0s autopkgtest [11:05:25]: starting date and time: 2025-03-15 11:05:25+0000 0s autopkgtest [11:05:25]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [11:05:25]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._t2ab2az/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade transtermhp --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-15@bos03-arm64-14.secgroup --name adt-plucky-arm64-transtermhp-20250315-110525-juju-7f2275-prod-proposed-migration-environment-15-f1bb5486-98e3-40f3-9010-1a685bf7cfac --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 170s autopkgtest [11:08:15]: testbed dpkg architecture: arm64 170s autopkgtest [11:08:15]: testbed apt version: 2.9.33 171s autopkgtest [11:08:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 171s autopkgtest [11:08:16]: testbed release detected to be: None 172s autopkgtest [11:08:17]: updating testbed package index (apt update) 172s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 173s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 173s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 173s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 173s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 173s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [410 kB] 173s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [46.2 kB] 173s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 173s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1888 B] 173s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 173s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [353 kB] 174s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.7 kB] 174s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 174s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 174s Fetched 1052 kB in 2s (620 kB/s) 175s Reading package lists... 176s + lsb_release --codename --short 176s + RELEASE=plucky 176s + cat 176s + [ plucky != trusty ] 176s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s Calculating upgrade... 177s Calculating upgrade... 177s The following packages will be upgraded: 177s python3-jinja2 strace 177s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Need to get 608 kB of archives. 177s After this operation, 11.3 kB of additional disk space will be used. 177s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 178s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 179s Fetched 608 kB in 1s (561 kB/s) 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 Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 179s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 179s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 179s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 179s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 180s Setting up strace (6.13+ds-1ubuntu1) ... 180s Processing triggers for man-db (2.13.0-1) ... 180s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 180s + /usr/lib/apt/apt-helper analyze-pattern ?true 180s + uname -r 180s + sed s/\./\\./g 180s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 180s + tail -n+2 180s + apt list ?obsolete 180s + + grep -v ^linux-.*6\.14\.0-10-generic.* 180s cut -d/ -f1 181s + obsolete_pkgs=linux-headers-6.11.0-8-generic 181s linux-headers-6.11.0-8 181s linux-image-6.11.0-8-generic 181s linux-modules-6.11.0-8-generic 181s linux-tools-6.11.0-8-generic 181s linux-tools-6.11.0-8 181s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 182s Solving dependencies... 183s The following packages will be REMOVED: 183s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 183s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 183s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 183s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 184s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 184s After this operation, 267 MB disk space will be freed. 184s (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.) 184s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 184s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 184s Removing libpython3.12t64:arm64 (3.12.9-1) ... 184s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 184s Removing libnsl2:arm64 (1.3.0-3build3) ... 184s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 184s Removing libunwind8:arm64 (1.6.2-3.1) ... 184s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 184s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 186s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 186s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 186s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 186s /etc/kernel/postrm.d/initramfs-tools: 186s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 186s /etc/kernel/postrm.d/zz-flash-kernel: 186s flash-kernel: Kernel 6.11.0-8-generic has been removed. 186s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 186s /etc/kernel/postrm.d/zz-update-grub: 186s Sourcing file `/etc/default/grub' 186s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 186s Generating grub configuration file ... 187s Found linux image: /boot/vmlinuz-6.14.0-10-generic 187s Found initrd image: /boot/initrd.img-6.14.0-10-generic 187s Warning: os-prober will not be executed to detect other bootable partitions. 187s Systems on them will not be added to the GRUB boot configuration. 187s Check GRUB_DISABLE_OS_PROBER documentation entry. 187s Adding boot menu entry for UEFI Firmware Settings ... 187s done 187s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 187s Processing triggers for libc-bin (2.41-1ubuntu1) ... 187s (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.) 187s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 188s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 188s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 188s + grep -q trusty /etc/lsb-release 188s + [ ! -d /usr/share/doc/unattended-upgrades ] 188s + [ ! -d /usr/share/doc/lxd ] 188s + [ ! -d /usr/share/doc/lxd-client ] 188s + [ ! -d /usr/share/doc/snapd ] 188s + type iptables 188s + cat 188s + chmod 755 /etc/rc.local 188s + . /etc/rc.local 188s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 188s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 188s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 188s + uname -m 188s + [ aarch64 = ppc64le ] 188s + [ -d /run/systemd/system ] 188s + systemd-detect-virt --quiet --vm 188s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 188s + cat 188s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 188s + echo COMPRESS=lz4 188s autopkgtest [11:08:33]: upgrading testbed (apt dist-upgrade and autopurge) 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 189s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 190s Entering ResolveByKeep 190s 190s Calculating upgrade... 191s The following packages will be upgraded: 191s libc-bin libc-dev-bin libc6 libc6-dev locales 191s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 9530 kB of archives. 191s After this operation, 0 B of additional disk space will be used. 191s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 193s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 193s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 197s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 197s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 203s Preconfiguring packages ... 203s Fetched 9530 kB in 11s (863 kB/s) 203s (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.) 203s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 203s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 203s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 203s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 203s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 204s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 204s Setting up libc6:arm64 (2.41-1ubuntu2) ... 204s (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.) 204s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 204s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 204s Setting up libc-bin (2.41-1ubuntu2) ... 204s (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.) 204s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 204s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 204s Setting up locales (2.41-1ubuntu2) ... 205s Generating locales (this might take a while)... 207s en_US.UTF-8... done 207s Generation complete. 207s Setting up libc-dev-bin (2.41-1ubuntu2) ... 207s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 207s Processing triggers for man-db (2.13.0-1) ... 208s Processing triggers for systemd (257.3-1ubuntu3) ... 209s Reading package lists... 209s Building dependency tree... 209s Reading state information... 210s Starting pkgProblemResolver with broken count: 0 210s Starting 2 pkgProblemResolver with broken count: 0 210s Done 210s Solving dependencies... 211s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 211s autopkgtest [11:08:56]: rebooting testbed after setup commands that affected boot 235s autopkgtest [11:09:20]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 238s autopkgtest [11:09:23]: @@@@@@@@@@@@@@@@@@@@ apt-source transtermhp 240s Get:1 http://ftpmaster.internal/ubuntu plucky/universe transtermhp 2.09-5 (dsc) [2099 B] 240s Get:2 http://ftpmaster.internal/ubuntu plucky/universe transtermhp 2.09-5 (tar) [71.3 kB] 240s Get:3 http://ftpmaster.internal/ubuntu plucky/universe transtermhp 2.09-5 (diff) [15.9 kB] 240s gpgv: Signature made Thu Aug 20 15:06:33 2020 UTC 240s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 240s gpgv: issuer "npatra974@gmail.com" 240s gpgv: Can't check signature: No public key 240s dpkg-source: warning: cannot verify inline signature for ./transtermhp_2.09-5.dsc: no acceptable signature found 240s autopkgtest [11:09:25]: testing package transtermhp version 2.09-5 241s autopkgtest [11:09:26]: build not needed 241s autopkgtest [11:09:26]: test run-unit-test: preparing testbed 241s Reading package lists... 242s Building dependency tree... 242s Reading state information... 242s Starting pkgProblemResolver with broken count: 0 242s Starting 2 pkgProblemResolver with broken count: 0 242s Done 243s The following NEW packages will be installed: 243s transtermhp 243s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 243s Need to get 121 kB of archives. 243s After this operation, 464 kB of additional disk space will be used. 243s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 transtermhp arm64 2.09-5 [121 kB] 244s Fetched 121 kB in 0s (307 kB/s) 244s Selecting previously unselected package transtermhp. 244s (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.) 244s Preparing to unpack .../transtermhp_2.09-5_arm64.deb ... 244s Unpacking transtermhp (2.09-5) ... 244s Setting up transtermhp (2.09-5) ... 244s Processing triggers for man-db (2.13.0-1) ... 246s autopkgtest [11:09:31]: test run-unit-test: [----------------------- 246s calibrate.sh 246s expterm.dat 246s infile.fasta 246s make_expterm.py 246s mfold_rna.sh 246s random_fasta.py 246s Test 1 246s TransTerm Options = 246s NOTE: warnings about 'using version 1.0 confidence' are expected and OK. 246s TransTermHP v2.08 (built on Aug 20 2020) 246s WARNING: USING VERSION 1.0 CONFIDENCE. 246s (use -p expterm.dat to use v2.0 confidence) 246s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 246s 246s --gc=-2.3 --au=-0.9 --gu=1.3 --mm=3.5 --gap=6 246s --max-len=59 --min-stem=4 --max-loop=13 --min-loop=3 246s --uwin-length=6 --uwin-require=3 --max-hp-score=-2 --max-tail-score=-2.5 246s --loop-penalty=1,2,3,4,5,6,7,8,9,10,11 246s --start-cut=0 --end-cut=25 246s 246s 246s warning: no examples in genes; can't compute conf. 246s 246s Each terminator entry starts in column 3 and is of the form: 246s term # start - end +/- regionconf hp tail | notes 246s Followed by the sequence of the 5' tail, 5' stem, loop, 3' stem, and 3' tail. 246s Genes are interspersed, and start the first column. 246s 246s 246s Wall clock time = 0 seconds. 246s calibrate.sh: Running TransTerm on random sequence with %AT = 0.26 259s WARNING: USING VERSION 1.0 CONFIDENCE. 259s (use -p expterm.dat to use v2.0 confidence) 259s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 274s Seq: random (length 20000000, 14751 genes) 274s 275s Wall clock time = 15 seconds. 275s calibrate.sh: Running TransTerm on random sequence with %AT = 0.28 288s WARNING: USING VERSION 1.0 CONFIDENCE. 288s (use -p expterm.dat to use v2.0 confidence) 288s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 306s Seq: random (length 20000000, 14726 genes) 306s 306s Wall clock time = 18 seconds. 306s calibrate.sh: Running TransTerm on random sequence with %AT = 0.30 320s WARNING: USING VERSION 1.0 CONFIDENCE. 320s (use -p expterm.dat to use v2.0 confidence) 320s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 339s Seq: random (length 20000000, 14701 genes) 339s 340s Wall clock time = 21 seconds. 340s calibrate.sh: Running TransTerm on random sequence with %AT = 0.32 353s WARNING: USING VERSION 1.0 CONFIDENCE. 353s (use -p expterm.dat to use v2.0 confidence) 353s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 375s Seq: random (length 20000000, 14789 genes) 375s 375s Wall clock time = 22 seconds. 375s calibrate.sh: Running TransTerm on random sequence with %AT = 0.34 388s WARNING: USING VERSION 1.0 CONFIDENCE. 388s (use -p expterm.dat to use v2.0 confidence) 388s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 412s Seq: random (length 20000000, 14838 genes) 412s 413s Wall clock time = 25 seconds. 413s calibrate.sh: Running TransTerm on random sequence with %AT = 0.36 426s WARNING: USING VERSION 1.0 CONFIDENCE. 426s (use -p expterm.dat to use v2.0 confidence) 426s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 451s Seq: random (length 20000000, 14802 genes) 451s 452s Wall clock time = 27 seconds. 452s calibrate.sh: Running TransTerm on random sequence with %AT = 0.38 464s WARNING: USING VERSION 1.0 CONFIDENCE. 464s (use -p expterm.dat to use v2.0 confidence) 464s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 492s Seq: random (length 20000000, 14747 genes) 492s 492s Wall clock time = 28 seconds. 492s calibrate.sh: Running TransTerm on random sequence with %AT = 0.40 506s WARNING: USING VERSION 1.0 CONFIDENCE. 506s (use -p expterm.dat to use v2.0 confidence) 506s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 534s Seq: random (length 20000000, 14721 genes) 534s 535s Wall clock time = 30 seconds. 535s calibrate.sh: Running TransTerm on random sequence with %AT = 0.42 548s WARNING: USING VERSION 1.0 CONFIDENCE. 548s (use -p expterm.dat to use v2.0 confidence) 548s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 579s Seq: random (length 20000000, 14849 genes) 579s 580s Wall clock time = 32 seconds. 580s calibrate.sh: Running TransTerm on random sequence with %AT = 0.44 592s WARNING: USING VERSION 1.0 CONFIDENCE. 592s (use -p expterm.dat to use v2.0 confidence) 592s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 625s Seq: random (length 20000000, 14772 genes) 625s 626s Wall clock time = 34 seconds. 626s calibrate.sh: Running TransTerm on random sequence with %AT = 0.46 639s WARNING: USING VERSION 1.0 CONFIDENCE. 639s (use -p expterm.dat to use v2.0 confidence) 639s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 672s Seq: random (length 20000000, 14775 genes) 672s 673s Wall clock time = 35 seconds. 673s calibrate.sh: Running TransTerm on random sequence with %AT = 0.48 686s WARNING: USING VERSION 1.0 CONFIDENCE. 686s (use -p expterm.dat to use v2.0 confidence) 686s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 721s Seq: random (length 20000000, 14812 genes) 721s 722s Wall clock time = 36 seconds. 722s calibrate.sh: Running TransTerm on random sequence with %AT = 0.50 735s WARNING: USING VERSION 1.0 CONFIDENCE. 735s (use -p expterm.dat to use v2.0 confidence) 735s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 771s Seq: random (length 20000000, 14788 genes) 771s 772s Wall clock time = 37 seconds. 772s calibrate.sh: Running TransTerm on random sequence with %AT = 0.52 785s WARNING: USING VERSION 1.0 CONFIDENCE. 785s (use -p expterm.dat to use v2.0 confidence) 785s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 823s Seq: random (length 20000000, 14801 genes) 823s 823s Wall clock time = 38 seconds. 823s calibrate.sh: Running TransTerm on random sequence with %AT = 0.54 837s WARNING: USING VERSION 1.0 CONFIDENCE. 837s (use -p expterm.dat to use v2.0 confidence) 837s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 876s Seq: random (length 20000000, 14816 genes) 876s 876s Wall clock time = 39 seconds. 876s calibrate.sh: Running TransTerm on random sequence with %AT = 0.56 890s WARNING: USING VERSION 1.0 CONFIDENCE. 890s (use -p expterm.dat to use v2.0 confidence) 890s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 930s Seq: random (length 20000000, 14709 genes) 930s 930s Wall clock time = 40 seconds. 930s calibrate.sh: Running TransTerm on random sequence with %AT = 0.58 943s WARNING: USING VERSION 1.0 CONFIDENCE. 943s (use -p expterm.dat to use v2.0 confidence) 943s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 984s Seq: random (length 20000000, 14855 genes) 984s 985s Wall clock time = 42 seconds. 985s calibrate.sh: Running TransTerm on random sequence with %AT = 0.60 998s WARNING: USING VERSION 1.0 CONFIDENCE. 998s (use -p expterm.dat to use v2.0 confidence) 998s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1039s Seq: random (length 20000000, 14828 genes) 1039s 1040s Wall clock time = 42 seconds. 1040s calibrate.sh: Running TransTerm on random sequence with %AT = 0.62 1053s WARNING: USING VERSION 1.0 CONFIDENCE. 1053s (use -p expterm.dat to use v2.0 confidence) 1053s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1095s Seq: random (length 20000000, 14777 genes) 1095s 1096s Wall clock time = 43 seconds. 1096s calibrate.sh: Running TransTerm on random sequence with %AT = 0.64 1109s WARNING: USING VERSION 1.0 CONFIDENCE. 1109s (use -p expterm.dat to use v2.0 confidence) 1109s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1152s Seq: random (length 20000000, 14804 genes) 1152s 1153s Wall clock time = 43 seconds. 1153s calibrate.sh: Running TransTerm on random sequence with %AT = 0.66 1166s WARNING: USING VERSION 1.0 CONFIDENCE. 1166s (use -p expterm.dat to use v2.0 confidence) 1166s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1209s Seq: random (length 20000000, 14786 genes) 1209s 1210s Wall clock time = 44 seconds. 1210s calibrate.sh: Running TransTerm on random sequence with %AT = 0.68 1223s WARNING: USING VERSION 1.0 CONFIDENCE. 1223s (use -p expterm.dat to use v2.0 confidence) 1223s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1267s Seq: random (length 20000000, 14761 genes) 1267s 1268s Wall clock time = 45 seconds. 1268s calibrate.sh: Running TransTerm on random sequence with %AT = 0.70 1281s WARNING: USING VERSION 1.0 CONFIDENCE. 1281s (use -p expterm.dat to use v2.0 confidence) 1281s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1326s Seq: random (length 20000000, 14706 genes) 1326s 1326s Wall clock time = 45 seconds. 1326s calibrate.sh: Running TransTerm on random sequence with %AT = 0.72 1339s WARNING: USING VERSION 1.0 CONFIDENCE. 1339s (use -p expterm.dat to use v2.0 confidence) 1339s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1385s Seq: random (length 20000000, 14764 genes) 1385s 1385s Wall clock time = 46 seconds. 1385s calibrate.sh: Running TransTerm on random sequence with %AT = 0.74 1399s WARNING: USING VERSION 1.0 CONFIDENCE. 1399s (use -p expterm.dat to use v2.0 confidence) 1399s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1445s Seq: random (length 20000000, 14793 genes) 1445s 1445s Wall clock time = 46 seconds. 1445s calibrate.sh: Running TransTerm on random sequence with %AT = 0.76 1459s WARNING: USING VERSION 1.0 CONFIDENCE. 1459s (use -p expterm.dat to use v2.0 confidence) 1459s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1505s Seq: random (length 20000000, 14772 genes) 1505s 1506s Wall clock time = 47 seconds. 1506s calibrate.sh: Running TransTerm on random sequence with %AT = 0.78 1520s WARNING: USING VERSION 1.0 CONFIDENCE. 1520s (use -p expterm.dat to use v2.0 confidence) 1520s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1566s Seq: random (length 20000000, 14710 genes) 1566s 1567s Wall clock time = 47 seconds. 1567s calibrate.sh: Running TransTerm on random sequence with %AT = 0.80 1581s WARNING: USING VERSION 1.0 CONFIDENCE. 1581s (use -p expterm.dat to use v2.0 confidence) 1581s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1628s Seq: random (length 20000000, 14781 genes) 1628s 1629s Wall clock time = 48 seconds. 1629s calibrate.sh: Running TransTerm on random sequence with %AT = 0.82 1642s WARNING: USING VERSION 1.0 CONFIDENCE. 1642s (use -p expterm.dat to use v2.0 confidence) 1642s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1689s Seq: random (length 20000000, 14839 genes) 1689s 1690s Wall clock time = 48 seconds. 1690s calibrate.sh: Running TransTerm on random sequence with %AT = 0.84 1703s WARNING: USING VERSION 1.0 CONFIDENCE. 1703s (use -p expterm.dat to use v2.0 confidence) 1703s Version 1 confidence scheme exists only for debugging andhistorical reasons. Use the updated scoring system. 1751s Seq: random (length 20000000, 14783 genes) 1751s 1752s Wall clock time = 49 seconds. 1752s Creating distribution file in expterm.dat 1754s You must specify a background distribution file with '-p expterm.dat'. 1754s Done. You can run transterm with this background distribution using '-r expterm.dat' 1754s PASS 1754s Test 2 1754s 2ndscore (Aug 20 2020) 1754s 1754s --gc=-2.1 --au=-1.3 --gu=-0.8 --mm=3.5 --gap=3.9 1754s --max-len=59 --max-loop=13 --min-loop=3 1754s --loop-penalty=4.1,4.9,4.4,4.7,5,5.1,5.2,5.3,5.4,5.5,5.6 1754s 1754s 1. Seq: 9258 (length 34) 1754s 2. Seq: 9361 (length 611) 1754s 3. Seq: 9365 (length 796) 1754s 4. Seq: 9371 (length 762) 1754s 5. Seq: 9544 (length 810) 1754s 6. Seq: 9598 (length 797) 1754s 7. Seq: 9606 (length 797) 1754s 8. Seq: 9615 (length 802) 1754s 9. Seq: 9685 (length 687) 1754s 10. Seq: 9785 (length 793) 1754s 11. Seq: 9796 (length 806) 1754s 12. Seq: 9913 (length 798) 1754s 13. Seq: 9986 (length 789) 1754s 14. Seq: 10090 (length 770) 1754s 15. Seq: 10116 (length 832) 1754s 16. Seq: 10141 (length 327) 1754s 17. Seq: 13616 (length 884) 1754s PASS 1754s 18. Seq: 28377 (length 87) 1754s 19. Seq: 42254 (length 372) 1754s autopkgtest [11:34:39]: test run-unit-test: -----------------------] 1755s autopkgtest [11:34:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1755s run-unit-test PASS 1755s autopkgtest [11:34:40]: @@@@@@@@@@@@@@@@@@@@ summary 1755s run-unit-test PASS 1772s nova [W] Using flock in prodstack6-arm64 1772s flock: timeout while waiting to get lock 1772s Creating nova instance adt-plucky-arm64-transtermhp-20250315-110525-juju-7f2275-prod-proposed-migration-environment-15-f1bb5486-98e3-40f3-9010-1a685bf7cfac from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 1772s nova [W] Timed out waiting for 563b35e0-4f10-4a5c-b3e6-c93ccad62d45 to get deleted.