0s autopkgtest [01:55:45]: starting date and time: 2026-02-10 01:55:45+0000
  0s autopkgtest [01:55:45]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [01:55:45]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5nlgqbbd/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:lattice --apt-upgrade r-bioc-deseq --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-15.secgroup --name adt-resolute-amd64-r-bioc-deseq-20260210-014136-juju-7f2275-prod-proposed-migration-environment-20-a3d0c4ea-4554-46d5-9828-6f7cd943c140 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  3s Creating nova instance adt-resolute-amd64-r-bioc-deseq-20260210-014136-juju-7f2275-prod-proposed-migration-environment-20-a3d0c4ea-4554-46d5-9828-6f7cd943c140 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)...
 85s autopkgtest [01:57:10]: testbed dpkg architecture: amd64
 85s autopkgtest [01:57:10]: testbed apt version: 3.1.14
 86s autopkgtest [01:57:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 86s autopkgtest [01:57:11]: testbed release detected to be: None
 86s autopkgtest [01:57:11]: updating testbed package index (apt update)
 87s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
 87s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 87s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 87s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 87s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1637 kB]
 87s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB]
 87s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [173 kB]
 87s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [201 kB]
 87s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [253 kB]
 87s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5996 B]
 87s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [316 B]
 87s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1584 kB]
 87s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [639 kB]
 87s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [33.3 kB]
 87s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B]
 87s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [25.2 kB]
 87s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B]
 88s Fetched 4710 kB in 1s (5690 kB/s)
 89s Reading package lists...
 89s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 89s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 89s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 89s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 90s Reading package lists...
 90s Reading package lists...
 90s Building dependency tree...
 90s Reading state information...
 90s Calculating upgrade...
 91s The following package was automatically installed and is no longer required:
 91s   libpython3.13
 91s Use 'sudo apt autoremove' to remove it.
 91s The following NEW packages will be installed:
 91s   gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib
 91s   linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic
 91s   linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic
 91s   linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic
 91s The following packages will be upgraded:
 91s   3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static
 91s   cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common
 91s   dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install
 91s   ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2
 91s   iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0
 91s   libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common
 91s   libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64
 91s   libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0
 91s   libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0
 91s   libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64
 91s   libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0
 91s   libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic
 91s   linux-headers-virtual linux-image-generic linux-image-virtual linux-perf
 91s   linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids
 91s   pollinate python3-linkify-it python3-markdown-it python3-referencing sed
 91s   shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget
 91s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
 91s Need to get 237 MB of archives.
 91s After this operation, 339 MB of additional disk space will be used.
 91s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB]
 91s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB]
 91s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB]
 91s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB]
 91s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB]
 91s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB]
 91s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB]
 91s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB]
 91s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB]
 91s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB]
 91s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB]
 91s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB]
 91s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB]
 91s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB]
 91s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB]
 91s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B]
 91s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB]
 91s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB]
 91s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB]
 91s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB]
 91s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB]
 92s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB]
 92s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB]
 92s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB]
 92s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB]
 92s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB]
 92s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB]
 92s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB]
 92s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB]
 92s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB]
 92s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB]
 92s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB]
 92s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB]
 92s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB]
 92s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB]
 92s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB]
 92s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB]
 92s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB]
 92s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB]
 92s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB]
 92s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB]
 92s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB]
 92s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB]
 92s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB]
 92s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B]
 92s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB]
 92s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB]
 92s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB]
 92s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB]
 92s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB]
 92s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB]
 92s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB]
 92s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB]
 92s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB]
 92s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB]
 92s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B]
 92s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB]
 92s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB]
 92s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B]
 92s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB]
 92s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB]
 92s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB]
 92s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB]
 92s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB]
 92s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB]
 92s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB]
 92s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB]
 92s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB]
 92s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB]
 92s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B]
 92s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB]
 92s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB]
 92s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB]
 92s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B]
 92s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB]
 92s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B]
 92s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB]
 92s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB]
 92s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB]
 92s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB]
 93s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB]
 93s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB]
 96s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB]
 96s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB]
 96s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B]
 96s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB]
 96s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B]
 96s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB]
 96s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B]
 96s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB]
 97s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB]
 97s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB]
 97s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB]
 97s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB]
 97s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB]
 97s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B]
 97s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB]
 97s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB]
 97s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB]
 97s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB]
 97s dpkg-preconfigure: unable to re-open stdin: No such file or directory
 97s Fetched 237 MB in 7s (36.2 MB/s)
 98s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 98s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ...
 98s Unpacking debianutils (5.23.2build1) over (5.23.2) ...
 98s Setting up debianutils (5.23.2build1) ...
 98s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 98s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ...
 98s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ...
 98s Setting up dash (0.5.12-12ubuntu3) ...
 98s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 98s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ...
 98s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ...
 98s Setting up findutils (4.10.0-3build2) ...
 98s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 98s Preparing to unpack .../sed_4.9-2build3_amd64.deb ...
 98s Unpacking sed (4.9-2build3) over (4.9-2build2) ...
 98s Setting up sed (4.9-2build3) ...
 98s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 83957 files and directories currently installed.)
 98s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ...
 98s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ...
 98s Setting up tar (1.35+dfsg-3.1build2) ...
 98s (Reading database ... 
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108s Setting up libglib2.0-data (2.87.2-2) ...
108s Setting up pollinate (4.33-4ubuntu5) ...
119s Setting up busybox-static (1:1.37.0-7ubuntu1) ...
119s Setting up libwrap0:amd64 (7.6.q-36build2) ...
119s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
120s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic
120s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic
120s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ...
120s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ...
120s Setting up patch (2.8-2build1) ...
120s Setting up libsensors5:amd64 (1:3.6.2-2build1) ...
120s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ...
120s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ...
120s Setting up lsof (4.99.4+dfsg-2build2) ...
120s Setting up libpci3:amd64 (1:3.14.0-1build2) ...
120s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ...
120s Setting up dracut-install (109-11ubuntu1) ...
120s Setting up dmsetup (2:1.02.205-2ubuntu3) ...
120s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ...
120s Setting up pnp.ids (0.394-1build1) ...
120s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ...
120s Setting up python3-linkify-it (2.0.3-1ubuntu3) ...
120s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ...
120s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ...
120s Setting up mawk (1.3.4.20260129-1) ...
120s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ...
120s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ...
120s Setting up linux-image-virtual (6.19.0-3.3) ...
120s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ...
120s Setting up libbsd0:amd64 (0.12.2-2build2) ...
120s Setting up libdrm-common (2.4.131-1) ...
120s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ...
120s Setting up dbus-bin (1.16.2-2ubuntu3) ...
120s Setting up libonig5:amd64 (6.9.10-1build1) ...
120s Setting up libbpf1:amd64 (1:1.6.2-1build1) ...
120s Setting up ethtool (1:6.15-3build1) ...
120s Setting up python3-referencing (0.36.2-1ubuntu2) ...
120s Setting up libxkbcommon0:amd64 (1.13.1-1) ...
120s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
120s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ...
120s Setting up tcpdump (4.99.5-2ubuntu3) ...
120s Setting up linux-image-generic (6.19.0-3.3) ...
121s Setting up wget (1.25.0-2ubuntu4) ...
121s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ...
121s Setting up iptables (1.8.11-2ubuntu3) ...
121s Setting up iproute2 (6.18.0-1ubuntu1) ...
121s Setting up linux-headers-generic (6.19.0-3.3) ...
121s Setting up dbus-daemon (1.16.2-2ubuntu3) ...
121s Setting up hwdata (0.394-1build1) ...
121s Setting up dbus-user-session (1.16.2-2ubuntu3) ...
121s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ...
121s No schema files found: doing nothing.
121s Setting up dbus (1.16.2-2ubuntu3) ...
121s A reboot is required to replace the running dbus-daemon.
121s Please reboot the system when convenient.
121s Setting up shared-mime-info (2.4-5build3) ...
122s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ...
122s Setting up pciutils (1:3.14.0-1build2) ...
122s Setting up python3-markdown-it (3.0.0-3build1) ...
122s Setting up libdrm2:amd64 (2.4.131-1) ...
122s Setting up libpython3.14:amd64 (3.14.2-1) ...
122s Setting up libapt-pkg7.0:amd64 (3.1.15) ...
122s Setting up linux-tools-common (6.19.0-3.3) ...
122s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ...
122s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ...
122s Setting up apt (3.1.15) ...
123s Setting up linux-headers-virtual (6.19.0-3.3) ...
123s Setting up linux-generic (6.19.0-3.3) ...
123s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ...
123s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ...
123s Setting up ubuntu-standard (1.564) ...
123s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ...
123s Setting up linux-virtual (6.19.0-3.3) ...
123s Setting up linux-perf (6.19.0-3.3) ...
123s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ...
123s Processing triggers for debianutils (5.23.2build1) ...
123s Processing triggers for install-info (7.2-5) ...
123s Processing triggers for initramfs-tools (0.150ubuntu7) ...
123s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic
128s Processing triggers for libc-bin (2.42-2ubuntu4) ...
128s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
128s /etc/kernel/postinst.d/initramfs-tools:
128s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic
132s /etc/kernel/postinst.d/zz-update-grub:
132s Sourcing file `/etc/default/grub'
132s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
132s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
132s Generating grub configuration file ...
133s Found linux image: /boot/vmlinuz-6.19.0-3-generic
133s Found initrd image: /boot/initrd.img-6.19.0-3-generic
133s Found linux image: /boot/vmlinuz-6.18.0-9-generic
133s Found initrd image: /boot/initrd.img-6.18.0-9-generic
133s Warning: os-prober will not be executed to detect other bootable partitions.
133s Systems on them will not be added to the GRUB boot configuration.
133s Check GRUB_DISABLE_OS_PROBER documentation entry.
133s Adding boot menu entry for UEFI Firmware Settings ...
133s done
133s autopkgtest [01:57:58]: upgrading testbed (apt dist-upgrade and autopurge)
134s Reading package lists...
134s Building dependency tree...
134s Reading state information...
134s Calculating upgrade...
134s The following package was automatically installed and is no longer required:
134s   libpython3.13
134s Use 'sudo apt autoremove' to remove it.
134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
134s Reading package lists...
135s Building dependency tree...
135s Reading state information...
135s Solving dependencies...
135s The following packages will be REMOVED:
135s   libpython3.13*
135s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
135s After this operation, 7599 kB disk space will be freed.
135s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 125273 files and directories currently installed.)
135s Removing libpython3.13:amd64 (3.13.11-1) ...
135s Processing triggers for libc-bin (2.42-2ubuntu4) ...
135s autopkgtest [01:58:00]: rebooting testbed after setup commands that affected boot
164s autopkgtest [01:58:29]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026
166s autopkgtest [01:58:31]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-deseq
168s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-deseq 1.39.0-17 (dsc) [2207 B]
168s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-deseq 1.39.0-17 (tar) [1692 kB]
168s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-deseq 1.39.0-17 (diff) [3244 B]
168s gpgv: Signature made Mon Jan 13 20:08:14 2025 UTC
168s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
168s gpgv:                issuer "crusoe@debian.org"
168s gpgv: Can't check signature: No public key
168s dpkg-source: warning: cannot verify inline signature for ./r-bioc-deseq_1.39.0-17.dsc: no acceptable signature found
168s autopkgtest [01:58:33]: testing package r-bioc-deseq version 1.39.0-17
168s autopkgtest [01:58:33]: build not needed
176s autopkgtest [01:58:41]: test pkg-r-autopkgtest: preparing testbed
176s Reading package lists...
176s Building dependency tree...
176s Reading state information...
176s Solving dependencies...
177s The following NEW packages will be installed:
177s   build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu
177s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
177s   g++ g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15
177s   gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15
177s   gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8
177s   libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 libcc1-0
177s   libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 libfontconfig1
177s   libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1 libgraphite2-3
177s   libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0
177s   libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev
177s   liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3
177s   libncurses-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
177s   libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev
177s   libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev libquadmath0
177s   libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libtcl8.6 libthai-data
177s   libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7
177s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 libzstd-dev
177s   linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev
177s   r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics
177s   r-bioc-biostrings r-bioc-deseq r-bioc-genefilter r-bioc-geneplotter
177s   r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-keggrest
177s   r-bioc-matrixgenerics r-bioc-s4vectors r-bioc-ucsc.utils r-bioc-xvector
177s   r-bioc-zlibbioc r-cran-askpass r-cran-bit r-cran-bit64 r-cran-bitops
177s   r-cran-blob r-cran-cachem r-cran-catools r-cran-cli r-cran-cpp11
177s   r-cran-crayon r-cran-curl r-cran-dbi r-cran-fastmap r-cran-gdata r-cran-glue
177s   r-cran-gplots r-cran-gtools r-cran-httr r-cran-jsonlite r-cran-kernsmooth
177s   r-cran-lattice r-cran-lifecycle r-cran-locfit r-cran-mass r-cran-matrix
177s   r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl
177s   r-cran-pkgconfig r-cran-plogr r-cran-png r-cran-r6 r-cran-rcolorbrewer
177s   r-cran-rlang r-cran-rsqlite r-cran-survival r-cran-sys r-cran-vctrs
177s   r-cran-xml r-cran-xtable rpcsvc-proto unzip x11-common xdg-utils zip
177s   zlib1g-dev
177s 0 upgraded, 163 newly installed, 0 to remove and 0 not upgraded.
177s Need to get 236 MB of archives.
177s After this operation, 607 MB of additional disk space will be used.
177s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB]
177s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB]
177s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB]
177s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB]
177s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB]
177s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB]
177s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB]
177s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB]
177s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B]
177s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B]
177s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB]
177s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB]
177s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB]
177s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB]
177s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB]
177s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB]
178s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB]
178s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB]
178s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB]
178s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB]
178s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB]
178s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB]
178s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB]
178s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B]
178s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B]
178s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB]
178s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB]
178s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB]
178s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B]
178s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B]
178s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B]
178s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB]
178s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB]
179s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB]
179s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB]
179s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB]
179s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB]
179s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB]
179s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB]
179s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB]
179s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB]
179s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B]
179s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B]
179s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB]
179s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB]
179s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB]
179s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB]
179s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
179s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB]
179s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B]
179s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
179s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB]
179s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB]
179s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB]
179s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB]
179s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB]
179s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB]
179s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
179s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB]
179s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB]
179s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB]
179s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB]
179s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B]
179s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B]
179s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B]
179s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB]
179s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB]
179s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB]
179s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB]
179s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB]
179s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB]
179s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB]
179s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB]
179s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB]
179s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB]
179s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB]
179s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB]
179s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB]
179s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B]
179s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB]
179s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB]
179s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB]
179s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB]
179s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB]
179s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB]
179s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB]
179s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB]
180s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB]
180s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB]
180s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
180s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB]
180s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B]
180s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB]
180s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB]
180s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB]
180s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB]
180s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB]
180s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
180s Get:99 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB]
180s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB]
180s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB]
180s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB]
180s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB]
180s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B]
180s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B]
180s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
180s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biobase amd64 2.66.0-2 [2332 kB]
180s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB]
181s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-iranges amd64 2.40.1-3 [2309 kB]
181s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1build1 [855 kB]
181s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB]
181s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit64 amd64 4.6.0-1-4 [491 kB]
181s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB]
181s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
181s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
181s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
181s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
181s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-blob all 1.3.0-1 [54.1 kB]
181s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
181s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
181s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1build1 [54.5 kB]
181s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB]
181s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plogr all 0.2.0-3build2 [15.8 kB]
181s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB]
181s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB]
181s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB]
181s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB]
181s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
181s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB]
181s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB]
181s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB]
181s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
181s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
181s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB]
181s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
181s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
181s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
181s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
181s Get:139 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
182s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB]
182s Get:141 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB]
182s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-keggrest all 1.46.0+dfsg-3 [183 kB]
182s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB]
183s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml amd64 3.99-0.20-1 [1751 kB]
183s Get:145 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xtable all 1:1.8-4-2build1 [691 kB]
183s Get:146 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-annotate all 1.84.0+dfsg-2 [1870 kB]
183s Get:147 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-lattice amd64 0.22-9-1 [1399 kB]
183s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-locfit amd64 1.5-9.12-1 [552 kB]
183s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB]
183s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB]
183s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB]
183s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-survival amd64 3.8-6-1 [8274 kB]
183s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genefilter amd64 1.88.0-2 [1243 kB]
183s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB]
183s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-geneplotter all 1.84.0+dfsg-2 [1508 kB]
183s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB]
183s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-deseq amd64 1.39.0-17 [2002 kB]
183s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB]
183s Get:159 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-catools amd64 1.18.3-1 [209 kB]
183s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtools amd64 3.9.5-1build1 [345 kB]
183s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gdata all 3.0.1-1build1 [491 kB]
183s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-kernsmooth amd64 2.23-26-1build1 [93.6 kB]
183s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gplots all 3.3.0-1 [3825 kB]
184s Preconfiguring packages ...
184s Fetched 236 MB in 7s (34.3 MB/s)
184s Selecting previously unselected package libc-dev-bin.
184s (Reading database ... 
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(Reading database ... 90%
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(Reading database ... 125269 files and directories currently installed.)
184s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_amd64.deb ...
184s Unpacking libc-dev-bin (2.42-2ubuntu4) ...
184s Selecting previously unselected package linux-libc-dev:amd64.
184s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_amd64.deb ...
184s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ...
184s Selecting previously unselected package libcrypt-dev:amd64.
184s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_amd64.deb ...
184s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ...
184s Selecting previously unselected package rpcsvc-proto.
184s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_amd64.deb ...
184s Unpacking rpcsvc-proto (1.4.3-1build1) ...
184s Selecting previously unselected package libc6-dev:amd64.
184s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_amd64.deb ...
184s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ...
184s Selecting previously unselected package libisl23:amd64.
184s Preparing to unpack .../005-libisl23_0.27-1build1_amd64.deb ...
184s Unpacking libisl23:amd64 (0.27-1build1) ...
184s Selecting previously unselected package libmpc3:amd64.
184s Preparing to unpack .../006-libmpc3_1.3.1-2_amd64.deb ...
184s Unpacking libmpc3:amd64 (1.3.1-2) ...
184s Selecting previously unselected package cpp-15-x86-64-linux-gnu.
184s Preparing to unpack .../007-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
184s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
184s Selecting previously unselected package cpp-15.
184s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_amd64.deb ...
184s Unpacking cpp-15 (15.2.0-12ubuntu1) ...
184s Selecting previously unselected package cpp-x86-64-linux-gnu.
184s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
184s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
184s Selecting previously unselected package cpp.
184s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ...
184s Unpacking cpp (4:15.2.0-4ubuntu1) ...
184s Selecting previously unselected package libcc1-0:amd64.
184s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_amd64.deb ...
184s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ...
184s Selecting previously unselected package libgomp1:amd64.
184s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_amd64.deb ...
184s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ...
184s Selecting previously unselected package libitm1:amd64.
184s Preparing to unpack .../013-libitm1_16-20260208-1ubuntu1_amd64.deb ...
184s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ...
185s Selecting previously unselected package libasan8:amd64.
185s Preparing to unpack .../014-libasan8_16-20260208-1ubuntu1_amd64.deb ...
185s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ...
185s Selecting previously unselected package liblsan0:amd64.
185s Preparing to unpack .../015-liblsan0_16-20260208-1ubuntu1_amd64.deb ...
185s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ...
185s Selecting previously unselected package libtsan2:amd64.
185s Preparing to unpack .../016-libtsan2_16-20260208-1ubuntu1_amd64.deb ...
185s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ...
185s Selecting previously unselected package libubsan1:amd64.
185s Preparing to unpack .../017-libubsan1_16-20260208-1ubuntu1_amd64.deb ...
185s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ...
185s Selecting previously unselected package libhwasan0:amd64.
185s Preparing to unpack .../018-libhwasan0_16-20260208-1ubuntu1_amd64.deb ...
185s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ...
185s Selecting previously unselected package libquadmath0:amd64.
185s Preparing to unpack .../019-libquadmath0_16-20260208-1ubuntu1_amd64.deb ...
185s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ...
185s Selecting previously unselected package libgcc-15-dev:amd64.
185s Preparing to unpack .../020-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ...
185s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ...
185s Selecting previously unselected package gcc-15-x86-64-linux-gnu.
185s Preparing to unpack .../021-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
185s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
185s Selecting previously unselected package gcc-15.
185s Preparing to unpack .../022-gcc-15_15.2.0-12ubuntu1_amd64.deb ...
185s Unpacking gcc-15 (15.2.0-12ubuntu1) ...
185s Selecting previously unselected package gcc-x86-64-linux-gnu.
185s Preparing to unpack .../023-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
185s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
185s Selecting previously unselected package gcc.
185s Preparing to unpack .../024-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ...
185s Unpacking gcc (4:15.2.0-4ubuntu1) ...
185s Selecting previously unselected package libstdc++-15-dev:amd64.
185s Preparing to unpack .../025-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ...
185s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ...
185s Selecting previously unselected package g++-15-x86-64-linux-gnu.
185s Preparing to unpack .../026-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
185s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
185s Selecting previously unselected package g++-15.
185s Preparing to unpack .../027-g++-15_15.2.0-12ubuntu1_amd64.deb ...
185s Unpacking g++-15 (15.2.0-12ubuntu1) ...
185s Selecting previously unselected package g++-x86-64-linux-gnu.
185s Preparing to unpack .../028-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
185s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
185s Selecting previously unselected package g++.
185s Preparing to unpack .../029-g++_4%3a15.2.0-4ubuntu1_amd64.deb ...
185s Unpacking g++ (4:15.2.0-4ubuntu1) ...
185s Selecting previously unselected package build-essential.
185s Preparing to unpack .../030-build-essential_12.12ubuntu2_amd64.deb ...
185s Unpacking build-essential (12.12ubuntu2) ...
185s Selecting previously unselected package dctrl-tools.
185s Preparing to unpack .../031-dctrl-tools_2.24-3build4_amd64.deb ...
185s Unpacking dctrl-tools (2.24-3build4) ...
185s Selecting previously unselected package fonts-dejavu-mono.
185s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8build1_all.deb ...
185s Unpacking fonts-dejavu-mono (2.37-8build1) ...
185s Selecting previously unselected package fonts-dejavu-core.
185s Preparing to unpack .../033-fonts-dejavu-core_2.37-8build1_all.deb ...
185s Unpacking fonts-dejavu-core (2.37-8build1) ...
185s Selecting previously unselected package fontconfig-config.
186s Preparing to unpack .../034-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ...
186s Unpacking fontconfig-config (2.17.1-3ubuntu1) ...
186s Selecting previously unselected package libfontconfig1:amd64.
186s Preparing to unpack .../035-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ...
186s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ...
186s Selecting previously unselected package fontconfig.
186s Preparing to unpack .../036-fontconfig_2.17.1-3ubuntu1_amd64.deb ...
186s Unpacking fontconfig (2.17.1-3ubuntu1) ...
186s Selecting previously unselected package libgfortran5:amd64.
186s Preparing to unpack .../037-libgfortran5_16-20260208-1ubuntu1_amd64.deb ...
186s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ...
186s Selecting previously unselected package libgfortran-15-dev:amd64.
186s Preparing to unpack .../038-libgfortran-15-dev_15.2.0-12ubuntu1_amd64.deb ...
186s Unpacking libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ...
186s Selecting previously unselected package gfortran-15-x86-64-linux-gnu.
186s Preparing to unpack .../039-gfortran-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
186s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
186s Selecting previously unselected package gfortran-15.
186s Preparing to unpack .../040-gfortran-15_15.2.0-12ubuntu1_amd64.deb ...
186s Unpacking gfortran-15 (15.2.0-12ubuntu1) ...
186s Selecting previously unselected package gfortran-x86-64-linux-gnu.
186s Preparing to unpack .../041-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
186s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
186s Selecting previously unselected package gfortran.
186s Preparing to unpack .../042-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ...
186s Unpacking gfortran (4:15.2.0-4ubuntu1) ...
186s Selecting previously unselected package icu-devtools.
186s Preparing to unpack .../043-icu-devtools_78.2-1ubuntu1_amd64.deb ...
186s Unpacking icu-devtools (78.2-1ubuntu1) ...
186s Selecting previously unselected package libblas3:amd64.
186s Preparing to unpack .../044-libblas3_3.12.1-7ubuntu1_amd64.deb ...
186s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ...
186s Selecting previously unselected package libblas-dev:amd64.
186s Preparing to unpack .../045-libblas-dev_3.12.1-7ubuntu1_amd64.deb ...
186s Unpacking libblas-dev:amd64 (3.12.1-7ubuntu1) ...
186s Selecting previously unselected package libbz2-dev:amd64.
186s Preparing to unpack .../046-libbz2-dev_1.0.8-6build2_amd64.deb ...
186s Unpacking libbz2-dev:amd64 (1.0.8-6build2) ...
186s Selecting previously unselected package libpixman-1-0:amd64.
186s Preparing to unpack .../047-libpixman-1-0_0.46.4-1_amd64.deb ...
186s Unpacking libpixman-1-0:amd64 (0.46.4-1) ...
186s Selecting previously unselected package libxcb-render0:amd64.
186s Preparing to unpack .../048-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ...
186s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ...
186s Selecting previously unselected package libxcb-shm0:amd64.
186s Preparing to unpack .../049-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ...
186s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ...
186s Selecting previously unselected package libxrender1:amd64.
186s Preparing to unpack .../050-libxrender1_1%3a0.9.12-1_amd64.deb ...
186s Unpacking libxrender1:amd64 (1:0.9.12-1) ...
186s Selecting previously unselected package libcairo2:amd64.
186s Preparing to unpack .../051-libcairo2_1.18.4-3_amd64.deb ...
186s Unpacking libcairo2:amd64 (1.18.4-3) ...
186s Selecting previously unselected package libdatrie1:amd64.
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187s Selecting previously unselected package libtk8.6:amd64.
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187s Selecting previously unselected package r-base-core.
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187s Selecting previously unselected package liblzma-dev:amd64.
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187s Selecting previously unselected package pkgconf:amd64.
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188s Selecting previously unselected package r-bioc-biocgenerics.
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188s Selecting previously unselected package r-cran-dbi.
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188s Selecting previously unselected package r-cran-openssl.
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188s Selecting previously unselected package r-cran-r6.
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188s Selecting previously unselected package r-bioc-zlibbioc.
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188s Selecting previously unselected package r-bioc-ucsc.utils.
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188s Selecting previously unselected package r-bioc-genomeinfodbdata.
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188s Selecting previously unselected package r-cran-crayon.
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188s Selecting previously unselected package r-bioc-biostrings.
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188s Selecting previously unselected package r-cran-xml.
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188s Selecting previously unselected package r-cran-xtable.
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189s Selecting previously unselected package r-cran-lattice.
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189s Selecting previously unselected package r-cran-locfit.
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189s Selecting previously unselected package r-cran-matrixstats.
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189s Selecting previously unselected package r-bioc-matrixgenerics.
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189s Selecting previously unselected package r-cran-survival.
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189s Selecting previously unselected package r-bioc-genefilter.
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189s Selecting previously unselected package r-cran-rcolorbrewer.
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189s Selecting previously unselected package r-bioc-geneplotter.
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189s Selecting previously unselected package r-cran-mass.
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189s Selecting previously unselected package r-bioc-deseq.
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192s Setting up gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
192s Setting up libcairo2:amd64 (1.18.4-3) ...
192s Setting up gcc-15 (15.2.0-12ubuntu1) ...
192s Setting up libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ...
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192s Setting up gfortran-15 (15.2.0-12ubuntu1) ...
192s Setting up libpangocairo-1.0-0:amd64 (1.57.0-1) ...
192s Setting up g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
192s Setting up libpng-dev:amd64 (1.6.54-1) ...
192s Setting up libjpeg-dev:amd64 (8c-2ubuntu12) ...
192s Setting up gcc (4:15.2.0-4ubuntu1) ...
192s Setting up r-base-core (4.5.2-1ubuntu2) ...
192s Creating config file /etc/R/Renviron with new version
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192s Setting up r-cran-lattice (0.22-9-1) ...
192s Setting up r-cran-xml (3.99-0.20-1) ...
192s Setting up r-cran-locfit (1.5-9.12-1) ...
192s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
192s Setting up r-cran-r6 (2.6.1-1) ...
192s Setting up g++-15 (15.2.0-12ubuntu1) ...
192s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
192s Setting up r-cran-curl (7.0.0+dfsg-1) ...
192s Setting up r-bioc-biocgenerics (0.52.0-2) ...
192s Setting up r-cran-rlang (1.1.5-3) ...
192s Setting up r-cran-matrixstats (1.5.0-1) ...
192s Setting up r-bioc-matrixgenerics (1.18.1-1) ...
192s Setting up r-cran-sys (3.4.3-1) ...
192s Setting up r-cran-plogr (0.2.0-3build2) ...
192s Setting up r-cran-mime (0.12-2) ...
192s Setting up r-cran-dbi (1.2.3-1build1) ...
192s Setting up r-cran-mass (7.3-65-1) ...
192s Setting up r-cran-gtools (3.9.5-1build1) ...
192s Setting up r-cran-glue (1.8.0-1) ...
192s Setting up r-cran-bit (4.6.0+dfsg-1) ...
192s Setting up r-cran-xtable (1:1.8-4-2build1) ...
192s Setting up r-cran-cli (3.6.4-1) ...
192s Setting up gfortran (4:15.2.0-4ubuntu1) ...
192s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
192s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
192s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
192s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
192s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ...
192s Setting up r-cran-bitops (1.0-9-1) ...
192s Setting up r-cran-bit64 (4.6.0-1-4) ...
192s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
192s Setting up r-cran-askpass (1.2.1-1) ...
192s Setting up r-cran-fastmap (1.2.0-1) ...
192s Setting up r-cran-png (0.1-8-1build2) ...
192s Setting up r-bioc-biobase (2.66.0-2) ...
192s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
192s Setting up r-cran-pkgconfig (2.0.3-2build2) ...
192s Setting up r-cran-cpp11 (0.5.3-1) ...
192s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ...
192s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
192s Setting up r-cran-matrix (1.7-4-1) ...
192s Setting up r-cran-kernsmooth (2.23-26-1build1) ...
192s Setting up g++ (4:15.2.0-4ubuntu1) ...
192s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
192s Setting up r-cran-cachem (1.1.0-1) ...
192s Setting up build-essential (12.12ubuntu2) ...
192s Setting up r-cran-catools (1.18.3-1) ...
192s Setting up r-bioc-iranges (2.40.1-3) ...
192s Setting up r-cran-gdata (3.0.1-1build1) ...
192s Setting up r-cran-vctrs (0.6.5-1) ...
192s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
192s Setting up r-base-dev (4.5.2-1ubuntu2) ...
192s Setting up r-cran-survival (3.8-6-1) ...
192s Setting up r-cran-httr (1.4.7+dfsg-1) ...
192s Setting up r-cran-memoise (2.0.1-1build1) ...
192s Setting up r-cran-blob (1.3.0-1) ...
192s Setting up pkg-r-autopkgtest (20250812) ...
192s Setting up r-bioc-xvector (0.46.0-2) ...
192s Setting up r-cran-gplots (3.3.0-1) ...
192s Setting up r-cran-rsqlite (2.3.9-1) ...
192s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
192s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
192s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
192s Setting up r-bioc-keggrest (1.46.0+dfsg-3) ...
192s Setting up r-bioc-annotationdbi (1.68.0-2) ...
192s Setting up r-bioc-annotate (1.84.0+dfsg-2) ...
192s Setting up r-bioc-genefilter (1.88.0-2) ...
192s Setting up r-bioc-geneplotter (1.84.0+dfsg-2) ...
192s Setting up r-bioc-deseq (1.39.0-17) ...
192s Processing triggers for man-db (2.13.1-1build1) ...
193s Processing triggers for install-info (7.2-5) ...
193s Processing triggers for libc-bin (2.42-2ubuntu4) ...
194s autopkgtest [01:58:59]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
194s autopkgtest [01:58:59]: test pkg-r-autopkgtest: [-----------------------
194s Test: Try to load the R library DESeq
194s 
194s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
194s Copyright (C) 2025 The R Foundation for Statistical Computing
194s Platform: x86_64-pc-linux-gnu
194s 
194s R is free software and comes with ABSOLUTELY NO WARRANTY.
194s You are welcome to redistribute it under certain conditions.
194s Type 'license()' or 'licence()' for distribution details.
194s 
194s R is a collaborative project with many contributors.
194s Type 'contributors()' for more information and
194s 'citation()' on how to cite R or R packages in publications.
194s 
194s Type 'demo()' for some demos, 'help()' for on-line help, or
194s 'help.start()' for an HTML browser interface to help.
194s Type 'q()' to quit R.
194s 
194s > library('DESeq')
194s Loading required package: BiocGenerics
194s 
194s Attaching package: ‘BiocGenerics’
194s 
194s The following objects are masked from ‘package:stats’:
194s 
194s     IQR, mad, sd, var, xtabs
194s 
194s The following objects are masked from ‘package:base’:
194s 
194s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
194s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
194s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
194s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
194s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
194s     table, tapply, union, unique, unsplit, which.max, which.min
194s 
194s Loading required package: Biobase
194s Welcome to Bioconductor
194s 
194s     Vignettes contain introductory material; view with
194s     'browseVignettes()'. To cite Bioconductor, see
194s     'citation("Biobase")', and for packages 'citation("pkgname")'.
194s 
194s Loading required package: locfit
194s locfit 1.5-9.12 	 2025-03-05
194s Loading required package: lattice
197s     Welcome to 'DESeq'. For improved performance, usability and
197s     functionality, please consider migrating to 'DESeq2'.
197s > 
197s find: ‘tests’: No such file or directory
198s autopkgtest [01:59:03]: test pkg-r-autopkgtest: -----------------------]
198s autopkgtest [01:59:03]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
198s pkg-r-autopkgtest    PASS
198s autopkgtest [01:59:03]: @@@@@@@@@@@@@@@@@@@@ summary
198s pkg-r-autopkgtest    PASS