0s autopkgtest [16:58:14]: starting date and time: 2025-03-15 16:58:14+0000 0s autopkgtest [16:58:14]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:58:14]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yq3hgitz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade stringtie --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-arm64-42.secgroup --name adt-plucky-arm64-stringtie-20250315-165813-juju-7f2275-prod-proposed-migration-environment-15-2b9d3ac0-70e0-43a1-b323-24edfb69afef --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/ 193s autopkgtest [17:01:27]: testbed dpkg architecture: arm64 193s autopkgtest [17:01:27]: testbed apt version: 2.9.33 193s autopkgtest [17:01:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 194s autopkgtest [17:01:28]: testbed release detected to be: None 194s autopkgtest [17:01:28]: updating testbed package index (apt update) 195s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 195s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 195s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 195s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 195s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 196s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 196s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 196s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 196s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 196s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 196s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 196s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 196s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 196s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 197s Fetched 1078 kB in 2s (603 kB/s) 197s Reading package lists... 198s + lsb_release --codename --short 198s + RELEASE=plucky 198s + cat 198s + [ plucky != trusty ] 198s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 199s Calculating upgrade... 199s Calculating upgrade... 200s The following packages will be upgraded: 200s pinentry-curses python3-jinja2 strace 200s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 200s Need to get 647 kB of archives. 200s After this operation, 11.3 kB of additional disk space will be used. 200s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 201s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 201s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 201s Fetched 647 kB in 1s (595 kB/s) 202s (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.) 202s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 202s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 202s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 202s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 202s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 202s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 202s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 202s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 202s Setting up strace (6.13+ds-1ubuntu1) ... 202s Processing triggers for man-db (2.13.0-1) ... 203s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 203s + /usr/lib/apt/apt-helper analyze-pattern ?true 203s + uname -r 203s + sed s/\./\\./g 203s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 203s + apt list ?obsolete 203s + tail -n+2 203s + cut -d/ -f1 203s + grep -v ^linux-.*6\.14\.0-10-generic.* 203s + obsolete_pkgs=linux-headers-6.11.0-8-generic 203s linux-headers-6.11.0-8 203s linux-image-6.11.0-8-generic 203s linux-modules-6.11.0-8-generic 203s linux-tools-6.11.0-8-generic 203s linux-tools-6.11.0-8 203s + 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 203s Reading package lists... 203s Building dependency tree... 203s Reading state information... 204s Solving dependencies... 204s The following packages will be REMOVED: 204s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 204s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 204s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 204s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 205s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 205s After this operation, 267 MB disk space will be freed. 205s (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.) 205s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 205s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 205s Removing libpython3.12t64:arm64 (3.12.9-1) ... 205s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 205s Removing libnsl2:arm64 (1.3.0-3build3) ... 205s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 205s Removing libunwind8:arm64 (1.6.2-3.1) ... 205s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 205s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 207s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 207s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 207s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 207s /etc/kernel/postrm.d/initramfs-tools: 207s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 207s /etc/kernel/postrm.d/zz-flash-kernel: 207s flash-kernel: Kernel 6.11.0-8-generic has been removed. 207s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 207s /etc/kernel/postrm.d/zz-update-grub: 207s Sourcing file `/etc/default/grub' 207s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 207s Generating grub configuration file ... 208s Found linux image: /boot/vmlinuz-6.14.0-10-generic 208s Found initrd image: /boot/initrd.img-6.14.0-10-generic 208s Warning: os-prober will not be executed to detect other bootable partitions. 208s Systems on them will not be added to the GRUB boot configuration. 208s Check GRUB_DISABLE_OS_PROBER documentation entry. 208s Adding boot menu entry for UEFI Firmware Settings ... 208s done 208s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 208s Processing triggers for libc-bin (2.41-1ubuntu1) ... 208s (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.) 208s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 208s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 208s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 209s + grep -q trusty /etc/lsb-release 209s + [ ! -d /usr/share/doc/unattended-upgrades ] 209s + [ ! -d /usr/share/doc/lxd ] 209s + [ ! -d /usr/share/doc/lxd-client ] 209s + [ ! -d /usr/share/doc/snapd ] 209s + type iptables 209s + cat 209s + chmod 755 /etc/rc.local 209s + . /etc/rc.local 209s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 209s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 209s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 209s + uname -m 209s + [ aarch64 = ppc64le ] 209s + [ -d /run/systemd/system ] 209s + systemd-detect-virt --quiet --vm 209s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 209s + cat 209s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 209s + echo COMPRESS=lz4 209s autopkgtest [17:01:43]: upgrading testbed (apt dist-upgrade and autopurge) 209s Reading package lists... 209s Building dependency tree... 209s Reading state information... 210s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 210s Starting 2 pkgProblemResolver with broken count: 0 210s Done 210s Entering ResolveByKeep 211s 211s Calculating upgrade... 211s The following packages will be upgraded: 211s libc-bin libc-dev-bin libc6 libc6-dev locales 211s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 211s Need to get 9530 kB of archives. 211s After this operation, 0 B of additional disk space will be used. 211s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 214s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 214s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 218s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 219s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 225s Preconfiguring packages ... 225s Fetched 9530 kB in 14s (699 kB/s) 225s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 225s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 225s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 226s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 226s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 226s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 226s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 226s Setting up libc6:arm64 (2.41-1ubuntu2) ... 226s (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.) 226s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 226s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 226s Setting up libc-bin (2.41-1ubuntu2) ... 226s (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.) 226s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 226s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 227s Setting up locales (2.41-1ubuntu2) ... 227s Generating locales (this might take a while)... 229s en_US.UTF-8... done 229s Generation complete. 229s Setting up libc-dev-bin (2.41-1ubuntu2) ... 229s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 229s Processing triggers for man-db (2.13.0-1) ... 230s Processing triggers for systemd (257.3-1ubuntu3) ... 231s Reading package lists... 231s Building dependency tree... 231s Reading state information... 232s Starting pkgProblemResolver with broken count: 0 232s Starting 2 pkgProblemResolver with broken count: 0 232s Done 232s Solving dependencies... 233s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 233s autopkgtest [17:02:07]: rebooting testbed after setup commands that affected boot 255s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 262s autopkgtest [17:02:36]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 265s autopkgtest [17:02:39]: @@@@@@@@@@@@@@@@@@@@ apt-source stringtie 269s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stringtie 2.2.1+ds-3build2 (dsc) [2469 B] 269s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stringtie 2.2.1+ds-3build2 (tar) [1756 kB] 269s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stringtie 2.2.1+ds-3build2 (tar) [295 kB] 269s Get:4 http://ftpmaster.internal/ubuntu plucky/universe stringtie 2.2.1+ds-3build2 (diff) [12.0 kB] 270s gpgv: Signature made Mon Apr 1 08:20:58 2024 UTC 270s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 270s gpgv: Can't check signature: No public key 270s dpkg-source: warning: cannot verify inline signature for ./stringtie_2.2.1+ds-3build2.dsc: no acceptable signature found 270s autopkgtest [17:02:44]: testing package stringtie version 2.2.1+ds-3build2 270s autopkgtest [17:02:44]: build not needed 272s autopkgtest [17:02:46]: test run-unit-test: preparing testbed 272s Reading package lists... 272s Building dependency tree... 272s Reading state information... 273s Starting pkgProblemResolver with broken count: 0 273s Starting 2 pkgProblemResolver with broken count: 0 273s Done 273s The following NEW packages will be installed: 273s libdeflate0 libhts3t64 libhtscodecs2 samtools stringtie 274s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 274s Need to get 1469 kB of archives. 274s After this operation, 4023 kB of additional disk space will be used. 274s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 274s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 274s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 274s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.21-1 [609 kB] 275s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 stringtie arm64 2.2.1+ds-3build2 [290 kB] 276s Fetched 1469 kB in 2s (823 kB/s) 276s Selecting previously unselected package libdeflate0:arm64. 276s (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.) 276s Preparing to unpack .../libdeflate0_1.23-1_arm64.deb ... 276s Unpacking libdeflate0:arm64 (1.23-1) ... 276s Selecting previously unselected package libhtscodecs2:arm64. 276s Preparing to unpack .../libhtscodecs2_1.6.1-2_arm64.deb ... 276s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 276s Selecting previously unselected package libhts3t64:arm64. 276s Preparing to unpack .../libhts3t64_1.21+ds-1_arm64.deb ... 276s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 276s Selecting previously unselected package samtools. 276s Preparing to unpack .../samtools_1.21-1_arm64.deb ... 276s Unpacking samtools (1.21-1) ... 276s Selecting previously unselected package stringtie. 276s Preparing to unpack .../stringtie_2.2.1+ds-3build2_arm64.deb ... 276s Unpacking stringtie (2.2.1+ds-3build2) ... 276s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 276s Setting up libdeflate0:arm64 (1.23-1) ... 276s Setting up libhts3t64:arm64 (1.21+ds-1) ... 276s Setting up samtools (1.21-1) ... 276s Setting up stringtie (2.2.1+ds-3build2) ... 276s Processing triggers for man-db (2.13.0-1) ... 277s Processing triggers for libc-bin (2.41-1ubuntu2) ... 278s autopkgtest [17:02:52]: test run-unit-test: [----------------------- 279s + pkg=stringtie 279s ++ pwd 279s + CUR_DIR=/tmp/autopkgtest.x4AFI6/build.d2s/src 279s + '[' /tmp/autopkgtest.x4AFI6/autopkgtest_tmp = '' ']' 279s + cp /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/README.md /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/human-chr19_P.gff /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/long_reads.out_expected.gtf /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/long_reads.sam /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/long_reads_guided.out_expected.gtf /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/mix_guides.gff /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/mix_long.sam /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/mix_reads.out_expected.gtf /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/mix_reads_guided.out_expected.gtf /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/mix_short.sam /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/short_reads.out_expected.gtf /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/short_reads.sam /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/short_reads_and_superreads.out_expected.gtf /tmp/autopkgtest.x4AFI6/build.d2s/src/debian-tests-data/short_reads_and_superreads.sam -a /tmp/autopkgtest.x4AFI6/autopkgtest_tmp 279s + cd /tmp/autopkgtest.x4AFI6/autopkgtest_tmp 279s + gunzip -r README.md human-chr19_P.gff long_reads.out_expected.gtf long_reads.sam long_reads_guided.out_expected.gtf mix_guides.gff mix_long.sam mix_reads.out_expected.gtf mix_reads_guided.out_expected.gtf mix_short.sam short_reads.out_expected.gtf short_reads.sam short_reads_and_superreads.out_expected.gtf short_reads_and_superreads.sam 279s + for f in *.sam 279s + outfile=long_reads.bam 279s + cat long_reads.sam 279s + samtools view -Sb - 279s + for f in *.sam 279s + outfile=mix_long.bam 279s + cat mix_long.sam 279s + samtools view -Sb - 279s + for f in *.sam 279s + outfile=mix_short.bam 279s + cat mix_short.sam 279s + samtools view -Sb - 279s + for f in *.sam 279s + outfile=short_reads.bam 279s + cat short_reads.sam 279s + samtools view -Sb - 279s + for f in *.sam 279s + outfile=short_reads_and_superreads.bam 279s + cat short_reads_and_superreads.sam 279s + samtools view -Sb - 279s + arrins=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads" "mix_short mix_long" "mix_short mix_long") 279s + arrparms=("" "" "-L" "-L -G human-chr19_P.gff" "--mix" "--mix -G mix_guides.gff") 279s + arrout=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads_guided" "mix_reads" "mix_reads_guided") 279s + arrmsg=("Short reads" "Short reads and super-reads" "Long reads" "Long reads with annotation guides" "Mixed reads" "Mixed reads with annotation guides") 279s + for i in ${!arrmsg[@]} 279s + fout=short_reads.out.gtf 279s + /bin/rm -f short_reads.out.gtf 279s 0 279s Test 1: Short reads 279s + fcmp=short_reads.out_expected.gtf 279s + n=0 279s + echo 0 279s + n=1 279s + echo 'Test 1: Short reads' 279s + fin=short_reads.bam 279s + [[ short_reads =~ ^mix ]] 279s + echo short_reads.out.gtf short_reads.bam 279s + stringtie -o short_reads.out.gtf short_reads.bam 279s short_reads.out.gtf short_reads.bam 279s + '[' '!' -f short_reads.out.gtf ']' 279s OK. 279s + diff -q -I '^#' short_reads.out.gtf short_reads.out_expected.gtf 279s + echo ' OK.' 279s + for i in ${!arrmsg[@]} 279s + fout=short_reads_and_superreads.out.gtf 279s + /bin/rm -f short_reads_and_superreads.out.gtf 279s 1 279s + fcmp=short_reads_and_superreads.out_expected.gtf 279s + n=1 279s + echo 1 279s + n=2 279s Test 2: Short reads and super-reads 279s short_reads_and_superreads.out.gtf short_reads_and_superreads.bam 279s + echo 'Test 2: Short reads and super-reads' 279s + fin=short_reads_and_superreads.bam 279s + [[ short_reads_and_superreads =~ ^mix ]] 279s + echo short_reads_and_superreads.out.gtf short_reads_and_superreads.bam 279s + stringtie -o short_reads_and_superreads.out.gtf short_reads_and_superreads.bam 279s + '[' '!' -f short_reads_and_superreads.out.gtf ']' 279s + diff -q -I '^#' short_reads_and_superreads.out.gtf short_reads_and_superreads.out_expected.gtf 279s OK. 279s + echo ' OK.' 279s + for i in ${!arrmsg[@]} 279s + fout=long_reads.out.gtf 279s + /bin/rm -f long_reads.out.gtf 279s 2 279s Test 3: Long reads 279s -L long_reads.out.gtf long_reads.bam 279s + fcmp=long_reads.out_expected.gtf 279s + n=2 279s + echo 2 279s + n=3 279s + echo 'Test 3: Long reads' 279s + fin=long_reads.bam 279s + [[ long_reads =~ ^mix ]] 279s + echo -L long_reads.out.gtf long_reads.bam 279s + stringtie -L -o long_reads.out.gtf long_reads.bam 279s + '[' '!' -f long_reads.out.gtf ']' 279s + diff -q -I '^#' long_reads.out.gtf long_reads.out_expected.gtf 279s OK. 279s + echo ' OK.' 279s + for i in ${!arrmsg[@]} 279s + fout=long_reads_guided.out.gtf 279s + /bin/rm -f long_reads_guided.out.gtf 279s 3 279s Test 4: Long reads with annotation guides 279s + fcmp=long_reads_guided.out_expected.gtf 279s + n=3 279s + echo 3 279s + n=4 279s + echo 'Test 4: Long reads with annotation guides' 279s + fin=long_reads.bam 279s + [[ long_reads =~ ^mix ]] 279s + echo -L -G human-chr19_P.gff long_reads_guided.out.gtf long_reads.bam 279s + stringtie -L -G human-chr19_P.gff -o long_reads_guided.out.gtf long_reads.bam 279s -L -G human-chr19_P.gff long_reads_guided.out.gtf long_reads.bam 279s + '[' '!' -f long_reads_guided.out.gtf ']' 279s + diff -q -I '^#' long_reads_guided.out.gtf long_reads_guided.out_expected.gtf 279s OK. 279s + echo ' OK.' 279s + for i in ${!arrmsg[@]} 279s + fout=mix_reads.out.gtf 279s + /bin/rm -f mix_reads.out.gtf 279s + fcmp=mix_reads.out_expected.gtf 279s 4 279s + n=4 279s + echo 4 279s + n=5 279s + echo 'Test 5: Mixed reads' 279s Test 5: Mixed reads 279s + fin='mix_short mix_long.bam' 279s + [[ mix_short mix_long =~ ^mix ]] 279s + ins=(${arrins[$i]}) 279s + fin='mix_short.bam mix_long.bam' 279s --mix mix_reads.out.gtf mix_short.bam mix_long.bam 279s + echo --mix mix_reads.out.gtf mix_short.bam mix_long.bam 279s + stringtie --mix -o mix_reads.out.gtf mix_short.bam mix_long.bam 279s OK. 279s + '[' '!' -f mix_reads.out.gtf ']' 279s + diff -q -I '^#' mix_reads.out.gtf mix_reads.out_expected.gtf 279s + echo ' OK.' 279s + for i in ${!arrmsg[@]} 279s + fout=mix_reads_guided.out.gtf 279s + /bin/rm -f mix_reads_guided.out.gtf 279s + fcmp=mix_reads_guided.out_expected.gtf 279s + n=5 279s + echo 5 279s + n=6 279s + echo 'Test 6: Mixed reads with annotation guides' 279s 5 279s Test 6: Mixed reads with annotation guides 279s --mix -G mix_guides.gff mix_reads_guided.out.gtf mix_short.bam mix_long.bam 279s + fin='mix_short mix_long.bam' 279s + [[ mix_short mix_long =~ ^mix ]] 279s + ins=(${arrins[$i]}) 279s + fin='mix_short.bam mix_long.bam' 279s + echo --mix -G mix_guides.gff mix_reads_guided.out.gtf mix_short.bam mix_long.bam 279s + stringtie --mix -G mix_guides.gff -o mix_reads_guided.out.gtf mix_short.bam mix_long.bam 279s + '[' '!' -f mix_reads_guided.out.gtf ']' 279s + diff -q -I '^#' mix_reads_guided.out.gtf mix_reads_guided.out_expected.gtf 279s OK. 279s + echo ' OK.' 279s autopkgtest [17:02:53]: test run-unit-test: -----------------------] 280s autopkgtest [17:02:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 280s run-unit-test PASS 280s autopkgtest [17:02:54]: @@@@@@@@@@@@@@@@@@@@ summary 280s run-unit-test PASS 298s nova [W] Using flock in prodstack6-arm64 298s Creating nova instance adt-plucky-arm64-stringtie-20250315-165813-juju-7f2275-prod-proposed-migration-environment-15-2b9d3ac0-70e0-43a1-b323-24edfb69afef from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 298s nova [W] Timed out waiting for 7e4d0e3f-5010-4f1d-ab87-a4042f1bddac to get deleted.