0s autopkgtest [17:31:48]: starting date and time: 2025-03-15 17:31:48+0000 0s autopkgtest [17:31:48]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:31:48]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gu4ednlr/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 segemehl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.28 lxd-armhf-10.145.243.28:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [17:32:08]: testbed dpkg architecture: armhf 21s autopkgtest [17:32:09]: testbed apt version: 2.9.33 25s autopkgtest [17:32:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 27s autopkgtest [17:32:15]: testbed release detected to be: None 36s autopkgtest [17:32:24]: updating testbed package index (apt update) 39s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 39s 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/main Sources [99.7 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 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] 63s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 64s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 64s 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] 79s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 81s Fetched 41.0 MB in 41s (993 kB/s) 82s Reading package lists... 87s autopkgtest [17:33:15]: upgrading testbed (apt dist-upgrade and autopurge) 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 90s Starting 2 pkgProblemResolver with broken count: 0 90s Done 90s Entering ResolveByKeep 91s 91s Calculating upgrade... 91s The following packages will be upgraded: 91s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 92s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Need to get 8683 kB of archives. 92s After this operation, 23.6 kB of additional disk space will be used. 92s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 94s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 95s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 99s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 99s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 99s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 99s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 100s Preconfiguring packages ... 100s Fetched 8683 kB in 8s (1111 kB/s) 100s (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.) 100s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 100s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 100s Setting up libc6:armhf (2.41-1ubuntu2) ... 101s (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.) 101s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 101s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 101s Setting up libc-bin (2.41-1ubuntu2) ... 101s (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.) 101s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 101s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 101s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 101s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 101s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 101s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 101s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 101s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 102s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 102s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 102s Setting up sos (4.9.0-5) ... 103s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 103s Setting up locales (2.41-1ubuntu2) ... 103s Generating locales (this might take a while)... 105s en_US.UTF-8... done 105s Generation complete. 105s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 106s Setting up strace (6.13+ds-1ubuntu1) ... 106s Processing triggers for man-db (2.13.0-1) ... 107s Processing triggers for systemd (257.3-1ubuntu3) ... 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s Starting pkgProblemResolver with broken count: 0 110s Starting 2 pkgProblemResolver with broken count: 0 110s Done 110s Solving dependencies... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [17:33:41]: rebooting testbed after setup commands that affected boot 152s autopkgtest [17:34:20]: 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 176s autopkgtest [17:34:44]: @@@@@@@@@@@@@@@@@@@@ apt-source segemehl 186s Get:1 http://ftpmaster.internal/ubuntu plucky/universe segemehl 0.3.4-5build2 (dsc) [2106 B] 186s Get:2 http://ftpmaster.internal/ubuntu plucky/universe segemehl 0.3.4-5build2 (tar) [244 kB] 186s Get:3 http://ftpmaster.internal/ubuntu plucky/universe segemehl 0.3.4-5build2 (diff) [7960 B] 187s gpgv: Signature made Mon Apr 1 08:00:00 2024 UTC 187s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 187s gpgv: Can't check signature: No public key 187s dpkg-source: warning: cannot verify inline signature for ./segemehl_0.3.4-5build2.dsc: no acceptable signature found 187s autopkgtest [17:34:55]: testing package segemehl version 0.3.4-5build2 189s autopkgtest [17:34:57]: build not needed 191s autopkgtest [17:34:59]: test run-unit-test: preparing testbed 192s Reading package lists... 193s Building dependency tree... 193s Reading state information... 193s Starting pkgProblemResolver with broken count: 0 193s Starting 2 pkgProblemResolver with broken count: 0 193s Done 194s The following NEW packages will be installed: 194s libdeflate0 libhts3t64 libhtscodecs2 segemehl 194s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 194s Need to get 779 kB of archives. 194s After this operation, 1983 kB of additional disk space will be used. 194s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 195s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 195s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB] 195s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf segemehl armhf 0.3.4-5build2 [274 kB] 196s Fetched 779 kB in 1s (546 kB/s) 196s Selecting previously unselected package libdeflate0:armhf. 196s (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.) 196s Preparing to unpack .../libdeflate0_1.23-1_armhf.deb ... 196s Unpacking libdeflate0:armhf (1.23-1) ... 196s Selecting previously unselected package libhtscodecs2:armhf. 196s Preparing to unpack .../libhtscodecs2_1.6.1-2_armhf.deb ... 196s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 196s Selecting previously unselected package libhts3t64:armhf. 196s Preparing to unpack .../libhts3t64_1.21+ds-1_armhf.deb ... 196s Unpacking libhts3t64:armhf (1.21+ds-1) ... 196s Selecting previously unselected package segemehl. 196s Preparing to unpack .../segemehl_0.3.4-5build2_armhf.deb ... 196s Unpacking segemehl (0.3.4-5build2) ... 196s Setting up libhtscodecs2:armhf (1.6.1-2) ... 196s Setting up libdeflate0:armhf (1.23-1) ... 196s Setting up libhts3t64:armhf (1.21+ds-1) ... 196s Setting up segemehl (0.3.4-5build2) ... 196s Processing triggers for libc-bin (2.41-1ubuntu2) ... 196s Processing triggers for man-db (2.13.0-1) ... 204s autopkgtest [17:35:12]: test run-unit-test: [----------------------- 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading database sequences. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 1 database sequences found. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: total length of db sequences: 250 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: assigning all reads to default read group 'A1'. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: additional read group default values ' SM:sample1 LB:library1 PU:unit1 PL:illumina' 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reads assigned to read group 'A1' 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: compiled sam header. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alphabet of size (5): ACGT 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: size of db sequence: 251 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: constructing suftab. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusort: classify. 206s init bit array of 32 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusort: getting bit. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: bit alurusort: alloc B of size 124. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusort: initbitarray of size 124. 206s init bit array of 16 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusort: Qmaxdist in cl of size 251. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: enter alurusort: substringsort. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: setting bit array to zero 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: allocating space for buckets and buffers 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: memsetting 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: substring sort ... ok 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: checking valbitarray. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: enter Tprime calculation. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: tprime: init arrays. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: tprime: scan B 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: tprime: iterating i=251 elements with lenB=124. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: tprime: exit 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: enter alursortint. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: classify int. 206s init bit array of 16 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: getting bit. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: init bcktsA. 206s init bit array of 16 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: countingsort. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countingsortint: init buffers and A 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: setting buffer to zero 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: scanning buffer (1 of 3) 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: scanning buffer (2 of 3) 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: scanning buffer (3 of 3) 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: scanning buffer (to set borders) 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: exiting 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: Sorting type S suffixes. Init bcktsB. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 55 69 124. 206s 206s init bit array of 7 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: arrayB: allocating B with 55 elements. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: arrayB: iterating to lenA=124. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: arrayB: exiting 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter Qmaxdist. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter Qdist. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter distCount. 206s init bit array of 16 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter get listsS. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: memsetting list of 121 elements. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: iter up to 124. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: scan A 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: set accidst 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: exiting 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: freeing stuff. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter sortlistsS. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistS: allocating stuff. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistS: iterating 55 elems. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistS: looping 121 elems. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistS: iterating 124 elems. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistsS: exiting happily! 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter tprime. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: tprime: init arrays. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: tprime: scan B 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: tprime: iterating i=124 elements with lenB=55. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: tprime: exit 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter alurusortint. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: classify int. 206s init bit array of 7 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: getting bit. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: init bcktsA. 206s init bit array of 7 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: countingsort. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countingsortint: init buffers and A 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: setting buffer to zero 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: scanning buffer (1 of 3) 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: scanning buffer (2 of 3) 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: scanning buffer (3 of 3) 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: scanning buffer (to set borders) 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: countsortint: exiting 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: Sorting type S suffixes. Init bcktsB. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 27 28 55. 206s 206s init bit array of 4 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: arrayB: allocating B with 27 elements. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: arrayB: iterating to lenA=55. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: arrayB: exiting 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter Qmaxdist. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter Qdist. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter distCount. 206s init bit array of 7 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter get listsS. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: memsetting list of 54 elements. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: iter up to 55. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: scan A 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: set accidst 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: getlistsS: exiting 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: freeing stuff. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: enter sortlistsS. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistS: allocating stuff. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistS: iterating 27 elems. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistS: looping 54 elems. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistS: iterating 55 elems. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: sortlistsS: exiting happily! 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: alurusortint: valbitarraysortedS. 206s init bit array of 7 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reconstructintS. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reconstruct: init. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reconstruct: iteration over 124 elems. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reconstruct: scan B (size: 55). 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reconstruct: exit. 206s init bit array of 16 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: enter reconstruction. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reconstruct: init. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reconstruct: iteration over 251 elems. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reconstruct: scan B (size: 124). 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reconstruct: exit. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: enter aluruSuffixArrayL start. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: aluruSuffixArrayL: initalizning arrays. 206s init bit array of 32 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: aluruSuffixArrayL: memsetting count. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: aluruSuffixArrayL: setting b. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: aluruSuffixArrayL: iteration. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: aluruSuffixArrayL: exit ok. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: constructing inv_suftab (251). 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: inv_suftab constructed. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: constructing lcp. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: deleting inv_suftab 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: constructing child tab. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: constructing suffix links. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: constructing id. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: constructing suflinks - bottom up. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: constructing suflinks - top down. 206s suflink construction. pushes: 177, maxstack: 7 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: building the suffix array has taken 0.000000 seconds. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: total length of suffix array was 250. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: writing suffix array 'index.idx' to disk. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: Mapping stats: 206s total mapped (%) unique (%) multi (%) split (%) 206s all 0 0 nan% 0 nan% 0 nan% 0 nan% 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 206s Goodbye. 206s "Hab' ich gerade inner Bild gelesen!" (Bienchen) 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading queries in 'myseq.fa'. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 1 query sequences found. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading database sequences. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 1 database sequences found. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: total length of db sequences: 250 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: assigning all reads to default read group 'A1'. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: additional read group default values ' SM:sample1 LB:library1 PU:unit1 PL:illumina' 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reads assigned to read group 'A1' 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: compiled sam header. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading suffix array 'index.idx' from disk. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading lcpc/vtab. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading childtab. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading suflinks. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading lsint id. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: read suffix array 'index.idx' with 251 elements. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: md5 keys of index and db match. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading the suffix array has taken 0.000000 seconds. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: matching w/ suffixarray has taken 0.000000 seconds. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: Mapping stats: 206s total mapped (%) unique (%) multi (%) split (%) 206s all 1 0 0.00% 0 0.00% 0 0.00% 0 0.00% 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 206s Goodbye. 206s "Hab' ich gerade inner Bild gelesen!" (Bienchen) 206s PASS Test 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading queries in 'seq2.fa'. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 1 query sequences found. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading database sequences. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 1 database sequences found. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: total length of db sequences: 250 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: assigning all reads to default read group 'A1'. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: additional read group default values ' SM:sample1 LB:library1 PU:unit1 PL:illumina' 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reads assigned to read group 'A1' 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: compiled sam header. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading suffix array 'index.idx' from disk. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading lcpc/vtab. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading childtab. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading suflinks. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading lsint id. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: read suffix array 'index.idx' with 251 elements. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: md5 keys of index and db match. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: reading the suffix array has taken 0.000000 seconds. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: writing multi splits to 'seq2.mult.bed' 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: writing sngle splits to 'seq2.sngl.bed' 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: writing trans splits to 'seq2.trns.txt' 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: matching w/ suffixarray has taken 0.000000 seconds. 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: Mapping stats: 206s total mapped (%) unique (%) multi (%) split (%) 206s all 1 0 0.00% 0 0.00% 0 0.00% 0 0.00% 206s [SEGEMEHL] Sat Mar 15 17:35:14 2025: 206s Goodbye. 206s "Hab' ich gerade inner Bild gelesen!" (Bienchen) 207s autopkgtest [17:35:15]: test run-unit-test: -----------------------] 210s run-unit-test PASS 210s autopkgtest [17:35:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 215s autopkgtest [17:35:23]: @@@@@@@@@@@@@@@@@@@@ summary 215s run-unit-test PASS