0s autopkgtest [14:41:29]: starting date and time: 2025-03-15 14:41:29+0000 0s autopkgtest [14:41:29]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:41:29]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qisxqxhy/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 nxtrim --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.227 lxd-armhf-10.145.243.227:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [14:41:50]: testbed dpkg architecture: armhf 23s autopkgtest [14:41:52]: testbed apt version: 2.9.33 27s autopkgtest [14:41:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [14:41:58]: testbed release detected to be: None 36s autopkgtest [14:42:05]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 39s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 40s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 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 [332 B] 41s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 67s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 69s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 69s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 71s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 71s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 71s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 89s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 90s Fetched 41.0 MB in 52s (790 kB/s) 91s Reading package lists... 97s autopkgtest [14:43:06]: upgrading testbed (apt dist-upgrade and autopurge) 99s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 102s Starting 2 pkgProblemResolver with broken count: 0 102s Done 102s Entering ResolveByKeep 103s 103s Calculating upgrade... 103s The following packages will be upgraded: 103s libc-bin libc6 locales python3-jinja2 sos strace 104s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Need to get 8642 kB of archives. 104s After this operation, 23.6 kB of additional disk space will be used. 104s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 112s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 113s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 114s Preconfiguring packages ... 114s Fetched 8642 kB in 10s (875 kB/s) 114s (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.) 114s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 115s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Setting up libc6:armhf (2.41-1ubuntu2) ... 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 ... 64655 files and directories currently installed.) 115s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 115s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Setting up libc-bin (2.41-1ubuntu2) ... 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 ... 64655 files and directories currently installed.) 115s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 116s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 116s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 116s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 116s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 116s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 116s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 116s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 117s Setting up sos (4.9.0-5) ... 117s Setting up locales (2.41-1ubuntu2) ... 118s Generating locales (this might take a while)... 120s en_US.UTF-8... done 120s Generation complete. 120s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 120s Setting up strace (6.13+ds-1ubuntu1) ... 120s Processing triggers for man-db (2.13.0-1) ... 121s Processing triggers for systemd (257.3-1ubuntu3) ... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 125s Solving dependencies... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s autopkgtest [14:43:37]: rebooting testbed after setup commands that affected boot 170s autopkgtest [14:44:19]: 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 194s autopkgtest [14:44:43]: @@@@@@@@@@@@@@@@@@@@ apt-source nxtrim 204s Get:1 http://ftpmaster.internal/ubuntu plucky/universe nxtrim 0.4.3+dfsg-4 (dsc) [1983 B] 204s Get:2 http://ftpmaster.internal/ubuntu plucky/universe nxtrim 0.4.3+dfsg-4 (tar) [65.9 kB] 204s Get:3 http://ftpmaster.internal/ubuntu plucky/universe nxtrim 0.4.3+dfsg-4 (diff) [5092 B] 205s gpgv: Signature made Fri Dec 20 21:13:49 2024 UTC 205s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 205s gpgv: issuer "tille@debian.org" 205s gpgv: Can't check signature: No public key 205s dpkg-source: warning: cannot verify inline signature for ./nxtrim_0.4.3+dfsg-4.dsc: no acceptable signature found 205s autopkgtest [14:44:54]: testing package nxtrim version 0.4.3+dfsg-4 207s autopkgtest [14:44:56]: build not needed 209s autopkgtest [14:44:58]: test run-unit-test: preparing testbed 210s Reading package lists... 211s Building dependency tree... 211s Reading state information... 211s Starting pkgProblemResolver with broken count: 0 211s Starting 2 pkgProblemResolver with broken count: 0 211s Done 212s The following NEW packages will be installed: 212s nxtrim 212s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 212s Need to get 35.0 kB of archives. 212s After this operation, 88.1 kB of additional disk space will be used. 212s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf nxtrim armhf 0.4.3+dfsg-4 [35.0 kB] 213s Fetched 35.0 kB in 0s (139 kB/s) 213s Selecting previously unselected package nxtrim. 213s (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.) 213s Preparing to unpack .../nxtrim_0.4.3+dfsg-4_armhf.deb ... 213s Unpacking nxtrim (0.4.3+dfsg-4) ... 213s Setting up nxtrim (0.4.3+dfsg-4) ... 213s Processing triggers for man-db (2.13.0-1) ... 222s autopkgtest [14:45:10]: test run-unit-test: [----------------------- 223s + nxtrim -1 example/ENA_R1.fastq.gz -2 example/ENA_R2.fastq.gz --out example/ENA 223s Output: example/ENA.*.fastq.gz 223s Trimming: 223s R1: example/ENA_R1.fastq.gz 223s R2: example/ENA_R2.fastq.gz 223s 223s Trimming summary: 223s 1 / 1 ( 100.00% ) reads passed chastity/purity filters. 223s 0 / 1 ( 0.00% ) reads had multiple copies of adapter (filtered). 223s 0 / 1 ( 0.00% ) read pairs were ignored because template length appeared less than read length 223s 1 remaining reads were trimmed 223s 223s 0 / 1 ( 0.00% ) read pairs had MP orientation 223s 1 / 1 ( 100.00% ) read pairs had PE orientation 223s 0 / 1 ( 0.00% ) read pairs had unknown orientation 223s 0 / 1 ( 0.00% ) were single end reads 223s 223s 0 / 1 ( 0.00% ) extra single end reads were generated from overhangs 223s + nxtrim -1 example/example11_R1.fastq.gz -2 example/example11_R2.fastq.gz --out example/example11 223s Output: example/example11.*.fastq.gz 223s Trimming: 223s R1: example/example11_R1.fastq.gz 223s R2: example/example11_R2.fastq.gz 223s WARNING: reads with differing lengths. Has this data already been processed with nxtrim? 223s 223s Trimming summary: 223s 1 / 1 ( 100.00% ) reads passed chastity/purity filters. 223s 0 / 1 ( 0.00% ) reads had multiple copies of adapter (filtered). 223s 0 / 1 ( 0.00% ) read pairs were ignored because template length appeared less than read length 223s 1 remaining reads were trimmed 223s 223s 0 / 1 ( 0.00% ) read pairs had MP orientation 223s 0 / 1 ( 0.00% ) read pairs had PE orientation 223s 1 / 1 ( 100.00% ) read pairs had unknown orientation 223s 0 / 1 ( 0.00% ) were single end reads 223s 223s 0 / 1 ( 0.00% ) extra single end reads were generated from overhangs 223s + nxtrim -1 example/EXTERNAL_R1.fastq.gz -2 example/EXTERNAL_R2.fastq.gz --out example/EXTERNAL 223s Output: example/EXTERNAL.*.fastq.gz 223s Trimming: 223s R1: example/EXTERNAL_R1.fastq.gz 223s R2: example/EXTERNAL_R2.fastq.gz 223s 223s Trimming summary: 223s 1 / 1 ( 100.00% ) reads passed chastity/purity filters. 223s 0 / 1 ( 0.00% ) reads had multiple copies of adapter (filtered). 223s 0 / 1 ( 0.00% ) read pairs were ignored because template length appeared less than read length 223s 1 remaining reads were trimmed 223s 223s 0 / 1 ( 0.00% ) read pairs had MP orientation 223s 1 / 1 ( 100.00% ) read pairs had PE orientation 223s 0 / 1 ( 0.00% ) read pairs had unknown orientation 223s 0 / 1 ( 0.00% ) were single end reads 223s 223s 0 / 1 ( 0.00% ) extra single end reads were generated from overhangs 223s + nxtrim -1 example/FailPF_R1.fastq.gz -2 example/FailPF_R2.fastq.gz --out example/FailPF 223s Output: example/FailPF.*.fastq.gz 223s Trimming: 223s R1: example/FailPF_R1.fastq.gz 223s R2: example/FailPF_R2.fastq.gz 223s 223s Trimming summary: 223s 0 / 1 ( 0.00% ) reads passed chastity/purity filters. 223s 0 / 0 ( nan% ) reads had multiple copies of adapter (filtered). 223s 0 / 0 ( nan% ) read pairs were ignored because template length appeared less than read length 223s 0 remaining reads were trimmed 223s 223s 0 / 0 ( nan% ) read pairs had MP orientation 223s 0 / 0 ( nan% ) read pairs had PE orientation 223s 0 / 0 ( nan% ) read pairs had unknown orientation 223s 0 / 0 ( nan% ) were single end reads 223s 223s 0 / 0 ( nan% ) extra single end reads were generated from overhangs 223s + nxtrim -1 example/MP_R1.fastq.gz -2 example/MP_R2.fastq.gz --out example/MP 223s Output: example/MP.*.fastq.gz 223s Trimming: 223s R1: example/MP_R1.fastq.gz 223s R2: example/MP_R2.fastq.gz 223s 223s Trimming summary: 223s 54 / 54 ( 100.00% ) reads passed chastity/purity filters. 223s 0 / 54 ( 0.00% ) reads had multiple copies of adapter (filtered). 223s 0 / 54 ( 0.00% ) read pairs were ignored because template length appeared less than read length 223s 54 remaining reads were trimmed 223s 223s 54 / 54 ( 100.00% ) read pairs had MP orientation 223s 0 / 54 ( 0.00% ) read pairs had PE orientation 223s 0 / 54 ( 0.00% ) read pairs had unknown orientation 223s 0 / 54 ( 0.00% ) were single end reads 223s 223s 0 / 54 ( 0.00% ) extra single end reads were generated from overhangs 223s + nxtrim -1 example/PE_R1.fastq.gz -2 example/PE_R2.fastq.gz --out example/PE 223s Output: example/PE.*.fastq.gz 223s Trimming: 223s R1: example/PE_R1.fastq.gz 223s R2: example/PE_R2.fastq.gz 223s 223s Trimming summary: 223s 55 / 55 ( 100.00% ) reads passed chastity/purity filters. 223s 0 / 55 ( 0.00% ) reads had multiple copies of adapter (filtered). 223s 1 / 55 ( 1.82% ) read pairs were ignored because template length appeared less than read length 223s 54 remaining reads were trimmed 223s 223s 0 / 54 ( 0.00% ) read pairs had MP orientation 223s 54 / 54 ( 100.00% ) read pairs had PE orientation 223s 0 / 54 ( 0.00% ) read pairs had unknown orientation 223s 0 / 54 ( 0.00% ) were single end reads 223s 223s 0 / 54 ( 0.00% ) extra single end reads were generated from overhangs 223s + nxtrim -1 example/sample_R1.fastq.gz -2 example/sample_R2.fastq.gz --out example/sample 223s Output: example/sample.*.fastq.gz 223s Trimming: 223s R1: example/sample_R1.fastq.gz 223s R2: example/sample_R2.fastq.gz 223s 223s Trimming summary: 223s 163 / 163 ( 100.00% ) reads passed chastity/purity filters. 223s 0 / 163 ( 0.00% ) reads had multiple copies of adapter (filtered). 223s 1 / 163 ( 0.61% ) read pairs were ignored because template length appeared less than read length 223s 162 remaining reads were trimmed 223s 223s 54 / 162 ( 33.33% ) read pairs had MP orientation 223s 54 / 162 ( 33.33% ) read pairs had PE orientation 223s 54 / 162 ( 33.33% ) read pairs had unknown orientation 223s 0 / 162 ( 0.00% ) were single end reads 223s 223s 0 / 162 ( 0.00% ) extra single end reads were generated from overhangs 223s + nxtrim -1 example/UNKNOWN_R1.fastq.gz -2 example/UNKNOWN_R2.fastq.gz --out example/UNKNOWN 223s Output: example/UNKNOWN.*.fastq.gz 223s Trimming: 223s R1: example/UNKNOWN_R1.fastq.gz 223s R2: example/UNKNOWN_R2.fastq.gz 223s 223s Trimming summary: 223s 54 / 54 ( 100.00% ) reads passed chastity/purity filters. 223s 0 / 54 ( 0.00% ) reads had multiple copies of adapter (filtered). 223s 0 / 54 ( 0.00% ) read pairs were ignored because template length appeared less than read length 223s 54 remaining reads were trimmed 223s 223s 0 / 54 ( 0.00% ) read pairs had MP orientation 223s 0 / 54 ( 0.00% ) read pairs had PE orientation 223s 54 / 54 ( 100.00% ) read pairs had unknown orientation 223s 0 / 54 ( 0.00% ) were single end reads 223s 223s 0 / 54 ( 0.00% ) extra single end reads were generated from overhangs 223s autopkgtest [14:45:12]: test run-unit-test: -----------------------] 227s autopkgtest [14:45:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 227s run-unit-test PASS 231s autopkgtest [14:45:20]: @@@@@@@@@@@@@@@@@@@@ summary 231s run-unit-test PASS