0s autopkgtest [21:49:17]: starting date and time: 2024-03-13 21:49:17+0000
  0s autopkgtest [21:49:17]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [21:49:17]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o0w0ivmg/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-skbio --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-2@bos02-arm64-12.secgroup --name adt-noble-arm64-python-skbio-20240313-214917-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/
275s autopkgtest [21:53:52]: testbed dpkg architecture: arm64
276s autopkgtest [21:53:53]: testbed apt version: 2.7.12
276s autopkgtest [21:53:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup
276s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
278s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2818 kB]
279s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [42.3 kB]
279s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB]
279s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B]
279s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [603 kB]
279s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
279s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB]
279s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
279s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3218 kB]
280s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
280s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [42.3 kB]
280s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
289s Fetched 7327 kB in 5s (1451 kB/s)
289s Reading package lists...
291s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
293s Reading package lists...
308s Reading package lists...
309s Building dependency tree...
309s Reading state information...
310s Calculating upgrade...
312s The following packages will be REMOVED:
312s   libssl3
312s The following NEW packages will be installed:
312s   libssl3t64
312s The following packages will be upgraded:
312s   console-setup console-setup-linux keyboard-configuration openssl
312s 4 upgraded, 1 newly installed, 1 to remove and 0 not upgraded.
312s Need to get 4955 kB of archives.
312s After this operation, 74.8 kB of additional disk space will be used.
312s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
313s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
314s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup-linux all 1.226ubuntu1 [1880 kB]
315s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup all 1.226ubuntu1 [110 kB]
315s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 keyboard-configuration all 1.226ubuntu1 [212 kB]
316s Preconfiguring packages ...
317s Fetched 4955 kB in 3s (1748 kB/s)
317s (Reading database ... 
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(Reading database ... 75867 files and directories currently installed.)
317s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
317s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
318s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
318s  wget depends on libssl3 (>= 3.0.0).
318s  u-boot-tools depends on libssl3 (>= 3.0.0).
318s  tnftp depends on libssl3 (>= 3.0.0).
318s  tcpdump depends on libssl3 (>= 3.0.0).
318s  systemd-resolved depends on libssl3 (>= 3.0.0).
318s  systemd depends on libssl3 (>= 3.0.0).
318s  sudo depends on libssl3 (>= 3.0.0).
318s  sbsigntool depends on libssl3 (>= 3.0.0).
318s  rsync depends on libssl3 (>= 3.0.0).
318s  python3-cryptography depends on libssl3 (>= 3.0.0).
318s  openssh-server depends on libssl3 (>= 3.0.10).
318s  openssh-client depends on libssl3 (>= 3.0.10).
318s  mtd-utils depends on libssl3 (>= 3.0.0).
318s  mokutil depends on libssl3 (>= 3.0.0).
318s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
318s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
318s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
318s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
318s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
318s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
318s  libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0).
318s  libnvme1 depends on libssl3 (>= 3.0.0).
318s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
318s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
318s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
318s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
318s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
318s  kmod depends on libssl3 (>= 3.0.0).
318s  dhcpcd-base depends on libssl3 (>= 3.0.0).
318s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
318s 
318s (Reading database ... 
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(Reading database ... 75867 files and directories currently installed.)
318s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
318s Selecting previously unselected package libssl3t64:arm64.
318s (Reading database ... 
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(Reading database ... 75856 files and directories currently installed.)
319s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
319s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
319s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ...
319s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ...
320s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ...
320s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ...
320s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ...
320s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ...
320s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
320s Setting up keyboard-configuration (1.226ubuntu1) ...
324s Your console font configuration will be updated the next time your system
326s boots. If you want to update it now, run 'setupcon' from a virtual console.
326s update-initramfs: deferring update (trigger activated)
326s Setting up openssl (3.0.13-0ubuntu1) ...
326s Setting up console-setup-linux (1.226ubuntu1) ...
330s Setting up console-setup (1.226ubuntu1) ...
332s update-initramfs: deferring update (trigger activated)
333s Processing triggers for man-db (2.12.0-3) ...
334s Processing triggers for libc-bin (2.39-0ubuntu2) ...
334s Processing triggers for initramfs-tools (0.142ubuntu20) ...
334s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic
334s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
406s System running in EFI mode, skipping.
407s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
407s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
407s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
407s Reading package lists...
408s Building dependency tree...
408s Reading state information...
410s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
411s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
411s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
411s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
411s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
411s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease
426s Reading package lists...
426s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
426s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
426s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1
426s Reading package lists...
427s Building dependency tree...
427s Reading state information...
429s Calculating upgrade...
430s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
430s Reading package lists...
431s Building dependency tree...
431s Reading state information...
433s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
434s autopkgtest [21:56:31]: rebooting testbed after setup commands that affected boot
597s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
606s autopkgtest [21:59:23]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
610s autopkgtest [21:59:27]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio
616s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-skbio 0.5.9-4 (dsc) [2804 B]
616s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-skbio 0.5.9-4 (tar) [3559 kB]
616s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-skbio 0.5.9-4 (diff) [15.7 kB]
617s gpgv: Signature made Sun Feb 11 20:35:02 2024 UTC
617s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
617s gpgv:                issuer "tille@debian.org"
617s gpgv: Can't check signature: No public key
617s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.5.9-4.dsc: no acceptable signature found
618s autopkgtest [21:59:35]: testing package python-skbio version 0.5.9-4
618s autopkgtest [21:59:35]: build not needed
620s autopkgtest [21:59:37]: test import-skbio: preparing testbed
625s Reading package lists...
625s Building dependency tree...
625s Reading state information...
626s Starting pkgProblemResolver with broken count: 0
627s Starting 2 pkgProblemResolver with broken count: 0
627s Done
629s The following additional packages will be installed:
629s   blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libaec0
629s   libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3
629s   libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libjbig0
629s   libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0
629s   liblcms2-2 liblerc4 liblzf1 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0
629s   libssw0 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2
629s   libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data
629s   python3-appdirs python3-asttokens python3-brotli python3-contourpy
629s   python3-cycler python3-dateutil python3-decorator python3-executing
629s   python3-fonttools python3-fs python3-h5py python3-h5py-serial
629s   python3-hdmedians python3-iniconfig python3-ipython python3-jedi
629s   python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib
629s   python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy
629s   python3-packaging python3-pandas python3-pandas-lib python3-parso
629s   python3-pexpect python3-pil python3-pil.imagetk python3-pluggy
629s   python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest
629s   python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk
629s   python3-traitlets python3-ufolib2 python3-unicodedata2 python3-wcwidth
629s   tk8.6-blt2.5 unicode-data x11-common
629s Suggested packages:
629s   blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc
629s   python-h5py-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng
629s   ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3
629s   librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject
629s   python3-pyqt5 python3-sip python3-tornado texlive-extra-utils
629s   texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gcc
629s   gfortran python3-dev python-pandas-doc python3-statsmodels
629s   python-pexpect-doc python-pil-doc python-scipy-doc python-skbio-doc
629s   texlive-fonts-extra python-sympy-doc tix python3-tk-dbg
629s Recommended packages:
629s   javascript-common python3-bs4 python3-cssselect python3-html5lib
629s   python3-bottleneck python3-numexpr python3-odf python3-openpyxl
629s   python3-tables python3-olefile g++ | c++-compiler isympy-common
629s The following NEW packages will be installed:
629s   autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono
629s   fonts-lyx libaec0 libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1
629s   libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64
629s   libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui
629s   liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblzf1 libopenjp2-7 libqhull-r8.0
629s   libraqm0 libsharpyuv0 libssw0 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7
629s   libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1
629s   python-matplotlib-data python3-appdirs python3-asttokens python3-brotli
629s   python3-contourpy python3-cycler python3-dateutil python3-decorator
629s   python3-executing python3-fonttools python3-fs python3-h5py
629s   python3-h5py-serial python3-hdmedians python3-iniconfig python3-ipython
629s   python3-jedi python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib
629s   python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy
629s   python3-packaging python3-pandas python3-pandas-lib python3-parso
629s   python3-pexpect python3-pil python3-pil.imagetk python3-pluggy
629s   python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest
629s   python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk
629s   python3-traitlets python3-ufolib2 python3-unicodedata2 python3-wcwidth
629s   tk8.6-blt2.5 unicode-data x11-common
629s 0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded.
629s Need to get 78.2 MB/78.2 MB of archives.
629s After this operation, 381 MB of additional disk space will be used.
629s Get:1 /tmp/autopkgtest.rzxpkO/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B]
629s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB]
630s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
630s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
630s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
630s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
630s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
630s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB]
630s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
630s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B]
630s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB]
630s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB]
631s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B]
631s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC3-1 [170 kB]
631s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB]
631s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
631s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
631s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
631s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
631s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
631s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
631s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B]
631s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu2 [1192 kB]
631s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-3.1ubuntu2 [55.8 kB]
631s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB]
631s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
631s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
631s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
631s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
631s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
631s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB]
632s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB]
632s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
632s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B]
632s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB]
632s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB]
632s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
632s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 libssw0 arm64 1.1-14 [21.1 kB]
632s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
632s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
632s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
632s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB]
632s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB]
632s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.35-1 [161 kB]
632s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB]
632s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB]
632s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-asttokens all 2.4.1-1 [20.9 kB]
632s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB]
632s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
632s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB]
632s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B]
632s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB]
632s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
632s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-executing all 2.0.1-0.1 [23.3 kB]
632s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB]
634s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB]
634s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB]
634s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB]
634s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB]
634s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB]
634s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB]
634s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1 [362 kB]
634s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB]
634s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB]
634s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu2 [887 kB]
635s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py all 3.10.0-1ubuntu2 [7980 B]
635s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-hdmedians arm64 0.14.2-5.1 [170 kB]
635s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B]
635s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-parso all 0.8.3-1 [67.2 kB]
635s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jedi all 0.18.2-1ubuntu1 [692 kB]
635s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-traitlets all 5.5.0-2 [85.0 kB]
635s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B]
635s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 python3-ptyprocess all 0.7.0-5 [15.1 kB]
635s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pexpect all 4.9-2 [48.1 kB]
635s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB]
635s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-prompt-toolkit all 3.0.43-1 [256 kB]
635s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pure-eval all 0.2.2-1 [11.3 kB]
635s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB]
635s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ipython all 8.20.0-1 [561 kB]
635s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-1build2 [65.4 kB]
635s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB]
635s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB]
635s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB]
635s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B]
635s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB]
635s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB]
635s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB]
635s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB]
636s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB]
636s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB]
636s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB]
636s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-skbio arm64 0.5.9-4 [883 kB]
639s Fetched 78.2 MB in 7s (11.1 MB/s)
639s Selecting previously unselected package libtcl8.6:arm64.
639s (Reading database ... 
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639s Preparing to unpack .../00-libtcl8.6_8.6.13+dfsg-2_arm64.deb ...
639s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ...
639s Selecting previously unselected package fonts-dejavu-mono.
639s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ...
639s Unpacking fonts-dejavu-mono (2.37-8) ...
639s Selecting previously unselected package fonts-dejavu-core.
639s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ...
640s Unpacking fonts-dejavu-core (2.37-8) ...
640s Selecting previously unselected package fontconfig-config.
640s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
640s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
641s Selecting previously unselected package libfontconfig1:arm64.
641s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
641s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
641s Selecting previously unselected package libxrender1:arm64.
641s Preparing to unpack .../05-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
641s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
641s Selecting previously unselected package libxft2:arm64.
641s Preparing to unpack .../06-libxft2_2.3.6-1_arm64.deb ...
641s Unpacking libxft2:arm64 (2.3.6-1) ...
641s Selecting previously unselected package x11-common.
641s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu2_all.deb ...
641s Unpacking x11-common (1:7.7+23ubuntu2) ...
641s Selecting previously unselected package libxss1:arm64.
641s Preparing to unpack .../08-libxss1_1%3a1.2.3-1build2_arm64.deb ...
641s Unpacking libxss1:arm64 (1:1.2.3-1build2) ...
641s Selecting previously unselected package libtk8.6:arm64.
641s Preparing to unpack .../09-libtk8.6_8.6.13-2_arm64.deb ...
641s Unpacking libtk8.6:arm64 (8.6.13-2) ...
641s Selecting previously unselected package tk8.6-blt2.5.
641s Preparing to unpack .../10-tk8.6-blt2.5_2.5.3+dfsg-7_arm64.deb ...
641s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ...
642s Selecting previously unselected package blt.
642s Preparing to unpack .../11-blt_2.5.3+dfsg-7_arm64.deb ...
642s Unpacking blt (2.5.3+dfsg-7) ...
642s Selecting previously unselected package fonts-lyx.
642s Preparing to unpack .../12-fonts-lyx_2.4.0~RC3-1_all.deb ...
642s Unpacking fonts-lyx (2.4.0~RC3-1) ...
642s Selecting previously unselected package libaec0:arm64.
642s Preparing to unpack .../13-libaec0_1.1.2-1_arm64.deb ...
642s Unpacking libaec0:arm64 (1.1.2-1) ...
642s Selecting previously unselected package libblas3:arm64.
642s Preparing to unpack .../14-libblas3_3.12.0-3_arm64.deb ...
642s Unpacking libblas3:arm64 (3.12.0-3) ...
642s Selecting previously unselected package libdeflate0:arm64.
642s Preparing to unpack .../15-libdeflate0_1.19-1_arm64.deb ...
642s Unpacking libdeflate0:arm64 (1.19-1) ...
642s Selecting previously unselected package libgfortran5:arm64.
642s Preparing to unpack .../16-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
642s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
642s Selecting previously unselected package libgomp1:arm64.
642s Preparing to unpack .../17-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
642s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
642s Selecting previously unselected package libgraphite2-3:arm64.
642s Preparing to unpack .../18-libgraphite2-3_1.3.14-2_arm64.deb ...
642s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
643s Selecting previously unselected package libharfbuzz0b:arm64.
643s Preparing to unpack .../19-libharfbuzz0b_8.3.0-2_arm64.deb ...
643s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
643s Selecting previously unselected package libsz2:arm64.
643s Preparing to unpack .../20-libsz2_1.1.2-1_arm64.deb ...
643s Unpacking libsz2:arm64 (1.1.2-1) ...
643s Selecting previously unselected package libhdf5-103-1t64:arm64.
643s Preparing to unpack .../21-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_arm64.deb ...
643s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ...
643s Selecting previously unselected package libhdf5-hl-100t64:arm64.
643s Preparing to unpack .../22-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_arm64.deb ...
643s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ...
643s Selecting previously unselected package libimagequant0:arm64.
643s Preparing to unpack .../23-libimagequant0_2.18.0-1_arm64.deb ...
643s Unpacking libimagequant0:arm64 (2.18.0-1) ...
643s Selecting previously unselected package libjpeg-turbo8:arm64.
643s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
643s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
643s Selecting previously unselected package libjpeg8:arm64.
643s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_arm64.deb ...
643s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
643s Selecting previously unselected package libjs-jquery.
643s Preparing to unpack .../26-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
643s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
644s Selecting previously unselected package libjs-jquery-ui.
644s Preparing to unpack .../27-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
644s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
644s Selecting previously unselected package liblapack3:arm64.
644s Preparing to unpack .../28-liblapack3_3.12.0-3_arm64.deb ...
644s Unpacking liblapack3:arm64 (3.12.0-3) ...
644s Selecting previously unselected package liblbfgsb0:arm64.
644s Preparing to unpack .../29-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ...
644s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ...
644s Selecting previously unselected package liblcms2-2:arm64.
644s Preparing to unpack .../30-liblcms2-2_2.14-2_arm64.deb ...
644s Unpacking liblcms2-2:arm64 (2.14-2) ...
644s Selecting previously unselected package liblerc4:arm64.
644s Preparing to unpack .../31-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
644s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
645s Selecting previously unselected package liblzf1:arm64.
645s Preparing to unpack .../32-liblzf1_3.6-4_arm64.deb ...
645s Unpacking liblzf1:arm64 (3.6-4) ...
645s Selecting previously unselected package libqhull-r8.0:arm64.
645s Preparing to unpack .../33-libqhull-r8.0_2020.2-6_arm64.deb ...
645s Unpacking libqhull-r8.0:arm64 (2020.2-6) ...
645s Selecting previously unselected package libraqm0:arm64.
645s Preparing to unpack .../34-libraqm0_0.10.1-1_arm64.deb ...
645s Unpacking libraqm0:arm64 (0.10.1-1) ...
645s Selecting previously unselected package libsharpyuv0:arm64.
645s Preparing to unpack .../35-libsharpyuv0_1.3.2-0.4_arm64.deb ...
645s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
645s Selecting previously unselected package libssw0:arm64.
645s Preparing to unpack .../36-libssw0_1.1-14_arm64.deb ...
645s Unpacking libssw0:arm64 (1.1-14) ...
645s Selecting previously unselected package libjbig0:arm64.
645s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
645s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
645s Selecting previously unselected package libwebp7:arm64.
645s Preparing to unpack .../38-libwebp7_1.3.2-0.4_arm64.deb ...
645s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
645s Selecting previously unselected package libtiff6:arm64.
645s Preparing to unpack .../39-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
645s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
645s Selecting previously unselected package libwebpdemux2:arm64.
646s Preparing to unpack .../40-libwebpdemux2_1.3.2-0.4_arm64.deb ...
646s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ...
646s Selecting previously unselected package libwebpmux3:arm64.
646s Preparing to unpack .../41-libwebpmux3_1.3.2-0.4_arm64.deb ...
646s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ...
646s Selecting previously unselected package libxslt1.1:arm64.
646s Preparing to unpack .../42-libxslt1.1_1.1.35-1_arm64.deb ...
646s Unpacking libxslt1.1:arm64 (1.1.35-1) ...
646s Selecting previously unselected package python-matplotlib-data.
646s Preparing to unpack .../43-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ...
646s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ...
646s Selecting previously unselected package python3-appdirs.
646s Preparing to unpack .../44-python3-appdirs_1.4.4-4_all.deb ...
646s Unpacking python3-appdirs (1.4.4-4) ...
646s Selecting previously unselected package python3-asttokens.
646s Preparing to unpack .../45-python3-asttokens_2.4.1-1_all.deb ...
646s Unpacking python3-asttokens (2.4.1-1) ...
646s Selecting previously unselected package python3-brotli.
647s Preparing to unpack .../46-python3-brotli_1.1.0-2_arm64.deb ...
647s Unpacking python3-brotli (1.1.0-2) ...
647s Selecting previously unselected package python3-numpy.
647s Preparing to unpack .../47-python3-numpy_1%3a1.24.2-2_arm64.deb ...
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657s Selecting previously unselected package python3-iniconfig.
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659s Selecting previously unselected package python3-ptyprocess.
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667s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
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667s Setting up python3-iniconfig (1.1.1-2) ...
668s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
668s Setting up python3-pure-eval (0.2.2-1) ...
668s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
668s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
668s Setting up python3-parso (0.8.3-1) ...
669s Setting up python3-lz4 (4.0.2+dfsg-1build2) ...
670s Setting up python3-asttokens (2.4.1-1) ...
670s Setting up python3-unicodedata2 (15.1.0+ds-1) ...
670s Setting up fonts-lyx (2.4.0~RC3-1) ...
670s Setting up x11-common (1:7.7+23ubuntu2) ...
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672s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
672s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
672s Setting up libaec0:arm64 (1.1.2-1) ...
672s Setting up python3-natsort (8.0.2-2) ...
673s Setting up unicode-data (15.1.0-1) ...
673s Setting up python3-decorator (5.1.1-5) ...
674s Setting up libblas3:arm64 (3.12.0-3) ...
674s 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
674s Setting up python3-packaging (23.2-1) ...
675s Setting up python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ...
676s Setting up python3-executing (2.0.1-0.1) ...
676s Setting up python3-brotli (1.1.0-2) ...
677s Setting up liblzf1:arm64 (3.6-4) ...
677s Setting up python3-cycler (0.11.0-2) ...
678s Setting up libimagequant0:arm64 (2.18.0-1) ...
678s Setting up fonts-dejavu-mono (2.37-8) ...
678s Setting up python3-kiwisolver (1.4.4-1build2) ...
678s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ...
678s Setting up fonts-dejavu-core (2.37-8) ...
678s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
678s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
678s Setting up python3-pluggy (1.4.0-1) ...
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679s Setting up python3-traitlets (5.5.0-2) ...
680s Setting up libxslt1.1:arm64 (1.1.35-1) ...
680s Setting up libopenjp2-7:arm64 (2.5.0-2) ...
680s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
681s Setting up python3-dateutil (2.8.2-3) ...
681s Setting up libxss1:arm64 (1:1.2.3-1build2) ...
681s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
681s Setting up python3-mpmath (1.2.1-3) ...
684s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ...
684s Setting up libwebpmux3:arm64 (1.3.2-0.4) ...
684s Setting up python3-appdirs (1.4.4-4) ...
684s Setting up python3-stack-data (0.6.3-1) ...
685s Setting up libssw0:arm64 (1.1-14) ...
685s Setting up libsz2:arm64 (1.1.2-1) ...
685s Setting up python3-ptyprocess (0.7.0-5) ...
686s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
686s Setting up python3-prompt-toolkit (3.0.43-1) ...
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711s Setting up python3-jedi (0.18.2-1ubuntu1) ...
712s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
713s Setting up python3-pytest (7.4.4-1) ...
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714s Setting up python3-matplotlib-inline (0.1.6-2) ...
714s Setting up python3-fs (2.4.16-3) ...
715s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
715s Setting up python3-pexpect (4.9-2) ...
716s Setting up libraqm0:arm64 (0.10.1-1) ...
716s Setting up python3-numpy (1:1.24.2-2) ...
723s Setting up python3-hdmedians (0.14.2-5.1) ...
724s Setting up python3-lxml:arm64 (5.1.0-1) ...
725s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
725s Setting up python3-contourpy (1.0.7-1build2) ...
725s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
725s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ...
725s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ...
725s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ...
725s Setting up libxft2:arm64 (2.3.6-1) ...
725s Setting up python3-scipy (1.11.4-6) ...
737s Setting up libtk8.6:arm64 (8.6.13-2) ...
737s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ...
737s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ...
738s Setting up python3-pil:arm64 (10.2.0-1) ...
739s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ...
756s Setting up python3-ipython (8.20.0-1) ...
758s Setting up python3-h5py (3.10.0-1ubuntu2) ...
759s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ...
759s Setting up blt (2.5.3+dfsg-7) ...
759s Setting up python3-tk:arm64 (3.11.5-1) ...
760s Setting up python3-pil.imagetk:arm64 (10.2.0-1) ...
760s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ...
761s Setting up python3-fonttools (4.46.0-1) ...
765s Setting up python3-matplotlib (3.6.3-1ubuntu3) ...
770s Setting up python3-skbio (0.5.9-4) ...
773s Setting up autopkgtest-satdep (0) ...
773s Processing triggers for libc-bin (2.39-0ubuntu2) ...
773s Processing triggers for man-db (2.12.0-3) ...
788s (Reading database ... 88443 files and directories currently installed.)
788s Removing autopkgtest-satdep (0) ...
789s autopkgtest [22:02:26]: test import-skbio: [-----------------------
796s autopkgtest [22:02:33]: test import-skbio: -----------------------]
797s autopkgtest [22:02:34]: test import-skbio:  - - - - - - - - - - results - - - - - - - - - -
797s import-skbio         PASS
797s autopkgtest [22:02:34]: test testsuite: preparing testbed
803s Reading package lists...
804s Building dependency tree...
804s Reading state information...
805s Starting pkgProblemResolver with broken count: 0
805s Starting 2 pkgProblemResolver with broken count: 0
805s Done
807s The following NEW packages will be installed:
807s   autopkgtest-satdep
807s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
807s Need to get 0 B/712 B of archives.
807s After this operation, 0 B of additional disk space will be used.
807s Get:1 /tmp/autopkgtest.rzxpkO/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B]
809s Selecting previously unselected package autopkgtest-satdep.
809s (Reading database ... 
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810s Setting up autopkgtest-satdep (0) ...
817s (Reading database ... 88443 files and directories currently installed.)
817s Removing autopkgtest-satdep (0) ...
818s autopkgtest [22:02:55]: test testsuite: [-----------------------
819s + find . -name _hommola.py -exec sed -i /Run the cospeciation test with 99 permutations. Note that the correlation/,/After permuting host : parasite interactions, we find that the observed/d {} ;
819s + find . -name power.py -exec sed -i /Now, let's use random sampling to estimate the power of our test on/,/Based on this power estimate, as we increase our confidence that we have not/d {} ;
819s + http_proxy=http://127.0.0.1:9 python3 -m pytest --pyargs skbio
833s ============================= test session starts ==============================
833s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0
833s rootdir: /tmp/autopkgtest.rzxpkO/autopkgtest_tmp
833s collected 2390 items
833s 
835s skbio/alignment/tests/test_pairwise.py .........................         [  1%]
836s skbio/alignment/tests/test_ssw.py ...........................            [  2%]
836s skbio/alignment/tests/test_tabular_msa.py .............................. [  3%]
837s ........................................................................ [  6%]
843s ........................................................................ [  9%]
850s ........................................................................ [ 12%]
850s ........................................................................ [ 15%]
851s ........................................................................ [ 18%]
851s ..........                                                               [ 18%]
851s skbio/diversity/alpha/tests/test_ace.py ..                               [ 18%]
854s skbio/diversity/alpha/tests/test_base.py ........................        [ 20%]
854s skbio/diversity/alpha/tests/test_chao1.py ...                            [ 20%]
854s skbio/diversity/alpha/tests/test_faith_pd.py ........                    [ 20%]
855s skbio/diversity/alpha/tests/test_gini.py ....                            [ 20%]
858s skbio/diversity/alpha/tests/test_lladser.py ............                 [ 21%]
859s skbio/diversity/beta/tests/test_unifrac.py ............................  [ 22%]
859s skbio/diversity/tests/test_block.py ...........                          [ 22%]
860s skbio/diversity/tests/test_driver.py ................................... [ 24%]
860s                                                                          [ 24%]
860s skbio/diversity/tests/test_util.py ...........                           [ 24%]
860s skbio/io/format/tests/test_base.py ................................      [ 26%]
861s skbio/io/format/tests/test_binary_dm.py .........                        [ 26%]
861s skbio/io/format/tests/test_blast6.py ...........                         [ 26%]
863s skbio/io/format/tests/test_blast7.py ..............                      [ 27%]
863s skbio/io/format/tests/test_clustal.py .............                      [ 27%]
873s skbio/io/format/tests/test_embl.py ...............................       [ 29%]
873s skbio/io/format/tests/test_emptyfile.py ..                               [ 29%]
902s skbio/io/format/tests/test_fasta.py ................                     [ 30%]
923s skbio/io/format/tests/test_fastq.py ...............                      [ 30%]
926s skbio/io/format/tests/test_genbank.py .....................              [ 31%]
928s skbio/io/format/tests/test_gff3.py ........................              [ 32%]
928s skbio/io/format/tests/test_lsmat.py .......                              [ 32%]
928s skbio/io/format/tests/test_newick.py .......                             [ 33%]
931s skbio/io/format/tests/test_ordination.py .....                           [ 33%]
935s skbio/io/format/tests/test_phylip.py .......                             [ 33%]
938s skbio/io/format/tests/test_qseq.py ......                                [ 33%]
938s skbio/io/format/tests/test_sequence_feature_vocabulary.py ....           [ 34%]
942s skbio/io/format/tests/test_stockholm.py ................................ [ 35%]
944s ...........................................                              [ 37%]
944s skbio/io/format/tests/test_taxdump.py ......                             [ 37%]
944s skbio/io/tests/test_iosources.py ..........                              [ 37%]
945s skbio/io/tests/test_registry.py ........................................ [ 39%]
945s ......................................................                   [ 41%]
952s skbio/io/tests/test_util.py .......................................XXsss [ 43%]
960s sssssssssssssssssssssssssss..................................xx......... [ 46%]
974s .........................xx..................................xx......... [ 49%]
979s .........................xx.....                                         [ 51%]
984s skbio/metadata/tests/test_intersection.py ...............                [ 51%]
985s skbio/metadata/tests/test_interval.py .................................. [ 53%]
985s .....................................                                    [ 54%]
985s skbio/metadata/tests/test_mixin.py ..................................... [ 56%]
986s .............................................................            [ 58%]
986s skbio/sequence/tests/test_distance.py ..........................         [ 59%]
986s skbio/sequence/tests/test_dna.py ....                                    [ 59%]
986s skbio/sequence/tests/test_genetic_code.py ..........................     [ 61%]
986s skbio/sequence/tests/test_grammared_sequence.py ........................ [ 62%]
986s ...................                                                      [ 62%]
987s skbio/sequence/tests/test_nucleotide_sequences.py ...................... [ 63%]
987s .......                                                                  [ 64%]
987s skbio/sequence/tests/test_protein.py ..........                          [ 64%]
987s skbio/sequence/tests/test_rna.py ....                                    [ 64%]
987s skbio/sequence/tests/test_sequence.py .................................. [ 66%]
988s ........................................................................ [ 69%]
988s ........................................................................ [ 72%]
989s ........................................................................ [ 75%]
989s .......                                                                  [ 75%]
991s skbio/stats/distance/tests/test_anosim.py ....                           [ 75%]
991s skbio/stats/distance/tests/test_base.py ................................ [ 76%]
994s ...................................................................      [ 79%]
1032s skbio/stats/distance/tests/test_bioenv.py .................              [ 80%]
1047s skbio/stats/distance/tests/test_mantel.py .............................. [ 81%]
1048s ..............                                                           [ 82%]
1049s skbio/stats/distance/tests/test_permanova.py ....                        [ 82%]
1077s skbio/stats/distance/tests/test_permdisp.py .............                [ 82%]
1077s skbio/stats/evolve/tests/test_hommola.py ............                    [ 83%]
1077s skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ 83%]
1078s .....                                                                    [ 83%]
1078s skbio/stats/ordination/tests/test_correspondence_analysis.py ........    [ 84%]
1081s skbio/stats/ordination/tests/test_ordination_results.py ................ [ 84%]
1081s                                                                          [ 84%]
1081s skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 84%]
1082s .......                                                                  [ 85%]
1083s skbio/stats/ordination/tests/test_redundancy_analysis.py ....            [ 85%]
1083s skbio/stats/ordination/tests/test_util.py ..........                     [ 85%]
1084s skbio/stats/tests/test_composition.py .................................. [ 87%]
1085s ...............................                                          [ 88%]
1087s skbio/stats/tests/test_gradient.py ..........................            [ 89%]
1087s skbio/stats/tests/test_misc.py ...                                       [ 89%]
1099s skbio/stats/tests/test_power.py ........................................ [ 91%]
1100s ...                                                                      [ 91%]
1100s skbio/stats/tests/test_subsample.py ............                         [ 92%]
1100s skbio/tests/test_base.py .....                                           [ 92%]
1100s skbio/tests/test_workflow.py .................                           [ 92%]
1101s skbio/tree/tests/test_majority_rule.py ......                            [ 93%]
1101s skbio/tree/tests/test_nj.py ...........                                  [ 93%]
1101s skbio/tree/tests/test_tree.py .......................................... [ 95%]
1102s ...................................................                      [ 97%]
1102s skbio/util/tests/test_decorator.py .......................               [ 98%]
1102s skbio/util/tests/test_misc.py ....................                       [ 99%]
1103s skbio/util/tests/test_testing.py ...............                         [100%]
1103s 
1103s =============================== warnings summary ===============================
1103s ../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37
1103s   /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC).
1103s     EPOCH = datetime.datetime.utcfromtimestamp(0)
1103s 
1103s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type
1103s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type
1103s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_kwargs_are_usable
1103s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_DNA
1103s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_Protein
1103s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_type_mismatch
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: local_pairwise_align_ssw is deprecated as of scikit-bio version 0.5.8, and will be removed in version 0.6.0. This will be removed or replaced, in favor of more general-purpose performant aligners. Additional details at https://github.com/biocore/scikit-bio/issues/1814
1103s     warnings.warn('%s is deprecated as of scikit-bio version %s, and '
1103s 
1103s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata
1103s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_constructor_makes_shallow_copy_of_positional_metadata
1103s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/metadata/_testing.py:445: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
1103s     df['bar'][0].append(42)
1103s 
1103s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_positional_metadata_setter_makes_shallow_copy
1103s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_positional_metadata_setter_makes_shallow_copy
1103s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_positional_metadata_setter_makes_shallow_copy
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/metadata/_testing.py:823: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
1103s     df['bar'][0].append(42)
1103s 
1103s skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in divide
1103s     gap_freqs /= length
1103s 
1103s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: invalid value encountered in scalar divide
1103s     return shannon(counts, base=np.e) / np.log(observed_otus(counts))
1103s 
1103s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/diversity/alpha/_base.py:887: RuntimeWarning: invalid value encountered in divide
1103s     freqs = counts / counts.sum()
1103s 
1103s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: divide by zero encountered in log
1103s     return shannon(counts, base=np.e) / np.log(observed_otus(counts))
1103s 
1103s skbio/diversity/tests/test_block.py: 3 warnings
1103s skbio/diversity/tests/test_driver.py: 9 warnings
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: partial_beta_diversity is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. The return type is unstable. Developer caution is advised. The resulting DistanceMatrix object will include zeros when distance has not been calculated, and therefore can be misleading.
1103s     warnings.warn('%s is deprecated as of scikit-bio version %s, and '
1103s 
1103s skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_vector_invalid_input
1103s   /usr/lib/python3/dist-packages/numpy/lib/type_check.py:300: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
1103s     return imag(x) == 0
1103s 
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: has_nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to has_definites
1103s     warnings.warn('%s is deprecated as of scikit-bio version %s, and '
1103s 
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
1103s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
1103s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
1103s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
1103s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
1103s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
1103s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerate_chars is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definite_chars
1103s     warnings.warn('%s is deprecated as of scikit-bio version %s, and '
1103s 
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
1103s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definites
1103s     warnings.warn('%s is deprecated as of scikit-bio version %s, and '
1103s 
1103s skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/sequence/_sequence.py:1820: RuntimeWarning: invalid value encountered in divide
1103s     obs_counts = obs_counts / len(self)
1103s 
1103s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/distance/_mantel.py:354: ConstantInputWarning: All values in data are exactly equal; results may not be reliable.
1103s     warnings.warn(ConstantInputWarning())
1103s 
1103s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/distance/_mantel.py:473: ConstantInputWarning: All values in data are exactly equal; results may not be reliable.
1103s     warnings.warn(ConstantInputWarning())
1103s 
1103s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups
1103s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -13.541846544269621 and the largest is 16.587201374785895.
1103s     warn(
1103s 
1103s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups
1103s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -15.629533932395201 and the largest is 20.903154277938906.
1103s     warn(
1103s 
1103s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in divide
1103s     proportion_explained = eigvals / sum_eigenvalues
1103s 
1103s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
1103s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal
1103s   /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4167: ConstantInputWarning: Each of the input arrays is constant;the F statistic is not defined or infinite
1103s     warnings.warn(stats.ConstantInputWarning(msg))
1103s 
1103s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results
1103s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.007758325147780542 and the largest is 2.7077929489469237.
1103s     warn(
1103s 
1103s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata
1103s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options
1103s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options
1103s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png
1103s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png
1103s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg
1103s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:285: UserWarning: Tight layout not applied. The left and right margins cannot be made large enough to accommodate all axes decorations.
1103s     fig.tight_layout()
1103s 
1103s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:263: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
1103s     plot = scatter_fn(c=point_colors, cmap=cmap)
1103s 
1103s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape
1103s   /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (<bound method TestRDAErrors.test_shape of <skbio.stats.ordination.tests.test_redundancy_analysis.TestRDAErrors testMethod=test_shape>>)
1103s     return self.run(*args, **kwds)
1103s 
1103s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAResults_biplot_score::test_biplot_score
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/ordination/tests/test_redundancy_analysis.py:248: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
1103s     scaling = (rda_.eigvals[0] / rda_.eigvals[:6])
1103s 
1103s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test
1103s   /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:523: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable.
1103s     res = hypotest_fun_out(*samples, **kwds)
1103s 
1103s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/composition.py:982: RuntimeWarning: divide by zero encountered in log
1103s     X_log = np.log(mat)
1103s 
1103s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr
1103s   /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2699: RuntimeWarning: invalid value encountered in subtract
1103s     X -= avg[:, None]
1103s 
1103s skbio/stats/tests/test_composition.py::TestVLR::test_vlr
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/composition.py:837: RuntimeWarning: divide by zero encountered in log
1103s     x = np.log(x)
1103s 
1103s skbio/stats/tests/test_composition.py::TestVLR::test_vlr
1103s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:236: RuntimeWarning: invalid value encountered in subtract
1103s     x = asanyarray(arr - arrmean)
1103s 
1103s skbio/stats/tests/test_gradient.py: 13 warnings
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/gradient.py:168: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
1103s     np.abs((w_vector[i] - w_vector[i-1]))
1103s 
1103s skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/stats/gradient.py:166: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '6.357142857142857' has dtype incompatible with int64, please explicitly cast to a compatible dtype first.
1103s     trajectories.loc[idx] = (
1103s 
1103s skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output
1103s   /tmp/autopkgtest.rzxpkO/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: f is deprecated as of scikit-bio version 0.1.0, and will be removed in version 0.1.4. You should now use skbio.g().
1103s     warnings.warn('%s is deprecated as of scikit-bio version %s, and '
1103s 
1103s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
1103s = 2350 passed, 30 skipped, 8 xfailed, 2 xpassed, 94 warnings in 282.75s (0:04:42) =
1106s autopkgtest [22:07:43]: test testsuite: -----------------------]
1107s autopkgtest [22:07:43]: test testsuite:  - - - - - - - - - - results - - - - - - - - - -
1107s testsuite            PASS
1107s autopkgtest [22:07:44]: @@@@@@@@@@@@@@@@@@@@ summary
1107s import-skbio         PASS
1107s testsuite            PASS
1129s Creating nova instance adt-noble-arm64-python-skbio-20240313-214917-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240313.img (UUID 20618c62-409e-4a2f-a5b9-d20441a97bde)...