0s autopkgtest [12:22:28]: starting date and time: 2025-02-19 12:22:28+0000 0s autopkgtest [12:22:28]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:22:28]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o0e0v3au/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-21.secgroup --name adt-plucky-arm64-python-biom-format-20250219-122228-juju-7f2275-prod-proposed-migration-environment-15-9b7b5e1d-80f3-436f-986b-900f475463a3 --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/ 165s autopkgtest [12:25:13]: testbed dpkg architecture: arm64 166s autopkgtest [12:25:14]: testbed apt version: 2.9.29 166s autopkgtest [12:25:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 166s autopkgtest [12:25:14]: testbed release detected to be: None 167s autopkgtest [12:25:15]: updating testbed package index (apt update) 168s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 168s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 168s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 168s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 168s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 168s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 168s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 168s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 168s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [93.3 kB] 168s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 168s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [686 kB] 168s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 168s Fetched 1752 kB in 1s (1817 kB/s) 170s Reading package lists... 171s + lsb_release --codename --short 171s + RELEASE=plucky 171s + cat 171s + [ plucky != trusty ] 171s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 172s Calculating upgrade... 173s The following NEW packages will be installed: 173s libapt-pkg7.0 173s The following packages will be upgraded: 173s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 173s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 173s Need to get 4842 kB of archives. 173s After this operation, 3409 kB of additional disk space will be used. 173s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libapt-pkg7.0 arm64 2.9.30 [1023 kB] 174s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 apt arm64 2.9.30 [1364 kB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 apt-utils arm64 2.9.30 [207 kB] 174s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 174s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit0 arm64 0.25.5-2ubuntu3 [280 kB] 174s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 rsyslog arm64 8.2412.0-2ubuntu1 [521 kB] 174s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-1 [236 kB] 174s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-1 [53.9 kB] 174s Preconfiguring packages ... 175s Fetched 4842 kB in 1s (5982 kB/s) 175s Selecting previously unselected package libapt-pkg7.0:arm64. 175s (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 ... 116620 files and directories currently installed.) 175s Preparing to unpack .../libapt-pkg7.0_2.9.30_arm64.deb ... 175s Unpacking libapt-pkg7.0:arm64 (2.9.30) ... 175s Setting up libapt-pkg7.0:arm64 (2.9.30) ... 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 ... 116669 files and directories currently installed.) 176s Preparing to unpack .../archives/apt_2.9.30_arm64.deb ... 176s Unpacking apt (2.9.30) over (2.9.29) ... 176s Setting up apt (2.9.30) ... 177s (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 ... 116669 files and directories currently installed.) 177s Preparing to unpack .../0-apt-utils_2.9.30_arm64.deb ... 177s Unpacking apt-utils (2.9.30) over (2.9.29) ... 178s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_arm64.deb ... 178s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 178s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_arm64.deb ... 178s Unpacking libp11-kit0:arm64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 178s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_arm64.deb ... 178s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 178s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_arm64.deb ... 178s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 179s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_arm64.deb ... 179s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 179s Setting up apt-utils (2.9.30) ... 179s Setting up liblsof0 (4.99.4+dfsg-1) ... 179s Setting up iproute2 (6.13.0-1ubuntu1) ... 179s Setting up rsyslog (8.2412.0-2ubuntu1) ... 179s info: The user `syslog' is already a member of `adm'. 181s Setting up libp11-kit0:arm64 (0.25.5-2ubuntu3) ... 181s Setting up lsof (4.99.4+dfsg-1) ... 181s Processing triggers for man-db (2.13.0-1) ... 184s Processing triggers for libc-bin (2.40-4ubuntu1) ... 184s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 184s + /usr/lib/apt/apt-helper analyze-pattern ?true 185s + + sed s/\./\\./g 185s uname -r 185s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 185s + + apt list ?obsolete 185s + cut+ grep -v ^linux-.*6\.12\.0-15-generic.* 185s tail -n+2 185s -d/ -f1 187s + true 187s + obsolete_pkgs= 187s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 189s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s + grep -q trusty /etc/lsb-release 189s + [ ! -d /usr/share/doc/unattended-upgrades ] 189s + [ ! -d /usr/share/doc/lxd ] 189s + [ ! -d /usr/share/doc/lxd-client ] 189s + [ ! -d /usr/share/doc/snapd ] 189s + type iptables 189s + cat 189s + chmod 755 /etc/rc.local 189s + . /etc/rc.local 189s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 189s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 189s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 189s + uname -m 189s + [ aarch64 = ppc64le ] 189s + [ -d /run/systemd/system ] 189s + systemd-detect-virt --quiet --vm 189s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 189s + cat 189s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 189s + echo COMPRESS=lz4 189s autopkgtest [12:25:37]: upgrading testbed (apt dist-upgrade and autopurge) 189s 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 193s 194s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 194s Reading package lists... 195s Building dependency tree... 195s Reading state information... 196s Starting pkgProblemResolver with broken count: 0 196s Starting 2 pkgProblemResolver with broken count: 0 196s Done 197s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s autopkgtest [12:25:46]: rebooting testbed after setup commands that affected boot 232s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 239s autopkgtest [12:26:27]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 241s autopkgtest [12:26:29]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 247s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build2 (dsc) [2498 B] 247s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build2 (tar) [11.9 MB] 247s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build2 (diff) [11.7 kB] 248s gpgv: Signature made Wed Jan 29 22:35:10 2025 UTC 248s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 248s gpgv: Can't check signature: No public key 248s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1build2.dsc: no acceptable signature found 248s autopkgtest [12:26:36]: testing package python-biom-format version 2.1.16-1build2 249s autopkgtest [12:26:37]: build not needed 251s autopkgtest [12:26:39]: test run-unit-test: preparing testbed 251s Reading package lists... 252s Building dependency tree... 252s Reading state information... 253s Starting pkgProblemResolver with broken count: 0 253s Starting 2 pkgProblemResolver with broken count: 0 253s Done 255s The following NEW packages will be installed: 255s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 libjs-jquery 255s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 255s python-biom-format-doc python3-biom-format python3-click python3-dateutil 255s python3-decorator python3-h5py python3-h5py-serial python3-numpy 255s python3-pandas python3-pandas-lib python3-pytz python3-scipy python3-tz 255s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 255s Need to get 40.6 MB of archives. 255s After this operation, 225 MB of additional disk space will be used. 255s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 256s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 256s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 256s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 256s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 257s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 257s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 257s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 257s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 257s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 261s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 261s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 261s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biom-format-doc all 2.1.16-1build2 [57.5 kB] 261s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 261s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.12.1-1 [1453 kB] 261s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.12.1-1 [7970 B] 261s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.8-1 [79.8 kB] 261s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 261s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 261s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 261s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8 [6925 kB] 261s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 261s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 261s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 261s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1build2 [165 kB] 262s Fetched 40.6 MB in 6s (7279 kB/s) 262s Selecting previously unselected package libaec0:arm64. 262s (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 ... 116670 files and directories currently installed.) 262s Preparing to unpack .../00-libaec0_1.1.3-1_arm64.deb ... 262s Unpacking libaec0:arm64 (1.1.3-1) ... 262s Selecting previously unselected package libblas3:arm64. 262s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 262s Unpacking libblas3:arm64 (3.12.1-2) ... 262s Selecting previously unselected package libgfortran5:arm64. 262s Preparing to unpack .../02-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 262s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 262s Selecting previously unselected package libsz2:arm64. 262s Preparing to unpack .../03-libsz2_1.1.3-1_arm64.deb ... 262s Unpacking libsz2:arm64 (1.1.3-1) ... 262s Selecting previously unselected package libhdf5-310:arm64. 262s Preparing to unpack .../04-libhdf5-310_1.14.5+repack-3_arm64.deb ... 262s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 262s Selecting previously unselected package libhdf5-hl-310:arm64. 262s Preparing to unpack .../05-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 262s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 263s Selecting previously unselected package libjs-jquery. 263s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 263s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 263s Selecting previously unselected package libjs-underscore. 263s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 263s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 263s Selecting previously unselected package libjs-sphinxdoc. 263s Preparing to unpack .../08-libjs-sphinxdoc_8.1.3-5_all.deb ... 263s Unpacking libjs-sphinxdoc (8.1.3-5) ... 263s Selecting previously unselected package liblapack3:arm64. 263s Preparing to unpack .../09-liblapack3_3.12.1-2_arm64.deb ... 263s Unpacking liblapack3:arm64 (3.12.1-2) ... 263s Selecting previously unselected package liblbfgsb0:arm64. 263s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 263s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 263s Selecting previously unselected package liblzf1:arm64. 263s Preparing to unpack .../11-liblzf1_3.6-4_arm64.deb ... 263s Unpacking liblzf1:arm64 (3.6-4) ... 263s Selecting previously unselected package python-biom-format-doc. 263s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1build2_all.deb ... 263s Unpacking python-biom-format-doc (2.1.16-1build2) ... 263s Selecting previously unselected package python3-numpy. 263s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 263s Unpacking python3-numpy (1:1.26.4+ds-13) ... 263s Selecting previously unselected package python3-h5py-serial. 264s Preparing to unpack .../14-python3-h5py-serial_3.12.1-1_arm64.deb ... 264s Unpacking python3-h5py-serial (3.12.1-1) ... 264s Selecting previously unselected package python3-h5py. 264s Preparing to unpack .../15-python3-h5py_3.12.1-1_all.deb ... 264s Unpacking python3-h5py (3.12.1-1) ... 264s Selecting previously unselected package python3-click. 264s Preparing to unpack .../16-python3-click_8.1.8-1_all.deb ... 264s Unpacking python3-click (8.1.8-1) ... 264s Selecting previously unselected package python3-dateutil. 264s Preparing to unpack .../17-python3-dateutil_2.9.0-3_all.deb ... 264s Unpacking python3-dateutil (2.9.0-3) ... 264s Selecting previously unselected package python3-pytz. 264s Preparing to unpack .../18-python3-pytz_2025.1-3_all.deb ... 264s Unpacking python3-pytz (2025.1-3) ... 264s Selecting previously unselected package python3-tz. 264s Preparing to unpack .../19-python3-tz_2025.1-3_all.deb ... 264s Unpacking python3-tz (2025.1-3) ... 264s Selecting previously unselected package python3-pandas-lib:arm64. 264s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-8_arm64.deb ... 264s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 265s Selecting previously unselected package python3-pandas. 265s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-8_all.deb ... 265s Unpacking python3-pandas (2.2.3+dfsg-8) ... 265s Selecting previously unselected package python3-decorator. 265s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 265s Unpacking python3-decorator (5.1.1-5) ... 265s Selecting previously unselected package python3-scipy. 265s Preparing to unpack .../23-python3-scipy_1.14.1-4ubuntu1_arm64.deb ... 265s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 266s Selecting previously unselected package python3-biom-format. 266s Preparing to unpack .../24-python3-biom-format_2.1.16-1build2_arm64.deb ... 266s Unpacking python3-biom-format (2.1.16-1build2) ... 266s Setting up python3-pytz (2025.1-3) ... 267s Setting up python3-click (8.1.8-1) ... 267s Setting up libaec0:arm64 (1.1.3-1) ... 267s Setting up python3-tz (2025.1-3) ... 267s Setting up python3-decorator (5.1.1-5) ... 267s Setting up libblas3:arm64 (3.12.1-2) ... 267s 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 267s Setting up liblzf1:arm64 (3.6-4) ... 267s Setting up libgfortran5:arm64 (15-20250213-1ubuntu1) ... 267s Setting up python3-dateutil (2.9.0-3) ... 268s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 268s Setting up libsz2:arm64 (1.1.3-1) ... 268s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 268s Setting up liblapack3:arm64 (3.12.1-2) ... 268s 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 268s Setting up python3-numpy (1:1.26.4+ds-13) ... 270s Setting up libjs-sphinxdoc (8.1.3-5) ... 270s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 270s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 270s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 270s Setting up python3-scipy (1.14.1-4ubuntu1) ... 275s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 275s Setting up python3-h5py-serial (3.12.1-1) ... 275s Setting up python-biom-format-doc (2.1.16-1build2) ... 275s Setting up python3-pandas (2.2.3+dfsg-8) ... 280s Setting up python3-h5py (3.12.1-1) ... 280s Setting up python3-biom-format (2.1.16-1build2) ... 281s Processing triggers for man-db (2.13.0-1) ... 281s Processing triggers for libc-bin (2.40-4ubuntu1) ... 283s autopkgtest [12:27:11]: test run-unit-test: [----------------------- 284s 284s System information 284s ================== 284s Platform: linux 284s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 284s Python executable: /usr/bin/python3 284s 284s Dependency versions 284s =================== 284s click version: 8.1.8 284s NumPy version: 1.26.4 284s SciPy version: 1.14.1 284s h5py version: 3.12.1 284s 284s biom-format package information 284s =============================== 284s biom-format version: 2.1.16 284s 286s 286s The input file is a valid BIOM-formatted file. 287s 287s The input file is a valid BIOM-formatted file. 288s 288s The input file is a valid BIOM-formatted file. 289s 289s The input file is a valid BIOM-formatted file. 291s + table=examples/min_sparse_otu_table_hdf5.biom 291s + obsmd=examples/obs_md.txt 291s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 291s + biom show-install-info 292s 292s System information 292s ================== 292s Platform: linux 292s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 292s Python executable: /usr/bin/python3 292s 292s Dependency versions 292s =================== 292s click version: 8.1.8 292s NumPy version: 1.26.4 292s SciPy version: 1.14.1 292s h5py version: 3.12.1 292s 292s biom-format package information 292s =============================== 292s biom-format version: 2.1.16 292s 292s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 293s 293s The input file is a valid BIOM-formatted file. 293s + biom add-metadata -i examples/min_sparse_otu_table_hdf5.biom -o test_add_metadata.biom --observation-metadata-fp examples/obs_md.txt --sc-separated taxonomy 294s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 295s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 297s + biom validate-table -i test_json.biom 297s 297s The input file is a valid BIOM-formatted file. 298s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 299s + biom validate-table -i test_hdf5.biom 300s 300s The input file is a valid BIOM-formatted file. 300s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 302s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 302s + biom validate-table -i test_hdf5.biom 303s 303s The input file is a valid BIOM-formatted file. 303s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 304s + biom validate-table -i test_json.biom 305s 305s The input file is a valid BIOM-formatted file. 305s + biom head -i examples/min_sparse_otu_table_hdf5.biom 306s # Constructed from biom file 306s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 306s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 306s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 306s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 306s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 306s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 306s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 307s Sample1 307s Sample2 307s Sample3 307s Sample4 307s Sample5 307s Sample6 307s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 308s + cat 308s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 309s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 310s Num samples: 6 310s Num observations: 5 310s Total count: 27 310s Table density (fraction of non-zero values): 0.500 310s 310s Counts/sample summary: 310s Min: 3.000 310s Max: 7.000 310s Median: 4.000 310s Mean: 4.500 310s Std. dev.: 1.500 310s Sample Metadata Categories: None provided 310s Observation Metadata Categories: None provided 310s 310s Counts/sample detail: 310s Sample2: 3.000 310s Sample5: 3.000 310s Sample3: 4.000 310s Sample6: 4.000 310s Sample4: 6.000 310s Sample1: 7.000 310s + cat 310s + biom from-uc -i uctest -o test_uc.biom 311s If this message was shown, then all commands executed without failure 311s + echo If this message was shown, then all commands executed without failure 312s autopkgtest [12:27:40]: test run-unit-test: -----------------------] 314s run-unit-test PASS 314s autopkgtest [12:27:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 314s autopkgtest [12:27:42]: test autodep8-python3: preparing testbed 465s autopkgtest [12:30:13]: testbed dpkg architecture: arm64 466s autopkgtest [12:30:14]: testbed apt version: 2.9.29 466s autopkgtest [12:30:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 466s autopkgtest [12:30:14]: testbed release detected to be: plucky 467s autopkgtest [12:30:15]: updating testbed package index (apt update) 467s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 468s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 468s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 468s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 468s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 468s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 468s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 468s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 468s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [93.3 kB] 468s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 468s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [686 kB] 468s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 468s Fetched 1752 kB in 1s (1868 kB/s) 469s Reading package lists... 470s + lsb_release --codename --short 470s + RELEASE=plucky 470s + cat 470s + [ plucky != trusty ] 470s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 470s Reading package lists... 470s Building dependency tree... 470s Reading state information... 471s Calculating upgrade... 471s The following NEW packages will be installed: 471s libapt-pkg7.0 471s The following packages will be upgraded: 471s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 471s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 471s Need to get 4842 kB of archives. 471s After this operation, 3409 kB of additional disk space will be used. 471s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libapt-pkg7.0 arm64 2.9.30 [1023 kB] 472s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 apt arm64 2.9.30 [1364 kB] 472s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 apt-utils arm64 2.9.30 [207 kB] 472s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 472s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit0 arm64 0.25.5-2ubuntu3 [280 kB] 472s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 rsyslog arm64 8.2412.0-2ubuntu1 [521 kB] 472s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-1 [236 kB] 472s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-1 [53.9 kB] 472s Preconfiguring packages ... 473s Fetched 4842 kB in 1s (5891 kB/s) 473s Selecting previously unselected package libapt-pkg7.0:arm64. 473s (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 ... 116620 files and directories currently installed.) 473s Preparing to unpack .../libapt-pkg7.0_2.9.30_arm64.deb ... 473s Unpacking libapt-pkg7.0:arm64 (2.9.30) ... 473s Setting up libapt-pkg7.0:arm64 (2.9.30) ... 473s (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 ... 116669 files and directories currently installed.) 473s Preparing to unpack .../archives/apt_2.9.30_arm64.deb ... 473s Unpacking apt (2.9.30) over (2.9.29) ... 473s Setting up apt (2.9.30) ... 474s (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 ... 116669 files and directories currently installed.) 474s Preparing to unpack .../0-apt-utils_2.9.30_arm64.deb ... 474s Unpacking apt-utils (2.9.30) over (2.9.29) ... 474s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_arm64.deb ... 474s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 475s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_arm64.deb ... 475s Unpacking libp11-kit0:arm64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 475s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_arm64.deb ... 475s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 475s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_arm64.deb ... 475s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 475s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_arm64.deb ... 475s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 475s Setting up apt-utils (2.9.30) ... 475s Setting up liblsof0 (4.99.4+dfsg-1) ... 475s Setting up iproute2 (6.13.0-1ubuntu1) ... 475s Setting up rsyslog (8.2412.0-2ubuntu1) ... 475s info: The user `syslog' is already a member of `adm'. 476s Setting up libp11-kit0:arm64 (0.25.5-2ubuntu3) ... 476s Setting up lsof (4.99.4+dfsg-1) ... 476s Processing triggers for man-db (2.13.0-1) ... 479s Processing triggers for libc-bin (2.40-4ubuntu1) ... 479s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 479s + /usr/lib/apt/apt-helper analyze-pattern ?true 479s + + uname -r 479s sed s/\./\\./g 479s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 479s + + tail -n+2 479s apt list ?obsolete 479s + cut -d/ -f1 479s + grep -v ^linux-.*6\.12\.0-15-generic.* 480s + true 480s + obsolete_pkgs= 480s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 480s Reading package lists... 481s Building dependency tree... 481s Reading state information... 481s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 481s + grep -q trusty /etc/lsb-release 481s + [ ! -d /usr/share/doc/unattended-upgrades ] 481s + [ ! -d /usr/share/doc/lxd ] 481s + [ ! -d /usr/share/doc/lxd-client ] 481s + [ ! -d /usr/share/doc/snapd ] 481s + type iptables 481s + cat 481s + chmod 755 /etc/rc.local 481s + . /etc/rc.local 481s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 481s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 481s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 481s + uname -m 481s + [ aarch64 = ppc64le ] 481s + [ -d /run/systemd/system ] 481s + systemd-detect-virt --quiet --vm 481s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 481s + cat 481s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 481s + echo COMPRESS=lz4 481s autopkgtest [12:30:29]: upgrading testbed (apt dist-upgrade and autopurge) 482s Reading package lists... 482s Building dependency tree... 482s Reading state information... 482s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 483s Starting 2 pkgProblemResolver with broken count: 0 483s Done 483s Entering ResolveByKeep 484s 484s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 484s Reading package lists... 485s Building dependency tree... 485s Reading state information... 485s Starting pkgProblemResolver with broken count: 0 485s Starting 2 pkgProblemResolver with broken count: 0 485s Done 486s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 486s autopkgtest [12:30:34]: rebooting testbed after setup commands that affected boot 513s Reading package lists... 513s Building dependency tree... 513s Reading state information... 514s Starting pkgProblemResolver with broken count: 0 514s Starting 2 pkgProblemResolver with broken count: 0 514s Done 515s The following NEW packages will be installed: 515s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 515s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 515s python3-dateutil python3-decorator python3-h5py python3-h5py-serial 515s python3-numpy python3-pandas python3-pandas-lib python3-pytz python3-scipy 515s python3-tz python3.12 python3.12-minimal 515s 0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded. 515s Need to get 42.9 MB of archives. 515s After this operation, 232 MB of additional disk space will be used. 515s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB] 516s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB] 516s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 516s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 516s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 516s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 516s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 516s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 516s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 516s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 516s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 516s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.1-1~exp2 [894 B] 516s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 516s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.12.1-1 [1453 kB] 516s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.12.1-1 [7970 B] 516s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.8-1 [79.8 kB] 516s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 516s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 516s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 516s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8 [6925 kB] 516s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 516s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 516s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 517s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1build2 [165 kB] 518s Fetched 42.9 MB in 2s (17.5 MB/s) 518s Selecting previously unselected package python3.12-minimal. 518s (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 ... 116670 files and directories currently installed.) 518s Preparing to unpack .../00-python3.12-minimal_3.12.9-1_arm64.deb ... 518s Unpacking python3.12-minimal (3.12.9-1) ... 518s Selecting previously unselected package python3.12. 518s Preparing to unpack .../01-python3.12_3.12.9-1_arm64.deb ... 518s Unpacking python3.12 (3.12.9-1) ... 518s Selecting previously unselected package libaec0:arm64. 518s Preparing to unpack .../02-libaec0_1.1.3-1_arm64.deb ... 518s Unpacking libaec0:arm64 (1.1.3-1) ... 518s Selecting previously unselected package libblas3:arm64. 518s Preparing to unpack .../03-libblas3_3.12.1-2_arm64.deb ... 518s Unpacking libblas3:arm64 (3.12.1-2) ... 518s Selecting previously unselected package libgfortran5:arm64. 518s Preparing to unpack .../04-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 518s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 519s Selecting previously unselected package libsz2:arm64. 519s Preparing to unpack .../05-libsz2_1.1.3-1_arm64.deb ... 519s Unpacking libsz2:arm64 (1.1.3-1) ... 519s Selecting previously unselected package libhdf5-310:arm64. 519s Preparing to unpack .../06-libhdf5-310_1.14.5+repack-3_arm64.deb ... 519s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 519s Selecting previously unselected package libhdf5-hl-310:arm64. 519s Preparing to unpack .../07-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 519s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 519s Selecting previously unselected package liblapack3:arm64. 519s Preparing to unpack .../08-liblapack3_3.12.1-2_arm64.deb ... 519s Unpacking liblapack3:arm64 (3.12.1-2) ... 519s Selecting previously unselected package liblbfgsb0:arm64. 519s Preparing to unpack .../09-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 519s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 519s Selecting previously unselected package liblzf1:arm64. 519s Preparing to unpack .../10-liblzf1_3.6-4_arm64.deb ... 519s Unpacking liblzf1:arm64 (3.6-4) ... 519s Selecting previously unselected package python3-all. 519s Preparing to unpack .../11-python3-all_3.13.1-1~exp2_arm64.deb ... 519s Unpacking python3-all (3.13.1-1~exp2) ... 519s Selecting previously unselected package python3-numpy. 519s Preparing to unpack .../12-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 519s Unpacking python3-numpy (1:1.26.4+ds-13) ... 519s Selecting previously unselected package python3-h5py-serial. 519s Preparing to unpack .../13-python3-h5py-serial_3.12.1-1_arm64.deb ... 519s Unpacking python3-h5py-serial (3.12.1-1) ... 519s Selecting previously unselected package python3-h5py. 519s Preparing to unpack .../14-python3-h5py_3.12.1-1_all.deb ... 519s Unpacking python3-h5py (3.12.1-1) ... 519s Selecting previously unselected package python3-click. 519s Preparing to unpack .../15-python3-click_8.1.8-1_all.deb ... 519s Unpacking python3-click (8.1.8-1) ... 519s Selecting previously unselected package python3-dateutil. 519s Preparing to unpack .../16-python3-dateutil_2.9.0-3_all.deb ... 519s Unpacking python3-dateutil (2.9.0-3) ... 519s Selecting previously unselected package python3-pytz. 519s Preparing to unpack .../17-python3-pytz_2025.1-3_all.deb ... 519s Unpacking python3-pytz (2025.1-3) ... 519s Selecting previously unselected package python3-tz. 520s Preparing to unpack .../18-python3-tz_2025.1-3_all.deb ... 520s Unpacking python3-tz (2025.1-3) ... 520s Selecting previously unselected package python3-pandas-lib:arm64. 520s Preparing to unpack .../19-python3-pandas-lib_2.2.3+dfsg-8_arm64.deb ... 520s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 520s Selecting previously unselected package python3-pandas. 520s Preparing to unpack .../20-python3-pandas_2.2.3+dfsg-8_all.deb ... 520s Unpacking python3-pandas (2.2.3+dfsg-8) ... 520s Selecting previously unselected package python3-decorator. 520s Preparing to unpack .../21-python3-decorator_5.1.1-5_all.deb ... 520s Unpacking python3-decorator (5.1.1-5) ... 520s Selecting previously unselected package python3-scipy. 520s Preparing to unpack .../22-python3-scipy_1.14.1-4ubuntu1_arm64.deb ... 520s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 521s Selecting previously unselected package python3-biom-format. 521s Preparing to unpack .../23-python3-biom-format_2.1.16-1build2_arm64.deb ... 521s Unpacking python3-biom-format (2.1.16-1build2) ... 521s Setting up python3.12-minimal (3.12.9-1) ... 522s Setting up python3.12 (3.12.9-1) ... 524s Setting up python3-all (3.13.1-1~exp2) ... 524s Setting up python3-pytz (2025.1-3) ... 524s Setting up python3-click (8.1.8-1) ... 524s Setting up libaec0:arm64 (1.1.3-1) ... 524s Setting up python3-tz (2025.1-3) ... 524s Setting up python3-decorator (5.1.1-5) ... 524s Setting up libblas3:arm64 (3.12.1-2) ... 524s 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 524s Setting up liblzf1:arm64 (3.6-4) ... 524s Setting up libgfortran5:arm64 (15-20250213-1ubuntu1) ... 524s Setting up python3-dateutil (2.9.0-3) ... 525s Setting up libsz2:arm64 (1.1.3-1) ... 525s Setting up liblapack3:arm64 (3.12.1-2) ... 525s 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 525s Setting up python3-numpy (1:1.26.4+ds-13) ... 529s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 529s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 529s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 529s Setting up python3-scipy (1.14.1-4ubuntu1) ... 537s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 537s Setting up python3-h5py-serial (3.12.1-1) ... 537s Setting up python3-pandas (2.2.3+dfsg-8) ... 548s Setting up python3-h5py (3.12.1-1) ... 549s Setting up python3-biom-format (2.1.16-1build2) ... 549s Processing triggers for systemd (257.2-3ubuntu1) ... 549s Processing triggers for man-db (2.13.0-1) ... 550s Processing triggers for libc-bin (2.40-4ubuntu1) ... 558s autopkgtest [12:31:46]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import biom; print(biom)" ; done 558s autopkgtest [12:31:46]: test autodep8-python3: [----------------------- 558s Testing with python3.12: 559s 560s Testing with python3.13: 561s 561s autopkgtest [12:31:49]: test autodep8-python3: -----------------------] 562s autopkgtest [12:31:50]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 562s autodep8-python3 PASS (superficial) 562s autopkgtest [12:31:50]: @@@@@@@@@@@@@@@@@@@@ summary 562s run-unit-test PASS 562s autodep8-python3 PASS (superficial) 579s nova [W] Using flock in prodstack6-arm64 579s flock: timeout while waiting to get lock 579s Creating nova instance adt-plucky-arm64-python-biom-format-20250219-122228-juju-7f2275-prod-proposed-migration-environment-15-9b7b5e1d-80f3-436f-986b-900f475463a3 from image adt/ubuntu-plucky-arm64-server-20250219.img (UUID 02c92adb-9d9d-4b0e-b071-488d8ee6210f)... 579s nova [W] Timed out waiting for aee30cd7-d14e-4226-b415-915ec73bfc00 to get deleted. 579s nova [W] Using flock in prodstack6-arm64 579s Creating nova instance adt-plucky-arm64-python-biom-format-20250219-122228-juju-7f2275-prod-proposed-migration-environment-15-9b7b5e1d-80f3-436f-986b-900f475463a3 from image adt/ubuntu-plucky-arm64-server-20250219.img (UUID 02c92adb-9d9d-4b0e-b071-488d8ee6210f)... 579s nova [W] Timed out waiting for c9bd8635-5a06-4aba-8360-de294be931ef to get deleted.