0.000291 sec 236s Valid Reads: 2/5=40.00% 236s Valid Alignments: 3 236s *************************** 236s 236s see output3 for all valid alignments. 236s Passed 236s 236s Test 5 236s loading short reads... 236s loading WHAM indexes... 236s loading time: 0 sec 236s align reads using indexes... 236s [ ] 0%########## ] 25%#################### ] 50%############################## ] 75%########################################] 100% 236s 236s *************************** 236s Total Align Time: 0.000252 sec 236s Valid Reads: 4/5=80.00% 236s Valid Alignments: 4 236s *************************** 236s 236s see output4 for all valid alignments. 236s Passed 236s 236s Test 6 236s loading short reads... 236s loading WHAM indexes... 236s loading time: 0 sec 236s align reads using indexes... 236s [ ] 0%########## ] 25%#################### ] 50%############################## ] 75%########################################] 100% 236s 236s *************************** 236s Total Align Time: 0.000270 sec 236s Valid Reads: 0/5=0.00% 236s Valid Alignments: 0 236s *************************** 236s 236s see output5 for all valid alignments. 236s Passed 236s 236s Test 7 236s loading short reads... 236s loading WHAM indexes... 236s loading time: 0 sec 236s align reads using indexes... 236s [ ] 0%########## ] 25%#################### ] 50%############################## ] 75%########################################] 100% 236s 236s *************************** 236s Total Align Time: 0.000288 sec 236s Valid Reads: 3/5=60.00% 236s Valid Alignments: 3 236s *************************** 236s 236s see output6 for all valid alignments. 236s Passed 236s 236s Test 8 236s loading short reads... 236s loading WHAM indexes... 236s loading time: 0 sec 236s align reads using indexes... 236s [ ] 0% 236s 236s Thread 0: Valid Reads: 1/1, Valid Alignments: 1 236s Thread 1: Valid Reads: 1/1, Valid Alignments: 1 236s Thread 2: Valid Reads: 1/1, Valid Alignments: 1 236s Thread 3: Valid Reads: 0/1, Valid Alignments: 0 236s Thread 4: Valid Reads: 0/1, Valid Alignments: 0 236s Thread 5: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 6: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 7: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 8: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 9: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 10: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 11: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 12: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 13: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 14: Valid Reads: 0/0, Valid Alignments: 0 236s Thread 15: Valid Reads: 0/0, Valid Alignments: 0 236s collect results... 236s 236s *************************** 236s Total Align Time: 0.000747 sec 236s Valid Reads: 3/5=60.00% 236s Valid Alignments: 3 236s *************************** 236s 236s see output7 for all valid alignments. 236s Passed 236s 237s autopkgtest [17:08:17]: test run-unit-test: -----------------------] 241s run-unit-test PASS 241s autopkgtest [17:08:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 245s autopkgtest [17:08:25]: @@@@@@@@@@@@@@@@@@@@ summary 245s run-unit-test PASS