0s autopkgtest [17:37:06]: starting date and time: 2024-03-16 17:37:06+0000
  0s autopkgtest [17:37:06]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [17:37:06]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kgfrt7jx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-bioc-mofa --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-20.secgroup --name adt-noble-arm64-r-bioc-mofa-20240316-173705-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 81s autopkgtest [17:38:27]: testbed dpkg architecture: arm64
 81s autopkgtest [17:38:27]: testbed apt version: 2.7.12
 81s autopkgtest [17:38:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 82s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 82s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3670 kB]
 83s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
 83s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 83s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [473 kB]
 83s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB]
 83s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 83s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
 83s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 83s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3995 kB]
 83s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 83s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB]
 83s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
 85s Fetched 9060 kB in 2s (5049 kB/s)
 86s Reading package lists...
 89s Reading package lists...
 90s Building dependency tree...
 90s Reading state information...
 91s Calculating upgrade...
 92s The following packages will be REMOVED:
 92s   libglib2.0-0 libssl3
 92s The following NEW packages will be installed:
 92s   libglib2.0-0t64 libssl3t64 xdg-user-dirs
 92s The following packages have been kept back:
 92s   curl
 92s The following packages will be upgraded:
 92s   gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common
 92s   ubuntu-minimal ubuntu-standard
 92s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded.
 92s Need to get 4613 kB of archives.
 92s After this operation, 211 kB of additional disk space will be used.
 92s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB]
 92s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB]
 92s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
 92s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
 92s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB]
 92s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B]
 92s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB]
 92s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB]
 92s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB]
 92s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB]
 93s Fetched 4613 kB in 1s (6326 kB/s)
 93s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
 93s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ...
 93s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
 94s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested:
 94s  udisks2 depends on libglib2.0-0 (>= 2.77.0).
 94s  shared-mime-info depends on libglib2.0-0 (>= 2.75.3).
 94s  python3-gi depends on libglib2.0-0 (>= 2.77.0).
 94s  python3-dbus depends on libglib2.0-0 (>= 2.16.0).
 94s  netplan.io depends on libglib2.0-0 (>= 2.70.0).
 94s  netplan-generator depends on libglib2.0-0 (>= 2.70.0).
 94s  libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0).
 94s  libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0).
 94s  libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3).
 94s  libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56).
 94s  libqmi-proxy depends on libglib2.0-0 (>= 2.30.0).
 94s  libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0).
 94s  libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
 94s  libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
 94s  libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3).
 94s  libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0).
 94s  libmbim-proxy depends on libglib2.0-0 (>= 2.56).
 94s  libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56).
 94s  libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3).
 94s  libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3).
 94s  libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3).
 94s  libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
 94s  libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0).
 94s  libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0).
 94s  libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2).
 94s  libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3).
 94s  libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2).
 94s  libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2).
 94s  libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2).
 94s  libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2).
 94s  libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2).
 94s  libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2).
 94s  libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2).
 94s  fwupd depends on libglib2.0-0 (>= 2.79.0).
 94s  bolt depends on libglib2.0-0 (>= 2.56.0).
 94s 
 94s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
 94s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ...
 94s Selecting previously unselected package libglib2.0-0t64:arm64.
 94s (Reading database ... 
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(Reading database ... 74733 files and directories currently installed.)
 94s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ...
 94s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled...
 94s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm'
 94s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ...
 94s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
 94s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
 94s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
 94s  wget depends on libssl3 (>= 3.0.0).
 94s  u-boot-tools depends on libssl3 (>= 3.0.0).
 94s  tnftp depends on libssl3 (>= 3.0.0).
 94s  tcpdump depends on libssl3 (>= 3.0.0).
 94s  systemd-resolved depends on libssl3 (>= 3.0.0).
 94s  systemd depends on libssl3 (>= 3.0.0).
 94s  sudo depends on libssl3 (>= 3.0.0).
 94s  sbsigntool depends on libssl3 (>= 3.0.0).
 94s  rsync depends on libssl3 (>= 3.0.0).
 94s  python3-cryptography depends on libssl3 (>= 3.0.0).
 94s  openssh-server depends on libssl3 (>= 3.0.10).
 94s  openssh-client depends on libssl3 (>= 3.0.10).
 94s  mtd-utils depends on libssl3 (>= 3.0.0).
 94s  mokutil depends on libssl3 (>= 3.0.0).
 94s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
 94s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
 94s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
 94s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
 94s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
 94s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
 94s  libnvme1 depends on libssl3 (>= 3.0.0).
 94s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
 94s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
 94s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
 94s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
 94s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
 94s  kmod depends on libssl3 (>= 3.0.0).
 94s  dhcpcd-base depends on libssl3 (>= 3.0.0).
 94s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
 94s 
 94s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
 94s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
 94s Selecting previously unselected package libssl3t64:arm64.
 94s (Reading database ... 
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(Reading database ... 74747 files and directories currently installed.)
 94s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
 94s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
 94s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ...
 94s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
 94s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ...
 94s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ...
 94s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ...
 94s Unpacking readline-common (8.2-3.1) over (8.2-3) ...
 94s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ...
 94s Unpacking ubuntu-minimal (1.536) over (1.535) ...
 95s Selecting previously unselected package xdg-user-dirs.
 95s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ...
 95s Unpacking xdg-user-dirs (0.18-1) ...
 95s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ...
 95s Unpacking ubuntu-standard (1.536) over (1.535) ...
 95s Setting up ubuntu-minimal (1.536) ...
 95s Setting up xdg-user-dirs (0.18-1) ...
 95s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
 95s Setting up libtirpc-common (1.3.4+ds-1.1) ...
 95s Setting up ubuntu-standard (1.536) ...
 95s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ...
 95s No schema files found: doing nothing.
 95s Setting up libglib2.0-data (2.79.3-3ubuntu5) ...
 95s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ...
 95s Setting up openssl (3.0.13-0ubuntu1) ...
 95s Setting up readline-common (8.2-3.1) ...
 95s Processing triggers for man-db (2.12.0-3) ...
 95s Processing triggers for install-info (7.1-3) ...
 96s Processing triggers for libc-bin (2.39-0ubuntu2) ...
 96s Reading package lists...
 97s Building dependency tree...
 97s Reading state information...
 98s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
 99s sh: Attempting to set up Debian/Ubuntu apt sources automatically
 99s sh: Distribution appears to be Ubuntu
101s Reading package lists...
102s Building dependency tree...
102s Reading state information...
103s eatmydata is already the newest version (131-1).
103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
103s Reading package lists...
103s Building dependency tree...
103s Reading state information...
105s dbus is already the newest version (1.14.10-4ubuntu1).
105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
105s Reading package lists...
105s Building dependency tree...
105s Reading state information...
106s rng-tools-debian is already the newest version (2.4).
106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
106s Reading package lists...
107s Building dependency tree...
107s Reading state information...
107s The following packages will be REMOVED:
107s   cloud-init* python3-configobj* python3-debconf*
108s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
108s After this operation, 3252 kB disk space will be freed.
108s (Reading database ... 
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(Reading database ... 74774 files and directories currently installed.)
108s Removing cloud-init (24.1.1-0ubuntu1) ...
109s Removing python3-configobj (5.0.8-3) ...
109s Removing python3-debconf (1.5.86) ...
109s Processing triggers for man-db (2.12.0-3) ...
110s (Reading database ... 
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(Reading database ... 74385 files and directories currently installed.)
110s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ...
111s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
111s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
112s invoke-rc.d: policy-rc.d denied execution of try-restart.
112s Reading package lists...
112s Building dependency tree...
112s Reading state information...
114s linux-generic is already the newest version (6.8.0-11.11+1).
114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
114s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
114s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
115s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
117s Reading package lists...
117s Reading package lists...
117s Building dependency tree...
117s Reading state information...
118s Calculating upgrade...
118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
119s Reading package lists...
119s Building dependency tree...
119s Reading state information...
119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
120s autopkgtest [17:39:06]: rebooting testbed after setup commands that affected boot
159s autopkgtest [17:39:45]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
162s autopkgtest [17:39:48]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-mofa
167s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-bioc-mofa 1.6.1+dfsg-12 (dsc) [2554 B]
167s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-bioc-mofa 1.6.1+dfsg-12 (tar) [915 kB]
167s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-bioc-mofa 1.6.1+dfsg-12 (diff) [4216 B]
167s gpgv: Signature made Thu Nov 30 17:10:43 2023 UTC
167s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
167s gpgv:                issuer "tille@debian.org"
167s gpgv: Can't check signature: No public key
167s dpkg-source: warning: cannot verify inline signature for ./r-bioc-mofa_1.6.1+dfsg-12.dsc: no acceptable signature found
167s autopkgtest [17:39:53]: testing package r-bioc-mofa version 1.6.1+dfsg-12
168s autopkgtest [17:39:54]: build not needed
168s autopkgtest [17:39:54]: test autodep8-python3: preparing testbed
170s Reading package lists...
170s Building dependency tree...
170s Reading state information...
171s Starting pkgProblemResolver with broken count: 0
171s Starting 2 pkgProblemResolver with broken count: 0
171s Done
173s The following additional packages will be installed:
173s   libaec0 libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 liblapack3
173s   liblbfgsb0 liblzf1 libpython3.11-minimal libpython3.11-stdlib libsz2
173s   python3-all python3-dateutil python3-decorator python3-distutils
173s   python3-h5py python3-h5py-serial python3-lib2to3 python3-mofapy
173s   python3-numpy python3-pandas python3-pandas-lib python3-scipy python3.11
173s   python3.11-minimal
173s Suggested packages:
173s   python-h5py-doc r-bioc-mofa gcc gfortran python3-dev python3-pytest
173s   python-pandas-doc python3-statsmodels python-scipy-doc python3.11-venv
173s   python3.11-doc binfmt-support
173s Recommended packages:
173s   python3-sklearn python3-sklearn-pandas python3-matplotlib python3-bottleneck
173s   python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib
173s   python3-lxml python3-tables g++ | c++-compiler python3-pil
173s The following NEW packages will be installed:
173s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1
173s   libhdf5-hl-100 liblapack3 liblbfgsb0 liblzf1 libpython3.11-minimal
173s   libpython3.11-stdlib libsz2 python3-all python3-dateutil python3-decorator
173s   python3-distutils python3-h5py python3-h5py-serial python3-lib2to3
173s   python3-mofapy python3-numpy python3-pandas python3-pandas-lib python3-scipy
173s   python3.11 python3.11-minimal
173s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded.
173s Need to get 45.2 MB/45.2 MB of archives.
173s After this operation, 230 MB of additional disk space will be used.
173s Get:1 /tmp/autopkgtest.9RIXv9/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B]
173s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB]
174s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB]
174s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB]
174s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB]
174s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB]
174s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
174s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
174s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B]
174s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB]
174s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB]
174s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
174s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB]
174s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B]
174s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB]
174s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB]
174s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B]
174s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB]
174s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
174s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
174s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu1 [1462 kB]
174s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py all 3.10.0-1ubuntu1 [7970 B]
174s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB]
174s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB]
174s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB]
175s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mofapy all 1.6.1+dfsg-12 [34.8 kB]
176s Fetched 45.2 MB in 2s (25.7 MB/s)
176s Selecting previously unselected package libpython3.11-minimal:arm64.
177s (Reading database ... 
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177s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ...
177s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ...
177s Selecting previously unselected package python3.11-minimal.
177s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ...
177s Unpacking python3.11-minimal (3.11.8-1) ...
177s Selecting previously unselected package libpython3.11-stdlib:arm64.
177s Preparing to unpack .../02-libpython3.11-stdlib_3.11.8-1_arm64.deb ...
177s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ...
177s Selecting previously unselected package python3.11.
177s Preparing to unpack .../03-python3.11_3.11.8-1_arm64.deb ...
177s Unpacking python3.11 (3.11.8-1) ...
177s Selecting previously unselected package libaec0:arm64.
177s Preparing to unpack .../04-libaec0_1.1.2-1_arm64.deb ...
177s Unpacking libaec0:arm64 (1.1.2-1) ...
177s Selecting previously unselected package libblas3:arm64.
177s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ...
177s Unpacking libblas3:arm64 (3.12.0-3) ...
177s Selecting previously unselected package libgfortran5:arm64.
177s Preparing to unpack .../06-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
177s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
177s Selecting previously unselected package libsz2:arm64.
177s Preparing to unpack .../07-libsz2_1.1.2-1_arm64.deb ...
177s Unpacking libsz2:arm64 (1.1.2-1) ...
177s Selecting previously unselected package libhdf5-103-1:arm64.
177s Preparing to unpack .../08-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ...
177s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ...
177s Selecting previously unselected package libhdf5-hl-100:arm64.
177s Preparing to unpack .../09-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ...
177s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ...
178s Selecting previously unselected package liblapack3:arm64.
178s Preparing to unpack .../10-liblapack3_3.12.0-3_arm64.deb ...
178s Unpacking liblapack3:arm64 (3.12.0-3) ...
178s Selecting previously unselected package liblbfgsb0:arm64.
178s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ...
178s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ...
178s Selecting previously unselected package liblzf1:arm64.
178s Preparing to unpack .../12-liblzf1_3.6-4_arm64.deb ...
178s Unpacking liblzf1:arm64 (3.6-4) ...
178s Selecting previously unselected package python3-lib2to3.
178s Preparing to unpack .../13-python3-lib2to3_3.11.5-1_all.deb ...
178s Unpacking python3-lib2to3 (3.11.5-1) ...
178s Selecting previously unselected package python3-distutils.
178s Preparing to unpack .../14-python3-distutils_3.11.5-1_all.deb ...
178s Unpacking python3-distutils (3.11.5-1) ...
178s Selecting previously unselected package python3-all.
178s Preparing to unpack .../15-python3-all_3.12.1-0ubuntu2_arm64.deb ...
178s Unpacking python3-all (3.12.1-0ubuntu2) ...
178s Selecting previously unselected package python3-dateutil.
178s Preparing to unpack .../16-python3-dateutil_2.8.2-3_all.deb ...
178s Unpacking python3-dateutil (2.8.2-3) ...
178s Selecting previously unselected package python3-decorator.
178s Preparing to unpack .../17-python3-decorator_5.1.1-5_all.deb ...
178s Unpacking python3-decorator (5.1.1-5) ...
178s Selecting previously unselected package python3-numpy.
178s Preparing to unpack .../18-python3-numpy_1%3a1.24.2-2_arm64.deb ...
178s Unpacking python3-numpy (1:1.24.2-2) ...
179s Selecting previously unselected package python3-h5py-serial.
179s Preparing to unpack .../19-python3-h5py-serial_3.10.0-1ubuntu1_arm64.deb ...
179s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ...
179s Selecting previously unselected package python3-h5py.
179s Preparing to unpack .../20-python3-h5py_3.10.0-1ubuntu1_all.deb ...
179s Unpacking python3-h5py (3.10.0-1ubuntu1) ...
179s Selecting previously unselected package python3-pandas-lib:arm64.
179s Preparing to unpack .../21-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ...
179s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ...
179s Selecting previously unselected package python3-pandas.
179s Preparing to unpack .../22-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ...
179s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ...
180s Selecting previously unselected package python3-scipy.
180s Preparing to unpack .../23-python3-scipy_1.11.4-6_arm64.deb ...
180s Unpacking python3-scipy (1.11.4-6) ...
181s Selecting previously unselected package python3-mofapy.
181s Preparing to unpack .../24-python3-mofapy_1.6.1+dfsg-12_all.deb ...
181s Unpacking python3-mofapy (1.6.1+dfsg-12) ...
181s Selecting previously unselected package autopkgtest-satdep.
182s Preparing to unpack .../25-1-autopkgtest-satdep.deb ...
182s Unpacking autopkgtest-satdep (0) ...
182s Setting up libaec0:arm64 (1.1.2-1) ...
182s Setting up python3-decorator (5.1.1-5) ...
182s Setting up libblas3:arm64 (3.12.0-3) ...
183s 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
183s Setting up liblzf1:arm64 (3.6-4) ...
183s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
183s Setting up python3-dateutil (2.8.2-3) ...
183s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ...
183s Setting up python3-lib2to3 (3.11.5-1) ...
183s Setting up libsz2:arm64 (1.1.2-1) ...
183s Setting up python3-distutils (3.11.5-1) ...
184s python3.12: can't get files for byte-compilation
184s Setting up python3.11-minimal (3.11.8-1) ...
185s Setting up liblapack3:arm64 (3.12.0-3) ...
185s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
185s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ...
185s Setting up python3-all (3.12.1-0ubuntu2) ...
185s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ...
185s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ...
185s Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ...
185s Setting up python3.11 (3.11.8-1) ...
186s Setting up python3-numpy (1:1.24.2-2) ...
189s Setting up python3-scipy (1.11.4-6) ...
194s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ...
194s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ...
194s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ...
200s Setting up python3-h5py (3.10.0-1ubuntu1) ...
200s Setting up python3-mofapy (1.6.1+dfsg-12) ...
200s /usr/lib/python3/dist-packages/mofapy/core/entry_point.py:41: SyntaxWarning: invalid escape sequence '\/'
200s   banner = """
200s /usr/lib/python3/dist-packages/mofapy/core/nongaussian_nodes.py:144: SyntaxWarning: invalid escape sequence '\p'
200s   """
200s /usr/lib/python3/dist-packages/mofapy/core/utils.py:178: SyntaxWarning: invalid escape sequence '\m'
200s   """Diagonal of :math:`\mathrm A\mathrm B^\intercal`.
200s Setting up autopkgtest-satdep (0) ...
200s Processing triggers for systemd (255.2-3ubuntu2) ...
200s Processing triggers for man-db (2.12.0-3) ...
201s Processing triggers for libc-bin (2.39-0ubuntu2) ...
207s (Reading database ... 79736 files and directories currently installed.)
207s Removing autopkgtest-satdep (0) ...
208s autopkgtest [17:40:34]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import mofapy; print(mofapy)" ; done
208s autopkgtest [17:40:34]: test autodep8-python3: [-----------------------
208s Testing with python3.12:
208s <module 'mofapy' from '/usr/lib/python3/dist-packages/mofapy/__init__.py'>
209s autopkgtest [17:40:35]: test autodep8-python3: -----------------------]
209s autopkgtest [17:40:35]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
209s autodep8-python3     PASS (superficial)
210s autopkgtest [17:40:36]: @@@@@@@@@@@@@@@@@@@@ summary
210s autodep8-python3     PASS (superficial)
220s Creating nova instance adt-noble-arm64-r-bioc-mofa-20240316-173705-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...