0s autopkgtest [21:47:50]: starting date and time: 2024-03-13 21:47:50+0000 0s autopkgtest [21:47:50]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [21:47:50]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gsp6qmgo/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:hdf5,src:openmpi,src:openssl,src:pmix --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.10.0-1ubuntu2 hdf5/1.10.10+repack-3.1ubuntu2 openmpi/4.1.6-5.1ubuntu3 openssl/3.0.13-0ubuntu1 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-21.secgroup --name adt-noble-arm64-python-biom-format-20240313-214750-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 73s autopkgtest [21:49:03]: testbed dpkg architecture: arm64 73s autopkgtest [21:49:03]: testbed apt version: 2.7.12 73s autopkgtest [21:49:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 74s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 74s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [42.3 kB] 74s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2818 kB] 74s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB] 74s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [603 kB] 74s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 74s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 74s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 74s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3218 kB] 74s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 74s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [42.3 kB] 74s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 76s Fetched 7327 kB in 1s (4902 kB/s) 76s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 80s The following packages will be REMOVED: 80s libssl3 80s The following NEW packages will be installed: 80s libssl3t64 80s The following packages will be upgraded: 80s console-setup console-setup-linux keyboard-configuration openssl 80s 4 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 80s Need to get 4955 kB of archives. 80s After this operation, 74.8 kB of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 80s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 80s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup-linux all 1.226ubuntu1 [1880 kB] 81s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup all 1.226ubuntu1 [110 kB] 81s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 keyboard-configuration all 1.226ubuntu1 [212 kB] 81s Preconfiguring packages ... 82s Fetched 4955 kB in 1s (5980 kB/s) 82s (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 ... 74759 files and directories currently installed.) 82s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 82s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 83s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 83s wget depends on libssl3 (>= 3.0.0). 83s u-boot-tools depends on libssl3 (>= 3.0.0). 83s tnftp depends on libssl3 (>= 3.0.0). 83s tcpdump depends on libssl3 (>= 3.0.0). 83s systemd-resolved depends on libssl3 (>= 3.0.0). 83s systemd depends on libssl3 (>= 3.0.0). 83s sudo depends on libssl3 (>= 3.0.0). 83s sbsigntool depends on libssl3 (>= 3.0.0). 83s rsync depends on libssl3 (>= 3.0.0). 83s python3-cryptography depends on libssl3 (>= 3.0.0). 83s openssh-server depends on libssl3 (>= 3.0.10). 83s openssh-client depends on libssl3 (>= 3.0.10). 83s mtd-utils depends on libssl3 (>= 3.0.0). 83s mokutil depends on libssl3 (>= 3.0.0). 83s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 83s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 83s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 83s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 83s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 83s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 83s libnvme1 depends on libssl3 (>= 3.0.0). 83s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 83s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 83s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 83s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 83s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 83s kmod depends on libssl3 (>= 3.0.0). 83s dhcpcd-base depends on libssl3 (>= 3.0.0). 83s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 83s 83s (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 ... 74759 files and directories currently installed.) 83s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 83s Selecting previously unselected package libssl3t64:arm64. 83s (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 ... 74748 files and directories currently installed.) 83s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 83s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 84s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ... 84s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ... 84s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ... 84s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ... 84s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ... 84s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ... 84s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 84s Setting up keyboard-configuration (1.226ubuntu1) ... 86s Your console font configuration will be updated the next time your system 86s boots. If you want to update it now, run 'setupcon' from a virtual console. 86s update-initramfs: deferring update (trigger activated) 86s Setting up openssl (3.0.13-0ubuntu1) ... 86s Setting up console-setup-linux (1.226ubuntu1) ... 88s Setting up console-setup (1.226ubuntu1) ... 89s update-initramfs: deferring update (trigger activated) 89s Processing triggers for man-db (2.12.0-3) ... 90s Processing triggers for libc-bin (2.39-0ubuntu2) ... 90s Processing triggers for initramfs-tools (0.142ubuntu20) ... 90s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 90s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 120s System running in EFI mode, skipping. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 122s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 122s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 122s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 125s Reading package lists... 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s Calculating upgrade... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s autopkgtest [21:49:58]: rebooting testbed after setup commands that affected boot 402s autopkgtest [21:54:32]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 405s autopkgtest [21:54:35]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 410s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-biom-format 2.1.15.2-3 (dsc) [1883 B] 410s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-biom-format 2.1.15.2-3 (tar) [11.9 MB] 410s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-biom-format 2.1.15.2-3 (diff) [11.5 kB] 410s gpgv: Signature made Sun Feb 4 19:23:04 2024 UTC 410s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 410s gpgv: Can't check signature: No public key 410s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.15.2-3.dsc: no acceptable signature found 410s autopkgtest [21:54:40]: testing package python-biom-format version 2.1.15.2-3 411s autopkgtest [21:54:41]: build not needed 413s autopkgtest [21:54:43]: test run-unit-test: preparing testbed 418s Reading package lists... 419s Building dependency tree... 419s Reading state information... 419s Starting pkgProblemResolver with broken count: 0 419s Starting 2 pkgProblemResolver with broken count: 0 419s Done 420s The following additional packages will be installed: 420s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 420s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 420s libpython3.11-minimal libpython3.11-stdlib libsz2 python-biom-format-doc 420s python3-biom-format python3-click python3-colorama python3-dateutil 420s python3-decorator python3-h5py python3-h5py-serial python3-numpy 420s python3-pandas python3-pandas-lib python3-scipy python3.11 420s python3.11-minimal 420s Suggested packages: 420s python-h5py-doc gcc gfortran python3-dev python3-pytest python-pandas-doc 420s python3-statsmodels python-scipy-doc python3.11-venv python3.11-doc 420s binfmt-support 420s Recommended packages: 420s javascript-common python3-matplotlib python3-bottleneck python3-numexpr 420s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 420s python3-tables g++ | c++-compiler python3-pil 420s The following NEW packages will be installed: 420s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 420s libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 420s liblbfgsb0 liblzf1 libpython3.11-minimal libpython3.11-stdlib libsz2 420s python-biom-format-doc python3-biom-format python3-click python3-colorama 420s python3-dateutil python3-decorator python3-h5py python3-h5py-serial 420s python3-numpy python3-pandas python3-pandas-lib python3-scipy python3.11 420s python3.11-minimal 420s 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. 420s Need to get 45.4 MB/45.4 MB of archives. 420s After this operation, 229 MB of additional disk space will be used. 420s Get:1 /tmp/autopkgtest.GVR3BZ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 420s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 420s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 421s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 421s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 421s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 421s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 421s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 421s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 421s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu2 [1192 kB] 421s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-3.1ubuntu2 [55.8 kB] 421s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 421s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 421s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-sphinxdoc all 7.2.6-4 [149 kB] 421s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 421s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 421s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 421s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 python-biom-format-doc all 2.1.15.2-3 [57.1 kB] 421s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 421s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu2 [887 kB] 421s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py all 3.10.0-1ubuntu2 [7980 B] 421s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 421s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 python3-click all 8.1.6-1 [79.0 kB] 421s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 421s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 421s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 421s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 421s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 422s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biom-format arm64 2.1.15.2-3 [170 kB] 422s Fetched 45.4 MB in 2s (25.9 MB/s) 422s Selecting previously unselected package libpython3.11-minimal:arm64. 423s (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 ... 74761 files and directories currently installed.) 423s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ... 423s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 423s Selecting previously unselected package python3.11-minimal. 423s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ... 423s Unpacking python3.11-minimal (3.11.8-1) ... 423s Selecting previously unselected package libpython3.11-stdlib:arm64. 423s Preparing to unpack .../02-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 423s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 423s Selecting previously unselected package python3.11. 423s Preparing to unpack .../03-python3.11_3.11.8-1_arm64.deb ... 423s Unpacking python3.11 (3.11.8-1) ... 423s Selecting previously unselected package libaec0:arm64. 423s Preparing to unpack .../04-libaec0_1.1.2-1_arm64.deb ... 423s Unpacking libaec0:arm64 (1.1.2-1) ... 423s Selecting previously unselected package libblas3:arm64. 423s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ... 423s Unpacking libblas3:arm64 (3.12.0-3) ... 423s Selecting previously unselected package libgfortran5:arm64. 423s Preparing to unpack .../06-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 423s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 423s Selecting previously unselected package libsz2:arm64. 423s Preparing to unpack .../07-libsz2_1.1.2-1_arm64.deb ... 423s Unpacking libsz2:arm64 (1.1.2-1) ... 423s Selecting previously unselected package libhdf5-103-1t64:arm64. 423s Preparing to unpack .../08-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 423s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 423s Selecting previously unselected package libhdf5-hl-100t64:arm64. 423s Preparing to unpack .../09-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 423s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 423s Selecting previously unselected package libjs-jquery. 423s Preparing to unpack .../10-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 423s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 423s Selecting previously unselected package libjs-underscore. 423s Preparing to unpack .../11-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 423s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 423s Selecting previously unselected package libjs-sphinxdoc. 423s Preparing to unpack .../12-libjs-sphinxdoc_7.2.6-4_all.deb ... 423s Unpacking libjs-sphinxdoc (7.2.6-4) ... 423s Selecting previously unselected package liblapack3:arm64. 423s Preparing to unpack .../13-liblapack3_3.12.0-3_arm64.deb ... 423s Unpacking liblapack3:arm64 (3.12.0-3) ... 423s Selecting previously unselected package liblbfgsb0:arm64. 424s Preparing to unpack .../14-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 424s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 424s Selecting previously unselected package liblzf1:arm64. 424s Preparing to unpack .../15-liblzf1_3.6-4_arm64.deb ... 424s Unpacking liblzf1:arm64 (3.6-4) ... 424s Selecting previously unselected package python-biom-format-doc. 424s Preparing to unpack .../16-python-biom-format-doc_2.1.15.2-3_all.deb ... 424s Unpacking python-biom-format-doc (2.1.15.2-3) ... 424s Selecting previously unselected package python3-numpy. 424s Preparing to unpack .../17-python3-numpy_1%3a1.24.2-2_arm64.deb ... 424s Unpacking python3-numpy (1:1.24.2-2) ... 424s Selecting previously unselected package python3-h5py-serial. 424s Preparing to unpack .../18-python3-h5py-serial_3.10.0-1ubuntu2_arm64.deb ... 424s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ... 424s Selecting previously unselected package python3-h5py. 424s Preparing to unpack .../19-python3-h5py_3.10.0-1ubuntu2_all.deb ... 424s Unpacking python3-h5py (3.10.0-1ubuntu2) ... 424s Selecting previously unselected package python3-colorama. 424s Preparing to unpack .../20-python3-colorama_0.4.6-4_all.deb ... 424s Unpacking python3-colorama (0.4.6-4) ... 424s Selecting previously unselected package python3-click. 424s Preparing to unpack .../21-python3-click_8.1.6-1_all.deb ... 424s Unpacking python3-click (8.1.6-1) ... 424s Selecting previously unselected package python3-dateutil. 424s Preparing to unpack .../22-python3-dateutil_2.8.2-3_all.deb ... 424s Unpacking python3-dateutil (2.8.2-3) ... 424s Selecting previously unselected package python3-pandas-lib:arm64. 424s Preparing to unpack .../23-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 424s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 425s Selecting previously unselected package python3-pandas. 425s Preparing to unpack .../24-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 425s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 425s Selecting previously unselected package python3-decorator. 425s Preparing to unpack .../25-python3-decorator_5.1.1-5_all.deb ... 425s Unpacking python3-decorator (5.1.1-5) ... 425s Selecting previously unselected package python3-scipy. 425s Preparing to unpack .../26-python3-scipy_1.11.4-6_arm64.deb ... 425s Unpacking python3-scipy (1.11.4-6) ... 426s Selecting previously unselected package python3-biom-format. 426s Preparing to unpack .../27-python3-biom-format_2.1.15.2-3_arm64.deb ... 426s Unpacking python3-biom-format (2.1.15.2-3) ... 426s Selecting previously unselected package autopkgtest-satdep. 426s Preparing to unpack .../28-1-autopkgtest-satdep.deb ... 426s Unpacking autopkgtest-satdep (0) ... 426s Setting up python3-colorama (0.4.6-4) ... 426s Setting up python3-click (8.1.6-1) ... 426s Setting up libaec0:arm64 (1.1.2-1) ... 426s Setting up python3-decorator (5.1.1-5) ... 426s Setting up libblas3:arm64 (3.12.0-3) ... 426s 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 426s Setting up liblzf1:arm64 (3.6-4) ... 426s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 426s Setting up python3-dateutil (2.8.2-3) ... 426s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 426s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 426s Setting up libsz2:arm64 (1.1.2-1) ... 426s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 426s Setting up python3.11-minimal (3.11.8-1) ... 427s Setting up liblapack3:arm64 (3.12.0-3) ... 427s 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 427s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 427s Setting up libjs-sphinxdoc (7.2.6-4) ... 427s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 427s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 427s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 427s Setting up python3.11 (3.11.8-1) ... 428s Setting up python-biom-format-doc (2.1.15.2-3) ... 428s Setting up python3-numpy (1:1.24.2-2) ... 430s Setting up python3-scipy (1.11.4-6) ... 432s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 432s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ... 433s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 437s Setting up python3-h5py (3.10.0-1ubuntu2) ... 437s Setting up python3-biom-format (2.1.15.2-3) ... 437s Setting up autopkgtest-satdep (0) ... 437s Processing triggers for systemd (255.2-3ubuntu2) ... 437s Processing triggers for man-db (2.12.0-3) ... 439s Processing triggers for libc-bin (2.39-0ubuntu2) ... 443s (Reading database ... 80123 files and directories currently installed.) 443s Removing autopkgtest-satdep (0) ... 443s autopkgtest [21:55:13]: test run-unit-test: [----------------------- 446s 446s System information 446s ================== 446s Platform: linux 446s Python version: 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 446s Python executable: /usr/bin/python3 446s 446s Dependency versions 446s =================== 446s click version: 8.1.6 446s NumPy version: 1.24.2 446s SciPy version: 1.11.4 446s h5py version: 3.10.0 446s 446s biom-format package information 446s =============================== 446s biom-format version: 2.1.15 446s 447s 447s The input file is a valid BIOM-formatted file. 448s 448s The input file is a valid BIOM-formatted file. 449s 449s The input file is a valid BIOM-formatted file. 451s 451s The input file is a valid BIOM-formatted file. 453s + table=examples/min_sparse_otu_table_hdf5.biom 453s + obsmd=examples/obs_md.txt 453s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 453s + biom show-install-info 454s 454s System information 454s ================== 454s Platform: linux 454s Python version: 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 454s Python executable: /usr/bin/python3 454s 454s Dependency versions 454s =================== 454s click version: 8.1.6 454s NumPy version: 1.24.2 454s SciPy version: 1.11.4 454s h5py version: 3.10.0 454s 454s biom-format package information 454s =============================== 454s biom-format version: 2.1.15 454s 454s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 454s 454s The input file is a valid BIOM-formatted file. 454s + 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 455s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 456s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 457s + biom validate-table -i test_json.biom 458s 458s The input file is a valid BIOM-formatted file. 458s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 459s + biom validate-table -i test_hdf5.biom 459s 459s The input file is a valid BIOM-formatted file. 460s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 461s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 461s + biom validate-table -i test_hdf5.biom 462s 462s The input file is a valid BIOM-formatted file. 462s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 463s + biom validate-table -i test_json.biom 464s 464s The input file is a valid BIOM-formatted file. 464s + biom head -i examples/min_sparse_otu_table_hdf5.biom 466s # Constructed from biom file 466s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 466s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 466s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 466s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 466s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 466s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 466s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 468s Sample1 468s Sample2 468s Sample3 468s Sample4 468s Sample5 468s Sample6 468s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 470s + cat 470s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 471s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 472s Num samples: 6 472s Num observations: 5 472s Total count: 27 472s Table density (fraction of non-zero values): 0.500 472s 472s Counts/sample summary: 472s Min: 3.000 472s Max: 7.000 472s Median: 4.000 472s Mean: 4.500 472s Std. dev.: 1.500 472s Sample Metadata Categories: None provided 472s Observation Metadata Categories: None provided 472s 472s Counts/sample detail: 472s Sample2: 3.000 472s Sample5: 3.000 472s Sample3: 4.000 472s Sample6: 4.000 472s Sample4: 6.000 472s Sample1: 7.000 472s + cat 472s + biom from-uc -i uctest -o test_uc.biom 473s If this message was shown, then all commands executed without failure 473s + echo If this message was shown, then all commands executed without failure 474s autopkgtest [21:55:44]: test run-unit-test: -----------------------] 474s autopkgtest [21:55:44]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 474s run-unit-test PASS 474s autopkgtest [21:55:44]: test autodep8-python3: preparing testbed 570s autopkgtest [21:57:20]: testbed dpkg architecture: arm64 570s autopkgtest [21:57:20]: testbed apt version: 2.7.12 570s autopkgtest [21:57:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 570s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 571s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [42.3 kB] 571s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2818 kB] 571s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 571s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB] 571s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [603 kB] 571s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 571s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 571s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 571s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3218 kB] 571s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 571s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [42.3 kB] 571s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 573s Fetched 7327 kB in 2s (4669 kB/s) 573s Reading package lists... 576s Reading package lists... 577s Building dependency tree... 577s Reading state information... 577s Calculating upgrade... 577s The following packages will be REMOVED: 577s libssl3 577s The following NEW packages will be installed: 577s libssl3t64 577s The following packages will be upgraded: 577s console-setup console-setup-linux keyboard-configuration openssl 578s 4 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 578s Need to get 4955 kB of archives. 578s After this operation, 74.8 kB of additional disk space will be used. 578s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 578s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 578s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup-linux all 1.226ubuntu1 [1880 kB] 578s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup all 1.226ubuntu1 [110 kB] 578s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 keyboard-configuration all 1.226ubuntu1 [212 kB] 579s Preconfiguring packages ... 579s Fetched 4955 kB in 1s (6292 kB/s) 579s (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 ... 74759 files and directories currently installed.) 579s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 579s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 580s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 580s wget depends on libssl3 (>= 3.0.0). 580s u-boot-tools depends on libssl3 (>= 3.0.0). 580s tnftp depends on libssl3 (>= 3.0.0). 580s tcpdump depends on libssl3 (>= 3.0.0). 580s systemd-resolved depends on libssl3 (>= 3.0.0). 580s systemd depends on libssl3 (>= 3.0.0). 580s sudo depends on libssl3 (>= 3.0.0). 580s sbsigntool depends on libssl3 (>= 3.0.0). 580s rsync depends on libssl3 (>= 3.0.0). 580s python3-cryptography depends on libssl3 (>= 3.0.0). 580s openssh-server depends on libssl3 (>= 3.0.10). 580s openssh-client depends on libssl3 (>= 3.0.10). 580s mtd-utils depends on libssl3 (>= 3.0.0). 580s mokutil depends on libssl3 (>= 3.0.0). 580s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 580s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 580s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 580s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 580s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 580s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 580s libnvme1 depends on libssl3 (>= 3.0.0). 580s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 580s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 580s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 580s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 580s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 580s kmod depends on libssl3 (>= 3.0.0). 580s dhcpcd-base depends on libssl3 (>= 3.0.0). 580s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 580s 580s (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 ... 74759 files and directories currently installed.) 580s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 580s Selecting previously unselected package libssl3t64:arm64. 580s (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 ... 74748 files and directories currently installed.) 580s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 580s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 580s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ... 580s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ... 580s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ... 580s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ... 580s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ... 580s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ... 580s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 580s Setting up keyboard-configuration (1.226ubuntu1) ... 585s Your console font configuration will be updated the next time your system 585s boots. If you want to update it now, run 'setupcon' from a virtual console. 585s update-initramfs: deferring update (trigger activated) 585s Setting up openssl (3.0.13-0ubuntu1) ... 585s Setting up console-setup-linux (1.226ubuntu1) ... 586s Setting up console-setup (1.226ubuntu1) ... 587s update-initramfs: deferring update (trigger activated) 587s Processing triggers for man-db (2.12.0-3) ... 588s Processing triggers for libc-bin (2.39-0ubuntu2) ... 588s Processing triggers for initramfs-tools (0.142ubuntu20) ... 588s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 588s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 606s System running in EFI mode, skipping. 606s Reading package lists... 606s Building dependency tree... 606s Reading state information... 607s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 608s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 608s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 608s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 608s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 610s Reading package lists... 610s Reading package lists... 610s Building dependency tree... 610s Reading state information... 610s Calculating upgrade... 611s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 611s Reading package lists... 611s Building dependency tree... 611s Reading state information... 612s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 612s autopkgtest [21:58:02]: rebooting testbed after setup commands that affected boot 866s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 878s Reading package lists... 879s Building dependency tree... 879s Reading state information... 880s Starting pkgProblemResolver with broken count: 0 880s Starting 2 pkgProblemResolver with broken count: 0 880s Done 882s The following additional packages will be installed: 882s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 882s liblbfgsb0 liblzf1 libpython3.11-minimal libpython3.11-stdlib libsz2 882s python3-all python3-biom-format python3-click python3-colorama 882s python3-dateutil python3-decorator python3-distutils python3-h5py 882s python3-h5py-serial python3-lib2to3 python3-numpy python3-pandas 882s python3-pandas-lib python3-scipy python3.11 python3.11-minimal 882s Suggested packages: 882s python-biom-format-doc python-h5py-doc gcc gfortran python3-dev 882s python3-pytest python-pandas-doc python3-statsmodels python-scipy-doc 882s python3.11-venv python3.11-doc binfmt-support 882s Recommended packages: 882s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 882s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 882s g++ | c++-compiler python3-pil 883s The following NEW packages will be installed: 883s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 883s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libpython3.11-minimal 883s libpython3.11-stdlib libsz2 python3-all python3-biom-format python3-click 883s python3-colorama python3-dateutil python3-decorator python3-distutils 883s python3-h5py python3-h5py-serial python3-lib2to3 python3-numpy 883s python3-pandas python3-pandas-lib python3-scipy python3.11 883s python3.11-minimal 883s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. 883s Need to get 44.9 MB/44.9 MB of archives. 883s After this operation, 228 MB of additional disk space will be used. 883s Get:1 /tmp/autopkgtest.GVR3BZ/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 883s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 884s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 884s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 884s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 884s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 884s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 884s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 884s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 884s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu2 [1192 kB] 884s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-3.1ubuntu2 [55.8 kB] 884s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 884s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 884s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 884s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 884s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 884s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 884s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 884s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu2 [887 kB] 884s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py all 3.10.0-1ubuntu2 [7980 B] 884s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 884s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 python3-click all 8.1.6-1 [79.0 kB] 884s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 884s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 884s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 884s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 884s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 885s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biom-format arm64 2.1.15.2-3 [170 kB] 886s Fetched 44.9 MB in 2s (25.7 MB/s) 886s Selecting previously unselected package libpython3.11-minimal:arm64. 886s (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 ... 74761 files and directories currently installed.) 886s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ... 886s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 886s Selecting previously unselected package python3.11-minimal. 886s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ... 886s Unpacking python3.11-minimal (3.11.8-1) ... 886s Selecting previously unselected package libpython3.11-stdlib:arm64. 886s Preparing to unpack .../02-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 886s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 887s Selecting previously unselected package python3.11. 887s Preparing to unpack .../03-python3.11_3.11.8-1_arm64.deb ... 887s Unpacking python3.11 (3.11.8-1) ... 887s Selecting previously unselected package libaec0:arm64. 887s Preparing to unpack .../04-libaec0_1.1.2-1_arm64.deb ... 887s Unpacking libaec0:arm64 (1.1.2-1) ... 887s Selecting previously unselected package libblas3:arm64. 887s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ... 887s Unpacking libblas3:arm64 (3.12.0-3) ... 887s Selecting previously unselected package libgfortran5:arm64. 887s Preparing to unpack .../06-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 887s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 887s Selecting previously unselected package libsz2:arm64. 887s Preparing to unpack .../07-libsz2_1.1.2-1_arm64.deb ... 887s Unpacking libsz2:arm64 (1.1.2-1) ... 887s Selecting previously unselected package libhdf5-103-1t64:arm64. 887s Preparing to unpack .../08-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 887s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 887s Selecting previously unselected package libhdf5-hl-100t64:arm64. 887s Preparing to unpack .../09-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 887s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 887s Selecting previously unselected package liblapack3:arm64. 887s Preparing to unpack .../10-liblapack3_3.12.0-3_arm64.deb ... 887s Unpacking liblapack3:arm64 (3.12.0-3) ... 888s Selecting previously unselected package liblbfgsb0:arm64. 888s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 888s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 888s Selecting previously unselected package liblzf1:arm64. 888s Preparing to unpack .../12-liblzf1_3.6-4_arm64.deb ... 888s Unpacking liblzf1:arm64 (3.6-4) ... 888s Selecting previously unselected package python3-lib2to3. 888s Preparing to unpack .../13-python3-lib2to3_3.11.5-1_all.deb ... 888s Unpacking python3-lib2to3 (3.11.5-1) ... 888s Selecting previously unselected package python3-distutils. 888s Preparing to unpack .../14-python3-distutils_3.11.5-1_all.deb ... 888s Unpacking python3-distutils (3.11.5-1) ... 888s Selecting previously unselected package python3-all. 888s Preparing to unpack .../15-python3-all_3.12.1-0ubuntu2_arm64.deb ... 888s Unpacking python3-all (3.12.1-0ubuntu2) ... 888s Selecting previously unselected package python3-numpy. 888s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_arm64.deb ... 888s Unpacking python3-numpy (1:1.24.2-2) ... 888s Selecting previously unselected package python3-h5py-serial. 888s Preparing to unpack .../17-python3-h5py-serial_3.10.0-1ubuntu2_arm64.deb ... 888s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ... 889s Selecting previously unselected package python3-h5py. 889s Preparing to unpack .../18-python3-h5py_3.10.0-1ubuntu2_all.deb ... 889s Unpacking python3-h5py (3.10.0-1ubuntu2) ... 889s Selecting previously unselected package python3-colorama. 889s Preparing to unpack .../19-python3-colorama_0.4.6-4_all.deb ... 889s Unpacking python3-colorama (0.4.6-4) ... 889s Selecting previously unselected package python3-click. 889s Preparing to unpack .../20-python3-click_8.1.6-1_all.deb ... 889s Unpacking python3-click (8.1.6-1) ... 889s Selecting previously unselected package python3-dateutil. 889s Preparing to unpack .../21-python3-dateutil_2.8.2-3_all.deb ... 889s Unpacking python3-dateutil (2.8.2-3) ... 889s Selecting previously unselected package python3-pandas-lib:arm64. 889s Preparing to unpack .../22-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 889s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 889s Selecting previously unselected package python3-pandas. 889s Preparing to unpack .../23-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 889s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 890s Selecting previously unselected package python3-decorator. 890s Preparing to unpack .../24-python3-decorator_5.1.1-5_all.deb ... 890s Unpacking python3-decorator (5.1.1-5) ... 890s Selecting previously unselected package python3-scipy. 890s Preparing to unpack .../25-python3-scipy_1.11.4-6_arm64.deb ... 890s Unpacking python3-scipy (1.11.4-6) ... 890s Selecting previously unselected package python3-biom-format. 891s Preparing to unpack .../26-python3-biom-format_2.1.15.2-3_arm64.deb ... 891s Unpacking python3-biom-format (2.1.15.2-3) ... 891s Selecting previously unselected package autopkgtest-satdep. 892s Preparing to unpack .../27-2-autopkgtest-satdep.deb ... 892s Unpacking autopkgtest-satdep (0) ... 892s Setting up python3-colorama (0.4.6-4) ... 892s Setting up python3-click (8.1.6-1) ... 893s Setting up libaec0:arm64 (1.1.2-1) ... 893s Setting up python3-decorator (5.1.1-5) ... 893s Setting up libblas3:arm64 (3.12.0-3) ... 893s 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 893s Setting up liblzf1:arm64 (3.6-4) ... 893s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 893s Setting up python3-dateutil (2.8.2-3) ... 893s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 893s Setting up python3-lib2to3 (3.11.5-1) ... 894s Setting up libsz2:arm64 (1.1.2-1) ... 894s Setting up python3-distutils (3.11.5-1) ... 894s python3.12: can't get files for byte-compilation 894s Setting up python3.11-minimal (3.11.8-1) ... 895s Setting up liblapack3:arm64 (3.12.0-3) ... 895s 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 895s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 895s Setting up python3-all (3.12.1-0ubuntu2) ... 895s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 895s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 895s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 895s Setting up python3.11 (3.11.8-1) ... 896s Setting up python3-numpy (1:1.24.2-2) ... 899s Setting up python3-scipy (1.11.4-6) ... 902s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 902s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ... 902s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 906s Setting up python3-h5py (3.10.0-1ubuntu2) ... 906s Setting up python3-biom-format (2.1.15.2-3) ... 907s Setting up autopkgtest-satdep (0) ... 907s Processing triggers for systemd (255.2-3ubuntu2) ... 907s Processing triggers for man-db (2.12.0-3) ... 908s Processing triggers for libc-bin (2.39-0ubuntu2) ... 912s (Reading database ... 80239 files and directories currently installed.) 912s Removing autopkgtest-satdep (0) ... 916s autopkgtest [22:03:06]: 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 916s autopkgtest [22:03:06]: test autodep8-python3: [----------------------- 917s Testing with python3.12: 920s 921s autopkgtest [22:03:11]: test autodep8-python3: -----------------------] 922s autopkgtest [22:03:12]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 922s autodep8-python3 PASS (superficial) 922s autopkgtest [22:03:12]: @@@@@@@@@@@@@@@@@@@@ summary 922s run-unit-test PASS 922s autodep8-python3 PASS (superficial) 942s Creating nova instance adt-noble-arm64-python-biom-format-20240313-214750-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240313.img (UUID 363cdc04-8630-403e-ac93-f1c7b1a75157)... 942s Creating nova instance adt-noble-arm64-python-biom-format-20240313-214750-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240313.img (UUID 363cdc04-8630-403e-ac93-f1c7b1a75157)...