0s autopkgtest [16:40:03]: starting date and time: 2025-03-15 16:40:03+0000 0s autopkgtest [16:40:03]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:40:03]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fl4ddc0y/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-37.secgroup --name adt-plucky-arm64-segemehl-20250315-164002-juju-7f2275-prod-proposed-migration-environment-2-47d6d485-7405-4a7e-acec-19b9f9dc6677 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 168s autopkgtest [16:42:51]: testbed dpkg architecture: arm64 168s autopkgtest [16:42:51]: testbed apt version: 2.9.33 168s autopkgtest [16:42:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 168s autopkgtest [16:42:51]: testbed release detected to be: None 169s autopkgtest [16:42:52]: updating testbed package index (apt update) 170s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 170s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 170s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 170s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 170s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 170s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 171s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 171s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 171s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 171s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 171s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 171s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 171s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 171s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 171s Fetched 1078 kB in 2s (669 kB/s) 172s Reading package lists... 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Calculating upgrade... 174s Calculating upgrade... 174s The following packages will be upgraded: 174s pinentry-curses python3-jinja2 strace 174s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 647 kB of archives. 174s After this operation, 11.3 kB of additional disk space will be used. 174s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 175s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 175s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 176s Fetched 647 kB in 1s (660 kB/s) 176s (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 ... 117701 files and directories currently installed.) 176s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 176s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 176s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 176s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 176s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 176s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 176s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 176s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 176s Setting up strace (6.13+ds-1ubuntu1) ... 176s Processing triggers for man-db (2.13.0-1) ... 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 178s Solving dependencies... 178s The following packages will be REMOVED: 178s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 178s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 178s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 178s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 179s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 179s After this operation, 267 MB disk space will be freed. 179s (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 ... 117701 files and directories currently installed.) 179s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 179s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 179s Removing libpython3.12t64:arm64 (3.12.9-1) ... 179s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 179s Removing libnsl2:arm64 (1.3.0-3build3) ... 179s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 179s Removing libunwind8:arm64 (1.6.2-3.1) ... 179s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 179s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 181s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 181s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 181s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 181s /etc/kernel/postrm.d/initramfs-tools: 181s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 181s /etc/kernel/postrm.d/zz-flash-kernel: 181s flash-kernel: Kernel 6.11.0-8-generic has been removed. 181s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 182s /etc/kernel/postrm.d/zz-update-grub: 182s Sourcing file `/etc/default/grub' 182s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 182s Generating grub configuration file ... 182s Found linux image: /boot/vmlinuz-6.14.0-10-generic 182s Found initrd image: /boot/initrd.img-6.14.0-10-generic 182s Warning: os-prober will not be executed to detect other bootable partitions. 182s Systems on them will not be added to the GRUB boot configuration. 182s Check GRUB_DISABLE_OS_PROBER documentation entry. 182s Adding boot menu entry for UEFI Firmware Settings ... 182s done 182s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 182s Processing triggers for libc-bin (2.41-1ubuntu1) ... 183s (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 ... 81650 files and directories currently installed.) 183s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 183s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 183s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 183s autopkgtest [16:43:06]: upgrading testbed (apt dist-upgrade and autopurge) 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 184s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 184s Starting 2 pkgProblemResolver with broken count: 0 184s Done 185s Entering ResolveByKeep 185s 185s Calculating upgrade... 186s The following packages will be upgraded: 186s libc-bin libc-dev-bin libc6 libc6-dev locales 186s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s Need to get 9530 kB of archives. 186s After this operation, 0 B of additional disk space will be used. 186s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 187s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 187s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 190s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 191s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 195s Preconfiguring packages ... 195s Fetched 9530 kB in 9s (1055 kB/s) 195s (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 ... 81647 files and directories currently installed.) 195s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 195s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 195s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 196s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up libc6:arm64 (2.41-1ubuntu2) ... 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 ... 81647 files and directories currently installed.) 196s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 196s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up libc-bin (2.41-1ubuntu2) ... 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 ... 81647 files and directories currently installed.) 196s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 196s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up locales (2.41-1ubuntu2) ... 197s Generating locales (this might take a while)... 199s en_US.UTF-8... done 199s Generation complete. 199s Setting up libc-dev-bin (2.41-1ubuntu2) ... 199s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 199s Processing triggers for man-db (2.13.0-1) ... 200s Processing triggers for systemd (257.3-1ubuntu3) ... 201s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 202s Solving dependencies... 203s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 203s autopkgtest [16:43:26]: rebooting testbed after setup commands that affected boot 226s autopkgtest [16:43:49]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 229s autopkgtest [16:43:52]: @@@@@@@@@@@@@@@@@@@@ apt-source segemehl 231s Get:1 http://ftpmaster.internal/ubuntu plucky/universe segemehl 0.3.4-5build2 (dsc) [2106 B] 231s Get:2 http://ftpmaster.internal/ubuntu plucky/universe segemehl 0.3.4-5build2 (tar) [244 kB] 231s Get:3 http://ftpmaster.internal/ubuntu plucky/universe segemehl 0.3.4-5build2 (diff) [7960 B] 231s gpgv: Signature made Mon Apr 1 08:00:00 2024 UTC 231s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 231s gpgv: Can't check signature: No public key 231s dpkg-source: warning: cannot verify inline signature for ./segemehl_0.3.4-5build2.dsc: no acceptable signature found 232s autopkgtest [16:43:55]: testing package segemehl version 0.3.4-5build2 232s autopkgtest [16:43:55]: build not needed 233s autopkgtest [16:43:56]: test run-unit-test: preparing testbed 233s Reading package lists... 233s Building dependency tree... 233s Reading state information... 233s Starting pkgProblemResolver with broken count: 0 234s Starting 2 pkgProblemResolver with broken count: 0 234s Done 234s The following NEW packages will be installed: 234s libdeflate0 libhts3t64 libhtscodecs2 segemehl 234s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 234s Need to get 775 kB of archives. 234s After this operation, 2222 kB of additional disk space will be used. 234s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 235s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 235s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 235s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 segemehl arm64 0.3.4-5build2 [205 kB] 236s Fetched 775 kB in 1s (704 kB/s) 236s Selecting previously unselected package libdeflate0:arm64. 236s (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 ... 81647 files and directories currently installed.) 236s Preparing to unpack .../libdeflate0_1.23-1_arm64.deb ... 236s Unpacking libdeflate0:arm64 (1.23-1) ... 236s Selecting previously unselected package libhtscodecs2:arm64. 236s Preparing to unpack .../libhtscodecs2_1.6.1-2_arm64.deb ... 236s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 236s Selecting previously unselected package libhts3t64:arm64. 236s Preparing to unpack .../libhts3t64_1.21+ds-1_arm64.deb ... 236s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 236s Selecting previously unselected package segemehl. 236s Preparing to unpack .../segemehl_0.3.4-5build2_arm64.deb ... 236s Unpacking segemehl (0.3.4-5build2) ... 236s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 236s Setting up libdeflate0:arm64 (1.23-1) ... 236s Setting up libhts3t64:arm64 (1.21+ds-1) ... 236s Setting up segemehl (0.3.4-5build2) ... 236s Processing triggers for libc-bin (2.41-1ubuntu2) ... 236s Processing triggers for man-db (2.13.0-1) ... 239s autopkgtest [16:44:02]: test run-unit-test: [----------------------- 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading database sequences. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 1 database sequences found. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: total length of db sequences: 250 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: assigning all reads to default read group 'A1'. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: additional read group default values ' SM:sample1 LB:library1 PU:unit1 PL:illumina' 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reads assigned to read group 'A1' 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: compiled sam header. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alphabet of size (5): ACGT 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: size of db sequence: 251 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: constructing suftab. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusort: classify. 239s init bit array of 32 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusort: getting bit. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: bit alurusort: alloc B of size 124. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusort: initbitarray of size 124. 239s init bit array of 16 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusort: Qmaxdist in cl of size 251. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: enter alurusort: substringsort. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: setting bit array to zero 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: allocating space for buckets and buffers 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: memsetting 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: substring sort ... ok 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: checking valbitarray. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: enter Tprime calculation. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: tprime: init arrays. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: tprime: scan B 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: tprime: iterating i=251 elements with lenB=124. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: tprime: exit 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: enter alursortint. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: classify int. 239s init bit array of 16 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: getting bit. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: init bcktsA. 239s init bit array of 16 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: countingsort. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countingsortint: init buffers and A 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: setting buffer to zero 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: scanning buffer (1 of 3) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: scanning buffer (2 of 3) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: scanning buffer (3 of 3) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: scanning buffer (to set borders) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: exiting 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: Sorting type S suffixes. Init bcktsB. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 55 69 124. 239s 239s init bit array of 7 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: arrayB: allocating B with 55 elements. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: arrayB: iterating to lenA=124. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: arrayB: exiting 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter Qmaxdist. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter Qdist. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter distCount. 239s init bit array of 16 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter get listsS. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: memsetting list of 121 elements. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: iter up to 124. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: scan A 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: set accidst 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: exiting 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: freeing stuff. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter sortlistsS. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistS: allocating stuff. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistS: iterating 55 elems. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistS: looping 121 elems. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistS: iterating 124 elems. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistsS: exiting happily! 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter tprime. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: tprime: init arrays. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: tprime: scan B 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: tprime: iterating i=124 elements with lenB=55. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: tprime: exit 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter alurusortint. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: classify int. 239s init bit array of 7 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: getting bit. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: init bcktsA. 239s init bit array of 7 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: countingsort. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countingsortint: init buffers and A 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: setting buffer to zero 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: scanning buffer (1 of 3) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: scanning buffer (2 of 3) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: scanning buffer (3 of 3) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: scanning buffer (to set borders) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: countsortint: exiting 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: Sorting type S suffixes. Init bcktsB. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 27 28 55. 239s 239s init bit array of 4 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: arrayB: allocating B with 27 elements. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: arrayB: iterating to lenA=55. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: arrayB: exiting 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter Qmaxdist. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter Qdist. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter distCount. 239s init bit array of 7 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter get listsS. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: memsetting list of 54 elements. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: iter up to 55. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: scan A 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: set accidst 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: getlistsS: exiting 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: freeing stuff. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: enter sortlistsS. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistS: allocating stuff. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistS: iterating 27 elems. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistS: looping 54 elems. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistS: iterating 55 elems. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: sortlistsS: exiting happily! 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: alurusortint: valbitarraysortedS. 239s init bit array of 7 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reconstructintS. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reconstruct: init. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reconstruct: iteration over 124 elems. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reconstruct: scan B (size: 55). 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reconstruct: exit. 239s init bit array of 16 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: enter reconstruction. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reconstruct: init. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reconstruct: iteration over 251 elems. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reconstruct: scan B (size: 124). 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reconstruct: exit. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: enter aluruSuffixArrayL start. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: aluruSuffixArrayL: initalizning arrays. 239s init bit array of 32 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: aluruSuffixArrayL: memsetting count. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: aluruSuffixArrayL: setting b. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: aluruSuffixArrayL: iteration. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: aluruSuffixArrayL: exit ok. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: constructing inv_suftab (251). 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: inv_suftab constructed. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: constructing lcp. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: deleting inv_suftab 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: constructing child tab. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: constructing suffix links. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: constructing id. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: constructing suflinks - bottom up. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: constructing suflinks - top down. 239s suflink construction. pushes: 177, maxstack: 7 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: building the suffix array has taken 0.000000 seconds. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: total length of suffix array was 250. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: writing suffix array 'index.idx' to disk. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: Mapping stats: 239s total mapped (%) unique (%) multi (%) split (%) 239s all 0 0 nan% 0 nan% 0 nan% 0 nan% 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 239s Goodbye. 239s "Beertime!" (A. Torda) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading queries in 'myseq.fa'. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 1 query sequences found. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading database sequences. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 1 database sequences found. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: total length of db sequences: 250 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: assigning all reads to default read group 'A1'. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: additional read group default values ' SM:sample1 LB:library1 PU:unit1 PL:illumina' 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reads assigned to read group 'A1' 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: compiled sam header. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading suffix array 'index.idx' from disk. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading lcpc/vtab. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading childtab. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading suflinks. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading lsint id. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: read suffix array 'index.idx' with 251 elements. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: md5 keys of index and db match. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading the suffix array has taken 0.000000 seconds. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: matching w/ suffixarray has taken 0.000000 seconds. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: Mapping stats: 239s total mapped (%) unique (%) multi (%) split (%) 239s all 1 0 0.00% 0 0.00% 0 0.00% 0 0.00% 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 239s Goodbye. 239s "Beertime!" (A. Torda) 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading queries in 'seq2.fa'. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 1 query sequences found. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading database sequences. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 1 database sequences found. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: total length of db sequences: 250 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: assigning all reads to default read group 'A1'. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: additional read group default values ' SM:sample1 LB:library1 PU:unit1 PL:illumina' 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reads assigned to read group 'A1' 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: compiled sam header. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading suffix array 'index.idx' from disk. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading lcpc/vtab. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading childtab. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading suflinks. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading lsint id. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: read suffix array 'index.idx' with 251 elements. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: md5 keys of index and db match. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: reading the suffix array has taken 0.000000 seconds. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: writing multi splits to 'seq2.mult.bed' 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: writing sngle splits to 'seq2.sngl.bed' 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: writing trans splits to 'seq2.trns.txt' 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: matching w/ suffixarray has taken 0.000000 seconds. 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: Mapping stats: 239s total mapped (%) unique (%) multi (%) split (%) 239s all 1 0 0.00% 0 0.00% 0 0.00% 0 0.00% 239s [SEGEMEHL] Sat Mar 15 16:44:03 2025: 239s Goodbye. 239s "Beertime!" (A. Torda) 239s PASS Test 239s autopkgtest [16:44:02]: test run-unit-test: -----------------------] 240s run-unit-test PASS 240s autopkgtest [16:44:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 240s autopkgtest [16:44:03]: @@@@@@@@@@@@@@@@@@@@ summary 240s run-unit-test PASS 258s nova [W] Using flock in prodstack6-arm64 258s Creating nova instance adt-plucky-arm64-segemehl-20250315-164002-juju-7f2275-prod-proposed-migration-environment-2-47d6d485-7405-4a7e-acec-19b9f9dc6677 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 258s nova [W] Timed out waiting for b73d7d95-b45b-4fd8-ba45-76a6aa383b14 to get deleted.