0s autopkgtest [01:26:59]: starting date and time: 2025-03-16 01:26:59+0000 0s autopkgtest [01:26:59]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:26:59]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hqbivp_d/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scikit-learn --apt-upgrade macs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-8 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-39.secgroup --name adt-plucky-arm64-macs-20250316-012659-juju-7f2275-prod-proposed-migration-environment-15-74327ca1-b9e6-4f1c-b61d-0fe204b5b8a5 --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/ 167s autopkgtest [01:29:46]: testbed dpkg architecture: arm64 168s autopkgtest [01:29:47]: testbed apt version: 2.9.33 168s autopkgtest [01:29:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 168s autopkgtest [01:29:47]: testbed release detected to be: None 169s autopkgtest [01:29:48]: 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 [17.7 kB] 170s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 170s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 171s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [72.2 kB] 171s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1816 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 [316 kB] 171s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [13.9 kB] 171s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [16.8 kB] 171s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 171s Fetched 972 kB in 2s (596 kB/s) 173s Reading package lists... 173s + lsb_release --codename --short 173s + RELEASE=plucky 173s + cat 173s + [ plucky != trusty ] 173s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 176s Calculating upgrade... 176s Calculating upgrade... 177s The following packages will be upgraded: 177s pinentry-curses python3-jinja2 strace 177s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Need to get 647 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 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 178s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 179s Fetched 647 kB in 1s (672 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 .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 179s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 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 pinentry-curses (1.3.1-2ubuntu3) ... 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 + + sed s/\./\\./g 180s uname -r 180s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 181s + apt list ?obsolete 181s + tail -n+2 181s + cut -d/ -f1 181s + grep -v ^linux-.*6\.14\.0-10-generic.* 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... 182s Building dependency tree... 182s Reading state information... 183s Solving dependencies... 184s The following packages will be REMOVED: 184s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 184s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 184s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 184s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 184s 0 upgraded, 0 newly installed, 11 to remove and 0 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) ... 185s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 185s Removing libpython3.12t64:arm64 (3.12.9-1) ... 185s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 185s Removing libnsl2:arm64 (1.3.0-3build3) ... 185s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 185s Removing libunwind8:arm64 (1.6.2-3.1) ... 185s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 185s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 187s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 187s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 187s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 187s /etc/kernel/postrm.d/initramfs-tools: 187s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 188s /etc/kernel/postrm.d/zz-flash-kernel: 188s flash-kernel: Kernel 6.11.0-8-generic has been removed. 188s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 188s /etc/kernel/postrm.d/zz-update-grub: 188s Sourcing file `/etc/default/grub' 188s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 188s Generating grub configuration file ... 188s Found linux image: /boot/vmlinuz-6.14.0-10-generic 188s Found initrd image: /boot/initrd.img-6.14.0-10-generic 189s Warning: os-prober will not be executed to detect other bootable partitions. 189s Systems on them will not be added to the GRUB boot configuration. 189s Check GRUB_DISABLE_OS_PROBER documentation entry. 189s Adding boot menu entry for UEFI Firmware Settings ... 189s done 189s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 189s Processing triggers for libc-bin (2.41-1ubuntu1) ... 189s (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.) 189s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 189s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 190s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 190s + grep -q trusty /etc/lsb-release 190s + [ ! -d /usr/share/doc/unattended-upgrades ] 190s + [ ! -d /usr/share/doc/lxd ] 190s + [ ! -d /usr/share/doc/lxd-client ] 190s + [ ! -d /usr/share/doc/snapd ] 190s + type iptables 190s + cat 190s + chmod 755 /etc/rc.local 190s + . /etc/rc.local 190s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 190s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 190s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 190s + uname -m 190s + [ aarch64 = ppc64le ] 190s + [ -d /run/systemd/system ] 190s + systemd-detect-virt --quiet --vm 190s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 190s + cat 190s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 190s + echo COMPRESS=lz4 190s autopkgtest [01:30:09]: upgrading testbed (apt dist-upgrade and autopurge) 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 191s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 191s Starting 2 pkgProblemResolver with broken count: 0 191s Done 192s Entering ResolveByKeep 192s 193s Calculating upgrade... 193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s Reading package lists... 194s Building dependency tree... 194s Reading state information... 194s Starting pkgProblemResolver with broken count: 0 194s Starting 2 pkgProblemResolver with broken count: 0 194s Done 195s Solving dependencies... 195s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 195s autopkgtest [01:30:14]: rebooting testbed after setup commands that affected boot 220s autopkgtest [01:30:39]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 223s autopkgtest [01:30:42]: @@@@@@@@@@@@@@@@@@@@ apt-source macs 385s Get:1 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1build3 (dsc) [2176 B] 385s Get:2 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1build3 (tar) [197 MB] 385s Get:3 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1build3 (diff) [1268 kB] 385s gpgv: Signature made Tue Mar 4 15:51:08 2025 UTC 385s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 385s gpgv: Can't check signature: No public key 385s dpkg-source: warning: cannot verify inline signature for ./macs_3.0.2-1build3.dsc: no acceptable signature found 389s autopkgtest [01:33:28]: testing package macs version 3.0.2-1build3 390s autopkgtest [01:33:29]: build not needed 413s autopkgtest [01:33:52]: test run-unit-test: preparing testbed 414s Reading package lists... 414s Building dependency tree... 414s Reading state information... 414s Starting pkgProblemResolver with broken count: 0 415s Starting 2 pkgProblemResolver with broken count: 0 415s Done 415s The following NEW packages will be installed: 415s libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs python3-cykhash 415s python3-decorator python3-hmmlearn python3-joblib python3-numpy 415s python3-numpy-dev python3-scipy python3-sklearn python3-sklearn-lib 415s python3-threadpoolctl 415s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 415s Need to get 34.2 MB of archives. 415s After this operation, 146 MB of additional disk space will be used. 415s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 416s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 416s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 416s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 418s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 420s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 420s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 420s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cykhash arm64 2.0.0-3build3 [487 kB] 421s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 421s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 431s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.4.2-3 [205 kB] 431s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 431s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [4109 kB] 434s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 436s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hmmlearn arm64 0.3.2-2build2 [120 kB] 436s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 macs arm64 3.0.2-1build3 [3128 kB] 439s Fetched 34.2 MB in 23s (1463 kB/s) 439s Selecting previously unselected package python3-numpy-dev:arm64. 439s (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.) 439s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 439s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 439s Selecting previously unselected package libblas3:arm64. 439s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 439s Unpacking libblas3:arm64 (3.12.1-2) ... 439s Selecting previously unselected package libgfortran5:arm64. 440s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 440s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 440s Selecting previously unselected package liblapack3:arm64. 440s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 440s Unpacking liblapack3:arm64 (3.12.1-2) ... 440s Selecting previously unselected package python3-numpy. 440s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 440s Unpacking python3-numpy (1:2.2.3+ds-5) ... 440s Selecting previously unselected package libgomp1:arm64. 440s Preparing to unpack .../05-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 440s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 440s Selecting previously unselected package liblbfgsb0:arm64. 440s Preparing to unpack .../06-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 440s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 440s Selecting previously unselected package python3-cykhash. 440s Preparing to unpack .../07-python3-cykhash_2.0.0-3build3_arm64.deb ... 440s Unpacking python3-cykhash (2.0.0-3build3) ... 440s Selecting previously unselected package python3-decorator. 440s Preparing to unpack .../08-python3-decorator_5.1.1-5_all.deb ... 440s Unpacking python3-decorator (5.1.1-5) ... 440s Selecting previously unselected package python3-scipy. 440s Preparing to unpack .../09-python3-scipy_1.14.1-4ubuntu2_arm64.deb ... 440s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 440s Selecting previously unselected package python3-joblib. 440s Preparing to unpack .../10-python3-joblib_1.4.2-3_all.deb ... 440s Unpacking python3-joblib (1.4.2-3) ... 440s Selecting previously unselected package python3-threadpoolctl. 441s Preparing to unpack .../11-python3-threadpoolctl_3.1.0-1_all.deb ... 441s Unpacking python3-threadpoolctl (3.1.0-1) ... 441s Selecting previously unselected package python3-sklearn-lib:arm64. 441s Preparing to unpack .../12-python3-sklearn-lib_1.4.2+dfsg-8_arm64.deb ... 441s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 441s Selecting previously unselected package python3-sklearn. 441s Preparing to unpack .../13-python3-sklearn_1.4.2+dfsg-8_all.deb ... 441s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 441s Selecting previously unselected package python3-hmmlearn. 441s Preparing to unpack .../14-python3-hmmlearn_0.3.2-2build2_arm64.deb ... 441s Unpacking python3-hmmlearn (0.3.2-2build2) ... 441s Selecting previously unselected package macs. 441s Preparing to unpack .../15-macs_3.0.2-1build3_arm64.deb ... 441s Unpacking macs (3.0.2-1build3) ... 441s Setting up python3-joblib (1.4.2-3) ... 441s Setting up python3-threadpoolctl (3.1.0-1) ... 441s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 441s Setting up python3-cykhash (2.0.0-3build3) ... 442s Setting up python3-decorator (5.1.1-5) ... 442s Setting up libblas3:arm64 (3.12.1-2) ... 442s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 442s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 442s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 442s Setting up liblapack3:arm64 (3.12.1-2) ... 442s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 442s Setting up python3-numpy (1:2.2.3+ds-5) ... 444s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 444s Setting up python3-scipy (1.14.1-4ubuntu2) ... 447s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 447s Setting up python3-sklearn (1.4.2+dfsg-8) ... 449s Setting up python3-hmmlearn (0.3.2-2build2) ... 449s Setting up macs (3.0.2-1build3) ... 450s Processing triggers for man-db (2.13.0-1) ... 450s Processing triggers for libc-bin (2.41-1ubuntu1) ... 451s autopkgtest [01:34:30]: test run-unit-test: [----------------------- 452s + pkg=macs 452s + '[' /tmp/autopkgtest.2puIJU/autopkgtest_tmp = '' ']' 452s + cp -a /usr/share/doc/macs/examples/aluY.chr1.bed.gz /usr/share/doc/macs/examples/gerp.chr1.bed.gz /tmp/autopkgtest.2puIJU/autopkgtest_tmp 452s + cd /tmp/autopkgtest.2puIJU/autopkgtest_tmp 452s + gunzip aluY.chr1.bed.gz gerp.chr1.bed.gz 452s + macs3 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 452s INFO @ 16 Mar 2025 01:34:31: [30 MB] 452s # Command line: callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 452s # ARGUMENTS LIST: 452s # name = test 452s # format = AUTO 452s # ChIP-seq file = ['aluY.chr1.bed'] 452s # control file = None 452s # effective genome size = 2.91e+09 452s # band width = 300 452s # model fold = [5, 50] 452s # qvalue cutoff = 1.00e-02 452s # The maximum gap between significant sites is assigned as the read length/tag size. 452s # The minimum length of peaks is assigned as the predicted fragment length "d". 452s # Larger dataset will be scaled towards smaller dataset. 452s # Range for calculating regional lambda is: 10000 bps 452s # Broad region calling is off 452s # Paired-End mode is off 452s 452s INFO @ 16 Mar 2025 01:34:31: [30 MB] #1 read tag files... 452s INFO @ 16 Mar 2025 01:34:31: [30 MB] #1 read treatment tags... 452s INFO @ 16 Mar 2025 01:34:31: [31 MB] Detected format is: BED 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #1 tag size is determined as 294 bps 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #1 tag size = 294.0 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #1 total tags in treatment: 11628 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #1 user defined the maximum tags... 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #1 tags after filtering in treatment: 11628 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #1 Redundant rate of treatment: 0.00 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #1 finished! 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #2 Build Peak Model... 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #2 Skipped... 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #2 Use 200 as fragment length 452s INFO @ 16 Mar 2025 01:34:31: [32 MB] #3 Call peaks... 452s INFO @ 16 Mar 2025 01:34:31: [33 MB] #3 Pre-compute pvalue-qvalue table... 452s INFO @ 16 Mar 2025 01:34:31: [35 MB] #3 In the peak calling step, the following will be performed simultaneously: 452s INFO @ 16 Mar 2025 01:34:31: [35 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... test_treat_pileup.bdg 452s INFO @ 16 Mar 2025 01:34:31: [35 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... test_control_lambda.bdg 452s INFO @ 16 Mar 2025 01:34:31: [35 MB] #3 Pileup will be based on sequencing depth in treatment. 452s INFO @ 16 Mar 2025 01:34:31: [35 MB] #3 Call peaks for each chromosome... 452s INFO @ 16 Mar 2025 01:34:31: [35 MB] #4 Write output xls file... test_peaks.xls 452s INFO @ 16 Mar 2025 01:34:31: [35 MB] #4 Write peak in narrowPeak format file... test_peaks.narrowPeak 452s INFO @ 16 Mar 2025 01:34:31: [35 MB] #4 Write summits bed file... test_summits.bed 452s INFO @ 16 Mar 2025 01:34:31: [35 MB] Done! 452s + macs3 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 452s INFO @ 16 Mar 2025 01:34:31: [30 MB] 452s # Command line: callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 452s # ARGUMENTS LIST: 452s # name = NA 452s # format = AUTO 452s # ChIP-seq file = ['gerp.chr1.bed'] 452s # control file = None 452s # effective genome size = 2.91e+09 452s # band width = 300 452s # model fold = [5, 50] 452s # qvalue cutoff for narrow/strong regions = 5.00e-02 452s # qvalue cutoff for broad/weak regions = 1.00e-01 452s # The maximum gap between significant sites is assigned as the read length/tag size. 452s # The minimum length of peaks is assigned as the predicted fragment length "d". 452s # Larger dataset will be scaled towards smaller dataset. 452s # Range for calculating regional lambda is: 10000 bps 452s # Broad region calling is on 452s # Paired-End mode is off 452s 452s INFO @ 16 Mar 2025 01:34:31: [30 MB] #1 read tag files... 452s INFO @ 16 Mar 2025 01:34:31: [30 MB] #1 read treatment tags... 452s INFO @ 16 Mar 2025 01:34:31: [31 MB] Detected format is: BED 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #1 tag size is determined as 181 bps 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #1 tag size = 181.0 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #1 total tags in treatment: 88292 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #1 user defined the maximum tags... 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #1 tags after filtering in treatment: 88292 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #1 Redundant rate of treatment: 0.00 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #1 finished! 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #2 Build Peak Model... 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #2 Skipped... 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #2 Use 200 as fragment length 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #3 Call peaks... 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000... 452s INFO @ 16 Mar 2025 01:34:31: [41 MB] #3 Pre-compute pvalue-qvalue table... 453s INFO @ 16 Mar 2025 01:34:31: [58 MB] #3 Call peaks for each chromosome... 453s INFO @ 16 Mar 2025 01:34:32: [60 MB] #4 Write output xls file... NA_peaks.xls 453s INFO @ 16 Mar 2025 01:34:32: [60 MB] #4 Write broad peak in broadPeak format file... NA_peaks.broadPeak 453s INFO @ 16 Mar 2025 01:34:32: [60 MB] #4 Write broad peak in bed12/gappedPeak format file... NA_peaks.gappedPeak 453s INFO @ 16 Mar 2025 01:34:32: [60 MB] Done! 453s autopkgtest [01:34:32]: test run-unit-test: -----------------------] 454s autopkgtest [01:34:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 454s run-unit-test PASS 454s autopkgtest [01:34:33]: @@@@@@@@@@@@@@@@@@@@ summary 454s run-unit-test PASS 472s nova [W] Using flock in prodstack6-arm64 472s Creating nova instance adt-plucky-arm64-macs-20250316-012659-juju-7f2275-prod-proposed-migration-environment-15-74327ca1-b9e6-4f1c-b61d-0fe204b5b8a5 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 472s nova [W] Timed out waiting for 9a9f9d22-3156-4aeb-a0cd-3876cd15f462 to get deleted.