0s autopkgtest [14:45:37]: starting date and time: 2025-03-15 14:45:37+0000 0s autopkgtest [14:45:37]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:45:37]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xkpkubyf/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade python-biom-format --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-20@bos03-arm64-8.secgroup --name adt-plucky-arm64-python-biom-format-20250315-144537-juju-7f2275-prod-proposed-migration-environment-20-5fd66534-23e1-4fce-b94e-69ef46d8fad5 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 128s autopkgtest [14:47:45]: testbed dpkg architecture: arm64 128s autopkgtest [14:47:45]: testbed apt version: 2.9.33 128s autopkgtest [14:47:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 128s autopkgtest [14:47:45]: testbed release detected to be: None 129s autopkgtest [14:47:46]: updating testbed package index (apt update) 130s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 130s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 130s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 130s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 130s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 130s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 131s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 131s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 131s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 131s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 131s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 131s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 131s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 131s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 132s Fetched 1094 kB in 2s (617 kB/s) 132s Reading package lists... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s Calculating upgrade... 134s Calculating upgrade... 134s The following packages will be upgraded: 134s python3-jinja2 strace 135s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Need to get 608 kB of archives. 135s After this operation, 11.3 kB of additional disk space will be used. 135s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 135s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 136s Fetched 608 kB in 1s (607 kB/s) 136s (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.) 136s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 136s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 136s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 137s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 137s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 137s Setting up strace (6.13+ds-1ubuntu1) ... 137s Processing triggers for man-db (2.13.0-1) ... 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Solving dependencies... 139s The following packages will be REMOVED: 139s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 139s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 139s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 139s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 139s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 139s After this operation, 267 MB disk space will be freed. 139s (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.) 139s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 139s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 139s Removing libpython3.12t64:arm64 (3.12.9-1) ... 139s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 139s Removing libnsl2:arm64 (1.3.0-3build3) ... 140s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 140s Removing libunwind8:arm64 (1.6.2-3.1) ... 140s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 140s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 142s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 142s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 142s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 142s /etc/kernel/postrm.d/initramfs-tools: 142s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 142s /etc/kernel/postrm.d/zz-flash-kernel: 142s flash-kernel: Kernel 6.11.0-8-generic has been removed. 142s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 143s /etc/kernel/postrm.d/zz-update-grub: 143s Sourcing file `/etc/default/grub' 143s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 143s Generating grub configuration file ... 143s Found linux image: /boot/vmlinuz-6.14.0-10-generic 143s Found initrd image: /boot/initrd.img-6.14.0-10-generic 143s Warning: os-prober will not be executed to detect other bootable partitions. 143s Systems on them will not be added to the GRUB boot configuration. 143s Check GRUB_DISABLE_OS_PROBER documentation entry. 143s Adding boot menu entry for UEFI Firmware Settings ... 143s done 143s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 143s Processing triggers for libc-bin (2.41-1ubuntu1) ... 144s (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.) 144s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 144s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 144s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 144s autopkgtest [14:48:01]: upgrading testbed (apt dist-upgrade and autopurge) 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 146s Entering ResolveByKeep 146s 146s Calculating upgrade... 147s The following packages will be upgraded: 147s libc-bin libc-dev-bin libc6 libc6-dev locales 147s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Need to get 9530 kB of archives. 147s After this operation, 0 B of additional disk space will be used. 147s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 149s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 149s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 152s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 152s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 158s Preconfiguring packages ... 158s Fetched 9530 kB in 11s (893 kB/s) 158s (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.) 158s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 158s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 158s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 158s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Setting up libc6:arm64 (2.41-1ubuntu2) ... 159s (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.) 159s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 159s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 159s Setting up libc-bin (2.41-1ubuntu2) ... 159s (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.) 159s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 159s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 159s Setting up locales (2.41-1ubuntu2) ... 160s Generating locales (this might take a while)... 162s en_US.UTF-8... done 162s Generation complete. 162s Setting up libc-dev-bin (2.41-1ubuntu2) ... 162s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 162s Processing triggers for man-db (2.13.0-1) ... 163s Processing triggers for systemd (257.3-1ubuntu3) ... 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Starting pkgProblemResolver with broken count: 0 164s Starting 2 pkgProblemResolver with broken count: 0 165s Done 165s Solving dependencies... 166s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s autopkgtest [14:48:23]: rebooting testbed after setup commands that affected boot 190s autopkgtest [14:48:47]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 192s autopkgtest [14:48:49]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 208s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build3 (dsc) [2498 B] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build3 (tar) [11.9 MB] 208s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build3 (diff) [11.7 kB] 209s gpgv: Signature made Tue Mar 4 15:18:02 2025 UTC 209s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 209s gpgv: Can't check signature: No public key 209s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1build3.dsc: no acceptable signature found 209s autopkgtest [14:49:06]: testing package python-biom-format version 2.1.16-1build3 210s autopkgtest [14:49:07]: build not needed 215s autopkgtest [14:49:12]: test run-unit-test: preparing testbed 216s Reading package lists... 216s Building dependency tree... 216s Reading state information... 216s Starting pkgProblemResolver with broken count: 0 216s Starting 2 pkgProblemResolver with broken count: 0 216s Done 217s The following NEW packages will be installed: 217s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 libjs-jquery 217s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 217s python-biom-format-doc python3-biom-format python3-click python3-dateutil 217s python3-decorator python3-h5py python3-h5py-serial python3-numpy 217s python3-numpy-dev python3-pandas python3-pandas-lib python3-pytz 217s python3-scipy python3-tz 217s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 217s Need to get 35.0 MB of archives. 217s After this operation, 157 MB of additional disk space will be used. 217s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 218s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 218s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 218s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 221s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 225s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 225s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 225s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 227s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 227s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 227s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 227s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 227s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 227s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 227s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biom-format-doc all 2.1.16-1build3 [57.5 kB] 227s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.13.0-1 [1126 kB] 228s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.13.0-1 [7978 B] 228s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 229s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 229s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 229s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 229s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8build1 [4586 kB] 234s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 238s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 238s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 256s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1build3 [142 kB] 256s Fetched 35.0 MB in 39s (897 kB/s) 256s Selecting previously unselected package python3-numpy-dev:arm64. 256s (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.) 256s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 256s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 257s Selecting previously unselected package libblas3:arm64. 257s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 257s Unpacking libblas3:arm64 (3.12.1-2) ... 257s Selecting previously unselected package libgfortran5:arm64. 257s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 257s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 257s Selecting previously unselected package liblapack3:arm64. 257s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 257s Unpacking liblapack3:arm64 (3.12.1-2) ... 257s Selecting previously unselected package python3-numpy. 257s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 257s Unpacking python3-numpy (1:2.2.3+ds-5) ... 257s Selecting previously unselected package libaec0:arm64. 257s Preparing to unpack .../05-libaec0_1.1.3-1_arm64.deb ... 257s Unpacking libaec0:arm64 (1.1.3-1) ... 257s Selecting previously unselected package libsz2:arm64. 257s Preparing to unpack .../06-libsz2_1.1.3-1_arm64.deb ... 257s Unpacking libsz2:arm64 (1.1.3-1) ... 257s Selecting previously unselected package libhdf5-310:arm64. 257s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_arm64.deb ... 257s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 257s Selecting previously unselected package libhdf5-hl-310:arm64. 257s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 257s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 257s Selecting previously unselected package libjs-jquery. 257s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 257s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 257s Selecting previously unselected package libjs-underscore. 257s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 257s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 257s Selecting previously unselected package libjs-sphinxdoc. 257s Preparing to unpack .../11-libjs-sphinxdoc_8.1.3-4_all.deb ... 257s Unpacking libjs-sphinxdoc (8.1.3-4) ... 257s Selecting previously unselected package liblbfgsb0:arm64. 257s Preparing to unpack .../12-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 257s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 257s Selecting previously unselected package liblzf1:arm64. 257s Preparing to unpack .../13-liblzf1_3.6-4_arm64.deb ... 257s Unpacking liblzf1:arm64 (3.6-4) ... 257s Selecting previously unselected package python-biom-format-doc. 257s Preparing to unpack .../14-python-biom-format-doc_2.1.16-1build3_all.deb ... 257s Unpacking python-biom-format-doc (2.1.16-1build3) ... 257s Selecting previously unselected package python3-h5py-serial. 257s Preparing to unpack .../15-python3-h5py-serial_3.13.0-1_arm64.deb ... 257s Unpacking python3-h5py-serial (3.13.0-1) ... 257s Selecting previously unselected package python3-h5py. 257s Preparing to unpack .../16-python3-h5py_3.13.0-1_all.deb ... 257s Unpacking python3-h5py (3.13.0-1) ... 257s Selecting previously unselected package python3-click. 257s Preparing to unpack .../17-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 257s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 257s Selecting previously unselected package python3-dateutil. 257s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 257s Unpacking python3-dateutil (2.9.0-3) ... 257s Selecting previously unselected package python3-pytz. 257s Preparing to unpack .../19-python3-pytz_2025.1-3_all.deb ... 257s Unpacking python3-pytz (2025.1-3) ... 258s Selecting previously unselected package python3-tz. 258s Preparing to unpack .../20-python3-tz_2025.1-3_all.deb ... 258s Unpacking python3-tz (2025.1-3) ... 258s Selecting previously unselected package python3-pandas-lib:arm64. 258s Preparing to unpack .../21-python3-pandas-lib_2.2.3+dfsg-8build1_arm64.deb ... 258s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 258s Selecting previously unselected package python3-pandas. 258s Preparing to unpack .../22-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 258s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 259s Selecting previously unselected package python3-decorator. 259s Preparing to unpack .../23-python3-decorator_5.1.1-5_all.deb ... 259s Unpacking python3-decorator (5.1.1-5) ... 259s Selecting previously unselected package python3-scipy. 259s Preparing to unpack .../24-python3-scipy_1.14.1-4ubuntu2_arm64.deb ... 259s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 259s Selecting previously unselected package python3-biom-format. 259s Preparing to unpack .../25-python3-biom-format_2.1.16-1build3_arm64.deb ... 259s Unpacking python3-biom-format (2.1.16-1build3) ... 259s Setting up python3-pytz (2025.1-3) ... 259s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 259s Setting up libaec0:arm64 (1.1.3-1) ... 259s Setting up python3-tz (2025.1-3) ... 259s Setting up python3-decorator (5.1.1-5) ... 259s Setting up libblas3:arm64 (3.12.1-2) ... 259s 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 259s Setting up liblzf1:arm64 (3.6-4) ... 259s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 259s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 259s Setting up python3-dateutil (2.9.0-3) ... 259s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 259s Setting up libsz2:arm64 (1.1.3-1) ... 259s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 259s Setting up liblapack3:arm64 (3.12.1-2) ... 259s 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 259s Setting up python3-numpy (1:2.2.3+ds-5) ... 261s Setting up libjs-sphinxdoc (8.1.3-4) ... 261s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 261s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 261s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 261s Setting up python3-scipy (1.14.1-4ubuntu2) ... 264s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 264s Setting up python3-h5py-serial (3.13.0-1) ... 265s Setting up python-biom-format-doc (2.1.16-1build3) ... 265s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 270s Setting up python3-h5py (3.13.0-1) ... 270s Setting up python3-biom-format (2.1.16-1build3) ... 270s Processing triggers for man-db (2.13.0-1) ... 270s Processing triggers for libc-bin (2.41-1ubuntu2) ... 272s autopkgtest [14:50:09]: test run-unit-test: [----------------------- 273s 273s System information 273s ================== 273s Platform: linux 273s Python version: 3.13.2 (main, Mar 13 2025, 14:29:07) [GCC 14.2.0] 273s Python executable: /usr/bin/python3 273s 273s Dependency versions 273s =================== 273s click version: 8.1.8 273s NumPy version: 2.2.3 273s SciPy version: 1.14.1 273s h5py version: 3.13.0 273s 273s biom-format package information 273s =============================== 273s biom-format version: 2.1.16 273s 274s 274s The input file is a valid BIOM-formatted file. 275s 275s The input file is a valid BIOM-formatted file. 276s 276s The input file is a valid BIOM-formatted file. 277s 277s The input file is a valid BIOM-formatted file. 279s + table=examples/min_sparse_otu_table_hdf5.biom 279s + obsmd=examples/obs_md.txt 279s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 279s + biom show-install-info 280s 280s System information 280s ================== 280s Platform: linux 280s Python version: 3.13.2 (main, Mar 13 2025, 14:29:07) [GCC 14.2.0] 280s Python executable: /usr/bin/python3 280s 280s Dependency versions 280s =================== 280s click version: 8.1.8 280s NumPy version: 2.2.3 280s SciPy version: 1.14.1 280s h5py version: 3.13.0 280s 280s biom-format package information 280s =============================== 280s biom-format version: 2.1.16 280s 280s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 281s 281s The input file is a valid BIOM-formatted file. 281s + 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 282s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 283s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 284s + biom validate-table -i test_json.biom 285s 285s The input file is a valid BIOM-formatted file. 285s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 286s + biom validate-table -i test_hdf5.biom 287s 287s The input file is a valid BIOM-formatted file. 287s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 288s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 289s + biom validate-table -i test_hdf5.biom 289s 289s The input file is a valid BIOM-formatted file. 290s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 290s + biom validate-table -i test_json.biom 291s 291s The input file is a valid BIOM-formatted file. 291s + biom head -i examples/min_sparse_otu_table_hdf5.biom 292s # Constructed from biom file 292s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 292s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 292s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 292s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 292s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 292s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 292s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 293s Sample1 293s Sample2 293s Sample3 293s Sample4 293s Sample5 293s Sample6 293s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 294s + cat 294s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 295s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 296s Num samples: 6 296s Num observations: 5 296s Total count: 27 296s Table density (fraction of non-zero values): 0.500 296s 296s Counts/sample summary: 296s Min: 3.000 296s Max: 7.000 296s Median: 4.000 296s Mean: 4.500 296s Std. dev.: 1.500 296s Sample Metadata Categories: None provided 296s Observation Metadata Categories: None provided 296s 296s Counts/sample detail: 296s Sample2: 3.000 296s Sample5: 3.000 296s Sample3: 4.000 296s Sample6: 4.000 296s Sample4: 6.000 296s Sample1: 7.000 296s + cat 296s + biom from-uc -i uctest -o test_uc.biom 297s + If this message was shown, then all commands executed without failure 297s echo If this message was shown, then all commands executed without failure 297s autopkgtest [14:50:34]: test run-unit-test: -----------------------] 298s autopkgtest [14:50:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 298s run-unit-test PASS 298s autopkgtest [14:50:35]: test autodep8-python3: preparing testbed 507s autopkgtest [14:54:03]: testbed dpkg architecture: arm64 507s autopkgtest [14:54:04]: testbed apt version: 2.9.33 507s autopkgtest [14:54:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 507s autopkgtest [14:54:04]: testbed release detected to be: plucky 508s autopkgtest [14:54:05]: updating testbed package index (apt update) 508s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 509s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 509s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 509s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 509s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 509s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 510s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 510s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 510s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 510s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 510s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 510s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 510s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 510s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 510s Fetched 1094 kB in 2s (634 kB/s) 511s Reading package lists... 512s Reading package lists... 512s Building dependency tree... 512s Reading state information... 513s Calculating upgrade... 513s Calculating upgrade... 513s The following packages will be upgraded: 513s python3-jinja2 strace 513s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 513s Need to get 608 kB of archives. 513s After this operation, 11.3 kB of additional disk space will be used. 513s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 514s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 515s Fetched 608 kB in 1s (601 kB/s) 515s (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.) 515s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 515s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 515s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 515s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 516s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 516s Setting up strace (6.13+ds-1ubuntu1) ... 516s Processing triggers for man-db (2.13.0-1) ... 517s Reading package lists... 517s Building dependency tree... 517s Reading state information... 517s Solving dependencies... 518s The following packages will be REMOVED: 518s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 518s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 518s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 518s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 518s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 518s After this operation, 267 MB disk space will be freed. 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 ... 117701 files and directories currently installed.) 518s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 518s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 518s Removing libpython3.12t64:arm64 (3.12.9-1) ... 518s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 518s Removing libnsl2:arm64 (1.3.0-3build3) ... 518s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 519s Removing libunwind8:arm64 (1.6.2-3.1) ... 519s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 519s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 521s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 521s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 521s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 521s /etc/kernel/postrm.d/initramfs-tools: 521s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 521s /etc/kernel/postrm.d/zz-flash-kernel: 521s flash-kernel: Kernel 6.11.0-8-generic has been removed. 521s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 522s /etc/kernel/postrm.d/zz-update-grub: 522s Sourcing file `/etc/default/grub' 522s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 522s Generating grub configuration file ... 522s Found linux image: /boot/vmlinuz-6.14.0-10-generic 522s Found initrd image: /boot/initrd.img-6.14.0-10-generic 522s Warning: os-prober will not be executed to detect other bootable partitions. 522s Systems on them will not be added to the GRUB boot configuration. 522s Check GRUB_DISABLE_OS_PROBER documentation entry. 522s Adding boot menu entry for UEFI Firmware Settings ... 522s done 522s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 523s Processing triggers for libc-bin (2.41-1ubuntu1) ... 523s (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.) 523s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 523s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 523s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 523s autopkgtest [14:54:20]: upgrading testbed (apt dist-upgrade and autopurge) 523s Reading package lists... 523s Building dependency tree... 523s Reading state information... 524s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 524s Starting 2 pkgProblemResolver with broken count: 0 524s Done 525s Entering ResolveByKeep 525s 525s Calculating upgrade... 526s The following packages will be upgraded: 526s libc-bin libc-dev-bin libc6 libc6-dev locales 526s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 526s Need to get 9530 kB of archives. 526s After this operation, 0 B of additional disk space will be used. 526s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 528s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 528s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 531s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 532s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 537s Preconfiguring packages ... 537s Fetched 9530 kB in 11s (887 kB/s) 537s (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.) 537s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 537s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 537s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 537s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 537s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 537s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 538s Setting up libc6:arm64 (2.41-1ubuntu2) ... 538s (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.) 538s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 538s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 538s Setting up libc-bin (2.41-1ubuntu2) ... 538s (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.) 538s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 538s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 538s Setting up locales (2.41-1ubuntu2) ... 539s Generating locales (this might take a while)... 541s en_US.UTF-8... done 541s Generation complete. 541s Setting up libc-dev-bin (2.41-1ubuntu2) ... 541s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 541s Processing triggers for man-db (2.13.0-1) ... 542s Processing triggers for systemd (257.3-1ubuntu3) ... 543s Reading package lists... 544s Building dependency tree... 544s Reading state information... 544s Starting pkgProblemResolver with broken count: 0 544s Starting 2 pkgProblemResolver with broken count: 0 544s Done 544s Solving dependencies... 545s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 545s autopkgtest [14:54:42]: rebooting testbed after setup commands that affected boot 571s Reading package lists... 571s Building dependency tree... 571s Reading state information... 572s Starting pkgProblemResolver with broken count: 0 572s Starting 2 pkgProblemResolver with broken count: 0 572s Done 573s The following NEW packages will be installed: 573s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 573s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 573s python3-dateutil python3-decorator python3-h5py python3-h5py-serial 573s python3-numpy python3-numpy-dev python3-pandas python3-pandas-lib 573s python3-pytz python3-scipy python3-tz 573s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 573s Need to get 34.5 MB of archives. 573s After this operation, 156 MB of additional disk space will be used. 573s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 573s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 574s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 574s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 579s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 586s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 586s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 586s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 588s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 588s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 588s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 588s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B] 588s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.13.0-1 [1126 kB] 590s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.13.0-1 [7978 B] 590s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 590s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 591s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 591s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 591s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8build1 [4586 kB] 600s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 606s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 606s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 638s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1build3 [142 kB] 639s Fetched 34.5 MB in 1min 6s (522 kB/s) 639s Selecting previously unselected package python3-numpy-dev:arm64. 639s (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.) 639s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 639s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 639s Selecting previously unselected package libblas3:arm64. 639s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 639s Unpacking libblas3:arm64 (3.12.1-2) ... 639s Selecting previously unselected package libgfortran5:arm64. 639s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 639s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 639s Selecting previously unselected package liblapack3:arm64. 639s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 639s Unpacking liblapack3:arm64 (3.12.1-2) ... 639s Selecting previously unselected package python3-numpy. 639s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 639s Unpacking python3-numpy (1:2.2.3+ds-5) ... 639s Selecting previously unselected package libaec0:arm64. 639s Preparing to unpack .../05-libaec0_1.1.3-1_arm64.deb ... 639s Unpacking libaec0:arm64 (1.1.3-1) ... 639s Selecting previously unselected package libsz2:arm64. 639s Preparing to unpack .../06-libsz2_1.1.3-1_arm64.deb ... 639s Unpacking libsz2:arm64 (1.1.3-1) ... 640s Selecting previously unselected package libhdf5-310:arm64. 640s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_arm64.deb ... 640s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 640s Selecting previously unselected package libhdf5-hl-310:arm64. 640s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 640s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 640s Selecting previously unselected package liblbfgsb0:arm64. 640s Preparing to unpack .../09-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 640s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 640s Selecting previously unselected package liblzf1:arm64. 640s Preparing to unpack .../10-liblzf1_3.6-4_arm64.deb ... 640s Unpacking liblzf1:arm64 (3.6-4) ... 640s Selecting previously unselected package python3-all. 640s Preparing to unpack .../11-python3-all_3.13.2-2_arm64.deb ... 640s Unpacking python3-all (3.13.2-2) ... 640s Selecting previously unselected package python3-h5py-serial. 640s Preparing to unpack .../12-python3-h5py-serial_3.13.0-1_arm64.deb ... 640s Unpacking python3-h5py-serial (3.13.0-1) ... 640s Selecting previously unselected package python3-h5py. 640s Preparing to unpack .../13-python3-h5py_3.13.0-1_all.deb ... 640s Unpacking python3-h5py (3.13.0-1) ... 640s Selecting previously unselected package python3-click. 640s Preparing to unpack .../14-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 640s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 640s Selecting previously unselected package python3-dateutil. 640s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 640s Unpacking python3-dateutil (2.9.0-3) ... 640s Selecting previously unselected package python3-pytz. 640s Preparing to unpack .../16-python3-pytz_2025.1-3_all.deb ... 640s Unpacking python3-pytz (2025.1-3) ... 640s Selecting previously unselected package python3-tz. 640s Preparing to unpack .../17-python3-tz_2025.1-3_all.deb ... 640s Unpacking python3-tz (2025.1-3) ... 640s Selecting previously unselected package python3-pandas-lib:arm64. 640s Preparing to unpack .../18-python3-pandas-lib_2.2.3+dfsg-8build1_arm64.deb ... 640s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 640s Selecting previously unselected package python3-pandas. 640s Preparing to unpack .../19-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 640s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 640s Selecting previously unselected package python3-decorator. 640s Preparing to unpack .../20-python3-decorator_5.1.1-5_all.deb ... 640s Unpacking python3-decorator (5.1.1-5) ... 640s Selecting previously unselected package python3-scipy. 640s Preparing to unpack .../21-python3-scipy_1.14.1-4ubuntu2_arm64.deb ... 640s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 642s Selecting previously unselected package python3-biom-format. 642s Preparing to unpack .../22-python3-biom-format_2.1.16-1build3_arm64.deb ... 642s Unpacking python3-biom-format (2.1.16-1build3) ... 642s Setting up python3-all (3.13.2-2) ... 642s Setting up python3-pytz (2025.1-3) ... 642s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 642s Setting up libaec0:arm64 (1.1.3-1) ... 642s Setting up python3-tz (2025.1-3) ... 642s Setting up python3-decorator (5.1.1-5) ... 642s Setting up libblas3:arm64 (3.12.1-2) ... 642s 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 642s Setting up liblzf1:arm64 (3.6-4) ... 642s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 642s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 642s Setting up python3-dateutil (2.9.0-3) ... 642s Setting up libsz2:arm64 (1.1.3-1) ... 642s Setting up liblapack3:arm64 (3.12.1-2) ... 642s 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 642s Setting up python3-numpy (1:2.2.3+ds-5) ... 644s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 644s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 644s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 644s Setting up python3-scipy (1.14.1-4ubuntu2) ... 647s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 647s Setting up python3-h5py-serial (3.13.0-1) ... 647s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 652s Setting up python3-h5py (3.13.0-1) ... 652s Setting up python3-biom-format (2.1.16-1build3) ... 652s Processing triggers for man-db (2.13.0-1) ... 653s Processing triggers for libc-bin (2.41-1ubuntu2) ... 657s autopkgtest [14:56:34]: 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 657s autopkgtest [14:56:34]: test autodep8-python3: [----------------------- 658s Testing with python3.13: 659s 659s autopkgtest [14:56:36]: test autodep8-python3: -----------------------] 660s autopkgtest [14:56:37]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 660s autodep8-python3 PASS (superficial) 660s autopkgtest [14:56:37]: @@@@@@@@@@@@@@@@@@@@ summary 660s run-unit-test PASS 660s autodep8-python3 PASS (superficial) 684s nova [W] Using flock in prodstack6-arm64 684s Creating nova instance adt-plucky-arm64-python-biom-format-20250315-144537-juju-7f2275-prod-proposed-migration-environment-20-5fd66534-23e1-4fce-b94e-69ef46d8fad5 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 684s nova [W] Timed out waiting for 65848bbc-eb28-40fa-abd4-d2f895c23e16 to get deleted. 684s nova [W] Using flock in prodstack6-arm64 684s Creating nova instance adt-plucky-arm64-python-biom-format-20250315-144537-juju-7f2275-prod-proposed-migration-environment-20-5fd66534-23e1-4fce-b94e-69ef46d8fad5 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 684s nova [W] Timed out waiting for 6acf59bc-6d31-4dba-ade3-2c773d4dc132 to get deleted.