0s autopkgtest [01:48:19]: starting date and time: 2025-05-04 01:48:19+0000
  0s autopkgtest [01:48:19]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production'
  0s autopkgtest [01:48:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gvc7obce/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:nlme --apt-upgrade r-cran-epi --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=nlme/3.1.168-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu4-ram8-disk100 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-8.secgroup --name adt-questing-amd64-r-cran-epi-20250504-014819-juju-7f2275-prod-proposed-migration-environment-15-7a6becfc-9143-4a93-bcab-315ca8db87c8 --image adt/ubuntu-questing-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
956s autopkgtest [02:04:15]: testbed dpkg architecture: amd64
956s autopkgtest [02:04:15]: testbed apt version: 3.0.0
956s autopkgtest [02:04:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup
956s autopkgtest [02:04:15]: testbed release detected to be: None
957s autopkgtest [02:04:16]: updating testbed package index (apt update)
957s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB]
958s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease
958s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease
958s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease
958s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [143 kB]
958s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1389 kB]
958s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.2 kB]
958s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [138 kB]
958s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [194 kB]
958s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1412 kB]
958s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [565 kB]
958s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [23.1 kB]
958s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [48.6 kB]
959s Fetched 4057 kB in 1s (3130 kB/s)
960s Reading package lists...
960s autopkgtest [02:04:19]: upgrading testbed (apt dist-upgrade and autopurge)
960s Reading package lists...
961s Building dependency tree...
961s Reading state information...
961s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
961s Starting 2 pkgProblemResolver with broken count: 0
961s Done
962s Entering ResolveByKeep
962s 
962s Calculating upgrade...
962s The following packages will be upgraded:
962s   cloud-init cloud-init-base debianutils libmbim-glib4 libmbim-proxy
962s   libnftnl11 libqmi-glib5 libqmi-proxy libsepol2 python3-lazr.restfulclient
962s   sos
962s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
962s Need to get 2693 kB of archives.
962s After this operation, 104 kB disk space will be freed.
962s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 debianutils amd64 5.22 [93.0 kB]
962s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libsepol2 amd64 3.8.1-1 [327 kB]
963s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 libnftnl11 amd64 1.2.9-1 [69.1 kB]
963s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init-base all 25.2~1g7a0265d3-0ubuntu1 [619 kB]
963s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-proxy amd64 1.32.0-1 [6276 B]
963s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-glib4 amd64 1.32.0-1 [233 kB]
963s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-proxy amd64 1.36.0-1 [6220 B]
963s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-glib5 amd64 1.36.0-1 [920 kB]
963s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 python3-lazr.restfulclient all 0.14.6-3 [51.0 kB]
963s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 sos all 4.9.1-1 [367 kB]
963s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init all 25.2~1g7a0265d3-0ubuntu1 [2106 B]
963s Preconfiguring packages ...
963s Fetched 2693 kB in 1s (3497 kB/s)
963s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 80514 files and directories currently installed.)
963s Preparing to unpack .../debianutils_5.22_amd64.deb ...
963s Unpacking debianutils (5.22) over (5.21) ...
964s Setting up debianutils (5.22) ...
964s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 80514 files and directories currently installed.)
964s Preparing to unpack .../libsepol2_3.8.1-1_amd64.deb ...
964s Unpacking libsepol2:amd64 (3.8.1-1) over (3.7-1) ...
964s Setting up libsepol2:amd64 (3.8.1-1) ...
964s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 80514 files and directories currently installed.)
964s Preparing to unpack .../0-libnftnl11_1.2.9-1_amd64.deb ...
964s Unpacking libnftnl11:amd64 (1.2.9-1) over (1.2.8-1) ...
964s Preparing to unpack .../1-cloud-init-base_25.2~1g7a0265d3-0ubuntu1_all.deb ...
964s Unpacking cloud-init-base (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ...
964s Preparing to unpack .../2-libmbim-proxy_1.32.0-1_amd64.deb ...
964s Unpacking libmbim-proxy (1.32.0-1) over (1.31.2-0ubuntu4) ...
964s Preparing to unpack .../3-libmbim-glib4_1.32.0-1_amd64.deb ...
964s Unpacking libmbim-glib4:amd64 (1.32.0-1) over (1.31.2-0ubuntu4) ...
964s Preparing to unpack .../4-libqmi-proxy_1.36.0-1_amd64.deb ...
964s Unpacking libqmi-proxy (1.36.0-1) over (1.35.6-1) ...
964s Preparing to unpack .../5-libqmi-glib5_1.36.0-1_amd64.deb ...
964s Unpacking libqmi-glib5:amd64 (1.36.0-1) over (1.35.6-1) ...
964s Preparing to unpack .../6-python3-lazr.restfulclient_0.14.6-3_all.deb ...
964s Unpacking python3-lazr.restfulclient (0.14.6-3) over (0.14.6-2) ...
964s Preparing to unpack .../7-sos_4.9.1-1_all.deb ...
965s Unpacking sos (4.9.1-1) over (4.9.0-6) ...
965s Preparing to unpack .../8-cloud-init_25.2~1g7a0265d3-0ubuntu1_all.deb ...
965s Unpacking cloud-init (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ...
965s Setting up sos (4.9.1-1) ...
965s Setting up libnftnl11:amd64 (1.2.9-1) ...
965s Setting up cloud-init-base (25.2~1g7a0265d3-0ubuntu1) ...
967s Setting up python3-lazr.restfulclient (0.14.6-3) ...
967s Setting up libmbim-glib4:amd64 (1.32.0-1) ...
967s Setting up cloud-init (25.2~1g7a0265d3-0ubuntu1) ...
967s Setting up libmbim-proxy (1.32.0-1) ...
967s Setting up libqmi-glib5:amd64 (1.36.0-1) ...
967s Setting up libqmi-proxy (1.36.0-1) ...
967s Processing triggers for libc-bin (2.41-6ubuntu1) ...
967s Processing triggers for rsyslog (8.2412.0-2ubuntu2) ...
967s Processing triggers for man-db (2.13.0-1) ...
969s Reading package lists...
969s Building dependency tree...
969s Reading state information...
970s Starting pkgProblemResolver with broken count: 0
970s Starting 2 pkgProblemResolver with broken count: 0
970s Done
970s Solving dependencies...
970s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
970s autopkgtest [02:04:29]: rebooting testbed after setup commands that affected boot
993s autopkgtest [02:04:52]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr  6 15:05:05 UTC 2025
996s autopkgtest [02:04:55]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-epi
998s Get:1 http://ftpmaster.internal/ubuntu questing/universe r-cran-epi 2.59-1 (dsc) [2265 B]
998s Get:2 http://ftpmaster.internal/ubuntu questing/universe r-cran-epi 2.59-1 (tar) [3198 kB]
998s Get:3 http://ftpmaster.internal/ubuntu questing/universe r-cran-epi 2.59-1 (diff) [5404 B]
998s gpgv: Signature made Thu Jan 23 00:05:30 2025 UTC
998s gpgv:                using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502
998s gpgv:                issuer "plessy@debian.org"
998s gpgv: Can't check signature: No public key
998s dpkg-source: warning: cannot verify inline signature for ./r-cran-epi_2.59-1.dsc: no acceptable signature found
998s autopkgtest [02:04:57]: testing package r-cran-epi version 2.59-1
999s autopkgtest [02:04:58]: build not needed
1000s autopkgtest [02:04:59]: test vignette: preparing testbed
1000s Reading package lists...
1001s Building dependency tree...
1001s Reading state information...
1001s Starting pkgProblemResolver with broken count: 0
1001s Starting 2 pkgProblemResolver with broken count: 0
1001s Done
1001s The following NEW packages will be installed:
1001s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3
1001s   libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1
1001s   libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8
1001s   liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0
1001s   libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6
1001s   libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0
1001s   libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core
1001s   r-cran-boot r-cran-cli r-cran-cmprsk r-cran-cpp11 r-cran-data.table
1001s   r-cran-dplyr r-cran-epi r-cran-etm r-cran-fansi r-cran-generics r-cran-glue
1001s   r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 r-cran-magrittr
1001s   r-cran-mass r-cran-matrix r-cran-mgcv r-cran-minqa r-cran-nlme r-cran-nloptr
1001s   r-cran-numderiv r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr
1001s   r-cran-popepi r-cran-purrr r-cran-r6 r-cran-rbibutils r-cran-rcpp
1001s   r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rdpack r-cran-reformulas
1001s   r-cran-rlang r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival
1001s   r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs
1001s   r-cran-withr r-cran-zoo unzip x11-common xdg-utils zip
1002s 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded.
1002s Need to get 95.0 MB of archives.
1002s After this operation, 188 MB of additional disk space will be used.
1002s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
1002s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
1002s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig-config amd64 2.15.0-2.2ubuntu1 [37.8 kB]
1002s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 libfontconfig1 amd64 2.15.0-2.2ubuntu1 [164 kB]
1002s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig amd64 2.15.0-2.2ubuntu1 [180 kB]
1002s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libblas3 amd64 3.12.1-2 [359 kB]
1002s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
1002s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
1002s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
1002s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
1002s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo2 amd64 1.18.4-1 [662 kB]
1002s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
1002s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB]
1002s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran5 amd64 15-20250404-0ubuntu1 [926 kB]
1002s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB]
1002s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
1002s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB]
1002s Get:18 http://ftpmaster.internal/ubuntu questing/main amd64 x11-common all 1:7.7+23ubuntu4 [21.8 kB]
1002s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB]
1002s Get:20 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB]
1002s Get:21 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
1002s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB]
1003s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
1003s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
1003s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
1003s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 libpango-1.0-0 amd64 1.56.3-1 [256 kB]
1003s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [52.9 kB]
1003s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [29.1 kB]
1003s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB]
1003s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB]
1003s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB]
1003s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB]
1003s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB]
1003s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
1003s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB]
1003s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 libtiff6 amd64 4.7.0-3ubuntu1 [204 kB]
1003s Get:37 http://ftpmaster.internal/ubuntu questing/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
1003s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
1003s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB]
1003s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
1003s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 zip amd64 3.0-14ubuntu2 [185 kB]
1003s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB]
1003s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
1003s Get:44 http://ftpmaster.internal/ubuntu questing/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB]
1004s Get:45 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB]
1004s Get:46 http://ftpmaster.internal/ubuntu questing/universe amd64 littler all 0.3.20-2 [2554 B]
1004s Get:47 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-boot all 1.3-31-1 [635 kB]
1004s Get:48 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
1004s Get:49 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB]
1004s Get:50 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB]
1004s Get:51 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB]
1005s Get:52 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-cmprsk amd64 2.2-12-1 [107 kB]
1005s Get:53 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-cpp11 all 0.5.2-1 [233 kB]
1005s Get:54 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB]
1005s Get:55 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB]
1005s Get:56 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
1005s Get:57 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB]
1005s Get:58 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
1005s Get:59 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
1005s Get:60 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB]
1005s Get:61 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
1005s Get:62 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
1005s Get:63 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
1005s Get:64 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-fansi amd64 1.0.6-1ubuntu1 [632 kB]
1005s Get:65 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
1005s Get:66 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB]
1005s Get:67 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
1005s Get:68 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB]
1005s Get:69 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB]
1005s Get:70 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
1005s Get:71 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB]
1005s Get:72 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rcpparmadillo amd64 14.4.0-1-1 [868 kB]
1005s Get:73 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-etm amd64 1.1.1-1 [478 kB]
1005s Get:74 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB]
1005s Get:75 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
1005s Get:76 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB]
1005s Get:77 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-zoo amd64 1.8-13-1 [999 kB]
1005s Get:78 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB]
1005s Get:79 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB]
1005s Get:80 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-epi amd64 2.59-1 [3401 kB]
1005s Get:81 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-minqa amd64 1.2.8-1 [119 kB]
1005s Get:82 http://ftpmaster.internal/ubuntu questing/universe amd64 libnlopt0 amd64 2.7.1-6ubuntu3 [251 kB]
1005s Get:83 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-nloptr amd64 2.2.1-1 [251 kB]
1005s Get:84 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rbibutils amd64 2.3-1 [1023 kB]
1005s Get:85 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rdpack all 2.6.3-1 [636 kB]
1005s Get:86 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-reformulas all 0.4.1-1 [128 kB]
1005s Get:87 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB]
1005s Get:88 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB]
1005s Get:89 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-lme4 amd64 1.1-36-1 [4135 kB]
1005s Get:90 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-popepi all 0.4.13+dfsg-1 [1151 kB]
1005s Get:91 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB]
1005s Get:92 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-stringi amd64 1.8.4-1build1 [927 kB]
1005s Get:93 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB]
1005s Get:94 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB]
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1010s Selecting previously unselected package r-cran-rcppeigen.
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1011s Selecting previously unselected package r-cran-lme4.
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1011s Selecting previously unselected package r-cran-popepi.
1011s Preparing to unpack .../89-r-cran-popepi_0.4.13+dfsg-1_all.deb ...
1011s Unpacking r-cran-popepi (0.4.13+dfsg-1) ...
1011s Selecting previously unselected package r-cran-purrr.
1011s Preparing to unpack .../90-r-cran-purrr_1.0.4-1_amd64.deb ...
1011s Unpacking r-cran-purrr (1.0.4-1) ...
1011s Selecting previously unselected package r-cran-stringi.
1011s Preparing to unpack .../91-r-cran-stringi_1.8.4-1build1_amd64.deb ...
1011s Unpacking r-cran-stringi (1.8.4-1build1) ...
1011s Selecting previously unselected package r-cran-stringr.
1011s Preparing to unpack .../92-r-cran-stringr_1.5.1-1_all.deb ...
1011s Unpacking r-cran-stringr (1.5.1-1) ...
1011s Selecting previously unselected package r-cran-tidyr.
1011s Preparing to unpack .../93-r-cran-tidyr_1.3.1-1_amd64.deb ...
1011s Unpacking r-cran-tidyr (1.3.1-1) ...
1011s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
1011s Setting up libpixman-1-0:amd64 (0.44.0-3) ...
1011s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ...
1011s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
1011s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
1011s Setting up libdatrie1:amd64 (0.2.13-3build1) ...
1011s Setting up libxcb-render0:amd64 (1.17.0-2) ...
1011s Setting up unzip (6.0-28ubuntu6) ...
1011s Setting up x11-common (1:7.7+23ubuntu4) ...
1011s Setting up libdeflate0:amd64 (1.23-2) ...
1011s Setting up libnlopt0:amd64 (2.7.1-6ubuntu3) ...
1011s Setting up libxcb-shm0:amd64 (1.17.0-2) ...
1011s Setting up libgomp1:amd64 (15-20250404-0ubuntu1) ...
1011s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ...
1011s Setting up zip (3.0-14ubuntu2) ...
1011s Setting up libblas3:amd64 (3.12.1-2) ...
1011s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
1011s Setting up fonts-dejavu-mono (2.37-8) ...
1011s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ...
1011s Setting up fonts-dejavu-core (2.37-8) ...
1011s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ...
1011s Setting up libgfortran5:amd64 (15-20250404-0ubuntu1) ...
1011s Setting up libwebp7:amd64 (1.5.0-0.1) ...
1011s Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
1011s Setting up libthai-data (0.1.29-2build1) ...
1011s Setting up libxss1:amd64 (1:1.2.3-1build3) ...
1011s Setting up libpaper2:amd64 (2.2.5-0.3) ...
1011s Setting up xdg-utils (1.2.1-2ubuntu1) ...
1011s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
1011s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
1011s Setting up libice6:amd64 (2:1.1.1-1) ...
1011s Setting up liblapack3:amd64 (3.12.1-2) ...
1011s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
1011s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ...
1012s Setting up libpaper-utils (2.2.5-0.3) ...
1012s Setting up libthai0:amd64 (0.1.29-2build1) ...
1012s Setting up libtiff6:amd64 (4.7.0-3ubuntu1) ...
1012s Setting up libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ...
1012s Setting up libsm6:amd64 (2:1.2.4-1) ...
1012s Setting up fontconfig (2.15.0-2.2ubuntu1) ...
1014s Regenerating fonts cache... done.
1014s Setting up libxft2:amd64 (2.3.6-1build1) ...
1014s Setting up libtk8.6:amd64 (8.6.16-1) ...
1014s Setting up libpango-1.0-0:amd64 (1.56.3-1) ...
1014s Setting up libcairo2:amd64 (1.18.4-1) ...
1014s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ...
1014s Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ...
1014s Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ...
1014s Setting up r-base-core (4.4.3-1) ...
1014s Creating config file /etc/R/Renviron with new version
1014s Setting up r-cran-lattice (0.22-6-1) ...
1014s Setting up r-cran-nlme (3.1.168-1) ...
1014s Setting up r-cran-statmod (1.5.0-1) ...
1014s Setting up r-cran-r6 (2.6.1-1) ...
1014s Setting up r-cran-pkgkitten (0.2.4-1) ...
1014s Setting up r-cran-numderiv (2016.8-1.1-3) ...
1014s Setting up r-cran-magrittr (2.0.3-1) ...
1014s Setting up r-cran-littler (0.3.20-2) ...
1014s Setting up r-cran-rcpp (1.0.14-1) ...
1014s Setting up r-cran-nloptr (2.2.1-1) ...
1014s Setting up r-cran-boot (1.3-31-1) ...
1014s Setting up r-cran-rlang (1.1.5-1) ...
1014s Setting up littler (0.3.20-2) ...
1014s Setting up r-cran-withr (3.0.2+dfsg-1) ...
1014s Setting up r-cran-generics (0.1.3-1) ...
1014s Setting up r-cran-fansi (1.0.6-1ubuntu1) ...
1014s Setting up r-cran-mass (7.3-65-1) ...
1014s Setting up r-cran-data.table (1.17.0+dfsg-1) ...
1014s Setting up r-cran-glue (1.8.0-1) ...
1014s Setting up r-cran-cli (3.6.4-1) ...
1014s Setting up r-cran-rbibutils (2.3-1) ...
1014s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
1014s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
1014s Setting up r-cran-utf8 (1.2.4-1) ...
1014s Setting up r-cran-stringi (1.8.4-1build1) ...
1014s Setting up r-cran-cpp11 (0.5.2-1) ...
1014s Setting up r-cran-plyr (1.8.9-1) ...
1014s Setting up r-cran-zoo (1.8-13-1) ...
1014s Setting up r-cran-matrix (1.7-3-1) ...
1014s Setting up r-cran-mgcv (1.9-1-1) ...
1014s Setting up r-cran-rcpparmadillo (14.4.0-1-1) ...
1014s Setting up r-cran-vctrs (0.6.5-1) ...
1014s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ...
1014s Setting up r-cran-pillar (1.10.1+dfsg-1) ...
1014s Setting up r-cran-minqa (1.2.8-1) ...
1014s Setting up r-cran-stringr (1.5.1-1) ...
1014s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
1014s Setting up r-cran-survival (3.8-3-1) ...
1014s Setting up r-cran-rdpack (2.6.3-1) ...
1014s Setting up r-cran-cmprsk (2.2-12-1) ...
1014s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
1014s Setting up r-cran-purrr (1.0.4-1) ...
1014s Setting up r-cran-dplyr (1.1.4-4) ...
1014s Setting up r-cran-reformulas (0.4.1-1) ...
1014s Setting up r-cran-etm (1.1.1-1) ...
1014s Setting up r-cran-lme4 (1.1-36-1) ...
1014s Setting up r-cran-tidyr (1.3.1-1) ...
1014s Setting up r-cran-epi (2.59-1) ...
1014s Setting up r-cran-popepi (0.4.13+dfsg-1) ...
1014s Processing triggers for libc-bin (2.41-6ubuntu1) ...
1014s Processing triggers for man-db (2.13.0-1) ...
1015s Processing triggers for install-info (7.1.1-1) ...
1017s autopkgtest [02:05:16]: test vignette: [-----------------------
1017s BEGIN VIGNETTE vignettes/crisk.rnw
1019s 
1019s Attaching package: ‘survival’
1019s 
1019s The following object is masked from ‘package:popEpi’:
1019s 
1019s     Surv
1019s 
1073s Output file:  crisk.tex
1074s BEGIN VIGNETTE vignettes/simLexis.rnw
1076s 
1076s Attaching package: ‘survival’
1076s 
1076s The following object is masked from ‘package:popEpi’:
1076s 
1076s     Surv
1076s 
1090s Output file:  simLexis.tex
1090s BEGIN VIGNETTE vignettes/addLexis.rnw
1092s 
1092s Attaching package: ‘dplyr’
1092s 
1092s The following objects are masked from ‘package:stats’:
1092s 
1092s     filter, lag
1092s 
1092s The following objects are masked from ‘package:base’:
1092s 
1092s     intersect, setdiff, setequal, union
1092s 
1093s Joining with `by = join_by(lex.id)`
1093s Joining with `by = join_by(lex.id)`
1094s Joining with `by = join_by(lex.id)`
1113s Output file:  addLexis.tex
1113s BEGIN VIGNETTE vignettes/yll.rnw
1114s 
1114s Attaching package: ‘survival’
1114s 
1114s The following object is masked from ‘package:popEpi’:
1114s 
1114s     Surv
1114s 
1126s Output file:  yll.tex
1126s BEGIN VIGNETTE vignettes/aaflup.rnw
1127s 
1127s Attaching package: ‘survival’
1127s 
1127s The following object is masked from ‘package:popEpi’:
1127s 
1127s     Surv
1127s 
1150s Output file:  aaflup.tex
1151s autopkgtest [02:07:30]: test vignette: -----------------------]
1151s autopkgtest [02:07:30]: test vignette:  - - - - - - - - - - results - - - - - - - - - -
1151s vignette             PASS
1152s autopkgtest [02:07:31]: test pkg-r-autopkgtest: preparing testbed
1152s Reading package lists...
1152s Building dependency tree...
1152s Reading state information...
1153s Starting pkgProblemResolver with broken count: 0
1153s Starting 2 pkgProblemResolver with broken count: 0
1153s Done
1153s The following NEW packages will be installed:
1153s   build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu
1153s   dctrl-tools g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc
1153s   gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14
1153s   gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8
1153s   libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev
1153s   libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev
1153s   libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3
1153s   libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
1153s   libpkgconf3 libpng-dev libquadmath0 libreadline-dev libstdc++-14-dev
1153s   libtirpc-dev libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin
1153s   r-base-dev zlib1g-dev
1153s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded.
1153s Need to get 103 MB of archives.
1153s After this operation, 363 MB of additional disk space will be used.
1153s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 libisl23 amd64 0.27-1 [685 kB]
1154s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB]
1154s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [11.9 MB]
1155s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-14 amd64 14.2.0-19ubuntu2 [1030 B]
1155s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B]
1155s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB]
1155s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libcc1-0 amd64 15-20250404-0ubuntu1 [47.1 kB]
1155s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libitm1 amd64 15-20250404-0ubuntu1 [29.5 kB]
1155s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 libasan8 amd64 15-20250404-0ubuntu1 [3076 kB]
1155s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 liblsan0 amd64 15-20250404-0ubuntu1 [1362 kB]
1155s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 libtsan2 amd64 15-20250404-0ubuntu1 [2760 kB]
1155s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libubsan1 amd64 15-20250404-0ubuntu1 [1211 kB]
1155s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 libhwasan0 amd64 15-20250404-0ubuntu1 [1687 kB]
1155s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libquadmath0 amd64 15-20250404-0ubuntu1 [153 kB]
1155s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libgcc-14-dev amd64 14.2.0-19ubuntu2 [2815 kB]
1156s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [23.3 MB]
1156s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-14 amd64 14.2.0-19ubuntu2 [540 kB]
1156s Get:18 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B]
1156s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B]
1156s Get:20 http://ftpmaster.internal/ubuntu questing/main amd64 libstdc++-14-dev amd64 14.2.0-19ubuntu2 [2510 kB]
1156s Get:21 http://ftpmaster.internal/ubuntu questing/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [13.4 MB]
1157s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 g++-14 amd64 14.2.0-19ubuntu2 [23.0 kB]
1157s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B]
1157s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B]
1157s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 build-essential amd64 12.12ubuntu1 [5080 B]
1157s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB]
1157s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran-14-dev amd64 14.2.0-19ubuntu2 [967 kB]
1157s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [12.5 MB]
1157s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran-14 amd64 14.2.0-19ubuntu2 [14.2 kB]
1157s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B]
1157s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B]
1157s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB]
1157s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libblas-dev amd64 3.12.1-2 [338 kB]
1157s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB]
1157s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate-dev amd64 1.23-2 [56.8 kB]
1157s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB]
1157s Get:37 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB]
1157s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B]
1157s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B]
1157s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB]
1157s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB]
1157s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB]
1157s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB]
1157s Get:44 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B]
1157s Get:45 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-dev amd64 10.45-1 [908 kB]
1157s Get:46 http://ftpmaster.internal/ubuntu questing/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB]
1157s Get:47 http://ftpmaster.internal/ubuntu questing/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB]
1157s Get:48 http://ftpmaster.internal/ubuntu questing/main amd64 libpng-dev amd64 1.6.47-1.1 [298 kB]
1158s Get:49 http://ftpmaster.internal/ubuntu questing/main amd64 libreadline-dev amd64 8.2-6 [184 kB]
1158s Get:50 http://ftpmaster.internal/ubuntu questing/main amd64 liblzma-dev amd64 5.6.4-1ubuntu1 [189 kB]
1158s Get:51 http://ftpmaster.internal/ubuntu questing/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB]
1158s Get:52 http://ftpmaster.internal/ubuntu questing/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB]
1158s Get:53 http://ftpmaster.internal/ubuntu questing/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB]
1158s Get:54 http://ftpmaster.internal/ubuntu questing/universe amd64 r-base-dev all 4.4.3-1 [4176 B]
1158s Get:55 http://ftpmaster.internal/ubuntu questing/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
1158s Fetched 103 MB in 4s (24.0 MB/s)
1158s Selecting previously unselected package libisl23:amd64.
1158s (Reading database ... 
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(Reading database ... 65%
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
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(Reading database ... 89098 files and directories currently installed.)
1158s Preparing to unpack .../00-libisl23_0.27-1_amd64.deb ...
1158s Unpacking libisl23:amd64 (0.27-1) ...
1158s Selecting previously unselected package libmpc3:amd64.
1158s Preparing to unpack .../01-libmpc3_1.3.1-1build2_amd64.deb ...
1158s Unpacking libmpc3:amd64 (1.3.1-1build2) ...
1158s Selecting previously unselected package cpp-14-x86-64-linux-gnu.
1158s Preparing to unpack .../02-cpp-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ...
1158s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ...
1158s Selecting previously unselected package cpp-14.
1158s Preparing to unpack .../03-cpp-14_14.2.0-19ubuntu2_amd64.deb ...
1158s Unpacking cpp-14 (14.2.0-19ubuntu2) ...
1158s Selecting previously unselected package cpp-x86-64-linux-gnu.
1158s Preparing to unpack .../04-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
1158s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
1158s Selecting previously unselected package cpp.
1158s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ...
1158s Unpacking cpp (4:14.2.0-1ubuntu1) ...
1158s Selecting previously unselected package libcc1-0:amd64.
1158s Preparing to unpack .../06-libcc1-0_15-20250404-0ubuntu1_amd64.deb ...
1158s Unpacking libcc1-0:amd64 (15-20250404-0ubuntu1) ...
1158s Selecting previously unselected package libitm1:amd64.
1158s Preparing to unpack .../07-libitm1_15-20250404-0ubuntu1_amd64.deb ...
1158s Unpacking libitm1:amd64 (15-20250404-0ubuntu1) ...
1158s Selecting previously unselected package libasan8:amd64.
1158s Preparing to unpack .../08-libasan8_15-20250404-0ubuntu1_amd64.deb ...
1158s Unpacking libasan8:amd64 (15-20250404-0ubuntu1) ...
1158s Selecting previously unselected package liblsan0:amd64.
1158s Preparing to unpack .../09-liblsan0_15-20250404-0ubuntu1_amd64.deb ...
1158s Unpacking liblsan0:amd64 (15-20250404-0ubuntu1) ...
1158s Selecting previously unselected package libtsan2:amd64.
1158s Preparing to unpack .../10-libtsan2_15-20250404-0ubuntu1_amd64.deb ...
1158s Unpacking libtsan2:amd64 (15-20250404-0ubuntu1) ...
1158s Selecting previously unselected package libubsan1:amd64.
1158s Preparing to unpack .../11-libubsan1_15-20250404-0ubuntu1_amd64.deb ...
1158s Unpacking libubsan1:amd64 (15-20250404-0ubuntu1) ...
1159s Selecting previously unselected package libhwasan0:amd64.
1159s Preparing to unpack .../12-libhwasan0_15-20250404-0ubuntu1_amd64.deb ...
1159s Unpacking libhwasan0:amd64 (15-20250404-0ubuntu1) ...
1159s Selecting previously unselected package libquadmath0:amd64.
1159s Preparing to unpack .../13-libquadmath0_15-20250404-0ubuntu1_amd64.deb ...
1159s Unpacking libquadmath0:amd64 (15-20250404-0ubuntu1) ...
1159s Selecting previously unselected package libgcc-14-dev:amd64.
1159s Preparing to unpack .../14-libgcc-14-dev_14.2.0-19ubuntu2_amd64.deb ...
1159s Unpacking libgcc-14-dev:amd64 (14.2.0-19ubuntu2) ...
1159s Selecting previously unselected package gcc-14-x86-64-linux-gnu.
1159s Preparing to unpack .../15-gcc-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ...
1159s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ...
1159s Selecting previously unselected package gcc-14.
1159s Preparing to unpack .../16-gcc-14_14.2.0-19ubuntu2_amd64.deb ...
1159s Unpacking gcc-14 (14.2.0-19ubuntu2) ...
1159s Selecting previously unselected package gcc-x86-64-linux-gnu.
1159s Preparing to unpack .../17-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
1159s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
1159s Selecting previously unselected package gcc.
1159s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ...
1159s Unpacking gcc (4:14.2.0-1ubuntu1) ...
1159s Selecting previously unselected package libstdc++-14-dev:amd64.
1159s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-19ubuntu2_amd64.deb ...
1159s Unpacking libstdc++-14-dev:amd64 (14.2.0-19ubuntu2) ...
1159s Selecting previously unselected package g++-14-x86-64-linux-gnu.
1159s Preparing to unpack .../20-g++-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ...
1159s Unpacking g++-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ...
1159s Selecting previously unselected package g++-14.
1159s Preparing to unpack .../21-g++-14_14.2.0-19ubuntu2_amd64.deb ...
1159s Unpacking g++-14 (14.2.0-19ubuntu2) ...
1159s Selecting previously unselected package g++-x86-64-linux-gnu.
1159s Preparing to unpack .../22-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
1159s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
1159s Selecting previously unselected package g++.
1160s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_amd64.deb ...
1160s Unpacking g++ (4:14.2.0-1ubuntu1) ...
1160s Selecting previously unselected package build-essential.
1160s Preparing to unpack .../24-build-essential_12.12ubuntu1_amd64.deb ...
1160s Unpacking build-essential (12.12ubuntu1) ...
1160s Selecting previously unselected package dctrl-tools.
1160s Preparing to unpack .../25-dctrl-tools_2.24-3build3_amd64.deb ...
1160s Unpacking dctrl-tools (2.24-3build3) ...
1160s Selecting previously unselected package libgfortran-14-dev:amd64.
1160s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-19ubuntu2_amd64.deb ...
1160s Unpacking libgfortran-14-dev:amd64 (14.2.0-19ubuntu2) ...
1160s Selecting previously unselected package gfortran-14-x86-64-linux-gnu.
1160s Preparing to unpack .../27-gfortran-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ...
1160s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ...
1160s Selecting previously unselected package gfortran-14.
1160s Preparing to unpack .../28-gfortran-14_14.2.0-19ubuntu2_amd64.deb ...
1160s Unpacking gfortran-14 (14.2.0-19ubuntu2) ...
1160s Selecting previously unselected package gfortran-x86-64-linux-gnu.
1160s Preparing to unpack .../29-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
1160s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
1160s Selecting previously unselected package gfortran.
1160s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ...
1160s Unpacking gfortran (4:14.2.0-1ubuntu1) ...
1160s Selecting previously unselected package icu-devtools.
1160s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_amd64.deb ...
1160s Unpacking icu-devtools (76.1-1ubuntu2) ...
1160s Selecting previously unselected package libblas-dev:amd64.
1160s Preparing to unpack .../32-libblas-dev_3.12.1-2_amd64.deb ...
1160s Unpacking libblas-dev:amd64 (3.12.1-2) ...
1160s Selecting previously unselected package libbz2-dev:amd64.
1160s Preparing to unpack .../33-libbz2-dev_1.0.8-6_amd64.deb ...
1160s Unpacking libbz2-dev:amd64 (1.0.8-6) ...
1160s Selecting previously unselected package libdeflate-dev:amd64.
1160s Preparing to unpack .../34-libdeflate-dev_1.23-2_amd64.deb ...
1160s Unpacking libdeflate-dev:amd64 (1.23-2) ...
1160s Selecting previously unselected package libicu-dev:amd64.
1160s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_amd64.deb ...
1160s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ...
1160s Selecting previously unselected package libjpeg-turbo8-dev:amd64.
1160s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ...
1160s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ...
1160s Selecting previously unselected package libjpeg8-dev:amd64.
1160s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_amd64.deb ...
1160s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ...
1160s Selecting previously unselected package libjpeg-dev:amd64.
1160s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_amd64.deb ...
1160s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ...
1160s Selecting previously unselected package liblapack-dev:amd64.
1160s Preparing to unpack .../39-liblapack-dev_3.12.1-2_amd64.deb ...
1160s Unpacking liblapack-dev:amd64 (3.12.1-2) ...
1161s Selecting previously unselected package libncurses-dev:amd64.
1161s Preparing to unpack .../40-libncurses-dev_6.5+20250216-2_amd64.deb ...
1161s Unpacking libncurses-dev:amd64 (6.5+20250216-2) ...
1161s Selecting previously unselected package libpcre2-16-0:amd64.
1161s Preparing to unpack .../41-libpcre2-16-0_10.45-1_amd64.deb ...
1161s Unpacking libpcre2-16-0:amd64 (10.45-1) ...
1161s Selecting previously unselected package libpcre2-32-0:amd64.
1161s Preparing to unpack .../42-libpcre2-32-0_10.45-1_amd64.deb ...
1161s Unpacking libpcre2-32-0:amd64 (10.45-1) ...
1161s Selecting previously unselected package libpcre2-posix3:amd64.
1161s Preparing to unpack .../43-libpcre2-posix3_10.45-1_amd64.deb ...
1161s Unpacking libpcre2-posix3:amd64 (10.45-1) ...
1161s Selecting previously unselected package libpcre2-dev:amd64.
1161s Preparing to unpack .../44-libpcre2-dev_10.45-1_amd64.deb ...
1161s Unpacking libpcre2-dev:amd64 (10.45-1) ...
1161s Selecting previously unselected package libpkgconf3:amd64.
1161s Preparing to unpack .../45-libpkgconf3_1.8.1-4_amd64.deb ...
1161s Unpacking libpkgconf3:amd64 (1.8.1-4) ...
1161s Selecting previously unselected package zlib1g-dev:amd64.
1161s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ...
1161s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
1161s Selecting previously unselected package libpng-dev:amd64.
1161s Preparing to unpack .../47-libpng-dev_1.6.47-1.1_amd64.deb ...
1161s Unpacking libpng-dev:amd64 (1.6.47-1.1) ...
1161s Selecting previously unselected package libreadline-dev:amd64.
1161s Preparing to unpack .../48-libreadline-dev_8.2-6_amd64.deb ...
1161s Unpacking libreadline-dev:amd64 (8.2-6) ...
1161s Selecting previously unselected package liblzma-dev:amd64.
1161s Preparing to unpack .../49-liblzma-dev_5.6.4-1ubuntu1_amd64.deb ...
1161s Unpacking liblzma-dev:amd64 (5.6.4-1ubuntu1) ...
1161s Selecting previously unselected package pkgconf-bin.
1161s Preparing to unpack .../50-pkgconf-bin_1.8.1-4_amd64.deb ...
1161s Unpacking pkgconf-bin (1.8.1-4) ...
1161s Selecting previously unselected package pkgconf:amd64.
1161s Preparing to unpack .../51-pkgconf_1.8.1-4_amd64.deb ...
1161s Unpacking pkgconf:amd64 (1.8.1-4) ...
1161s Selecting previously unselected package libtirpc-dev:amd64.
1161s Preparing to unpack .../52-libtirpc-dev_1.3.4+ds-1.3_amd64.deb ...
1161s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1.3) ...
1161s Selecting previously unselected package r-base-dev.
1161s Preparing to unpack .../53-r-base-dev_4.4.3-1_all.deb ...
1161s Unpacking r-base-dev (4.4.3-1) ...
1161s Selecting previously unselected package pkg-r-autopkgtest.
1161s Preparing to unpack .../54-pkg-r-autopkgtest_20231212ubuntu1_all.deb ...
1161s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ...
1161s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ...
1161s Setting up libncurses-dev:amd64 (6.5+20250216-2) ...
1161s Setting up libreadline-dev:amd64 (8.2-6) ...
1161s Setting up libpcre2-16-0:amd64 (10.45-1) ...
1161s Setting up libpcre2-32-0:amd64 (10.45-1) ...
1161s Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ...
1161s Setting up libpkgconf3:amd64 (1.8.1-4) ...
1161s Setting up libquadmath0:amd64 (15-20250404-0ubuntu1) ...
1161s Setting up libmpc3:amd64 (1.3.1-1build2) ...
1161s Setting up icu-devtools (76.1-1ubuntu2) ...
1161s Setting up pkgconf-bin (1.8.1-4) ...
1161s Setting up liblzma-dev:amd64 (5.6.4-1ubuntu1) ...
1161s Setting up libubsan1:amd64 (15-20250404-0ubuntu1) ...
1161s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
1161s Setting up libpcre2-posix3:amd64 (10.45-1) ...
1161s Setting up libhwasan0:amd64 (15-20250404-0ubuntu1) ...
1161s Setting up libasan8:amd64 (15-20250404-0ubuntu1) ...
1161s Setting up libtsan2:amd64 (15-20250404-0ubuntu1) ...
1161s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ...
1161s Setting up libisl23:amd64 (0.27-1) ...
1161s Setting up libdeflate-dev:amd64 (1.23-2) ...
1161s Setting up libicu-dev:amd64 (76.1-1ubuntu2) ...
1161s Setting up libcc1-0:amd64 (15-20250404-0ubuntu1) ...
1161s Setting up liblsan0:amd64 (15-20250404-0ubuntu1) ...
1161s Setting up libblas-dev:amd64 (3.12.1-2) ...
1161s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
1161s Setting up dctrl-tools (2.24-3build3) ...
1161s Setting up libitm1:amd64 (15-20250404-0ubuntu1) ...
1161s Setting up libbz2-dev:amd64 (1.0.8-6) ...
1161s Setting up libpcre2-dev:amd64 (10.45-1) ...
1161s Setting up libpng-dev:amd64 (1.6.47-1.1) ...
1161s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ...
1161s Setting up pkgconf:amd64 (1.8.1-4) ...
1161s Setting up liblapack-dev:amd64 (3.12.1-2) ...
1161s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
1161s Setting up cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ...
1161s Setting up cpp-14 (14.2.0-19ubuntu2) ...
1161s Setting up libgcc-14-dev:amd64 (14.2.0-19ubuntu2) ...
1161s Setting up libstdc++-14-dev:amd64 (14.2.0-19ubuntu2) ...
1161s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
1161s Setting up libgfortran-14-dev:amd64 (14.2.0-19ubuntu2) ...
1161s Setting up cpp (4:14.2.0-1ubuntu1) ...
1161s Setting up gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ...
1161s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
1161s Setting up gcc-14 (14.2.0-19ubuntu2) ...
1161s Setting up gfortran-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ...
1161s Setting up g++-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ...
1161s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
1161s Setting up g++-14 (14.2.0-19ubuntu2) ...
1161s Setting up gfortran-14 (14.2.0-19ubuntu2) ...
1161s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
1161s Setting up gcc (4:14.2.0-1ubuntu1) ...
1161s Setting up g++ (4:14.2.0-1ubuntu1) ...
1161s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
1161s Setting up build-essential (12.12ubuntu1) ...
1161s Setting up gfortran (4:14.2.0-1ubuntu1) ...
1161s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
1161s 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
1161s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
1161s 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
1161s Setting up r-base-dev (4.4.3-1) ...
1161s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
1161s Processing triggers for libc-bin (2.41-6ubuntu1) ...
1161s Processing triggers for man-db (2.13.0-1) ...
1162s Processing triggers for install-info (7.1.1-1) ...
1163s autopkgtest [02:07:42]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
1163s autopkgtest [02:07:42]: test pkg-r-autopkgtest: [-----------------------
1164s Test: Try to load the R library Epi
1164s 
1164s R version 4.4.3 (2025-02-28) -- "Trophy Case"
1164s Copyright (C) 2025 The R Foundation for Statistical Computing
1164s Platform: x86_64-pc-linux-gnu
1164s 
1164s R is free software and comes with ABSOLUTELY NO WARRANTY.
1164s You are welcome to redistribute it under certain conditions.
1164s Type 'license()' or 'licence()' for distribution details.
1164s 
1164s R is a collaborative project with many contributors.
1164s Type 'contributors()' for more information and
1164s 'citation()' on how to cite R or R packages in publications.
1164s 
1164s Type 'demo()' for some demos, 'help()' for on-line help, or
1164s 'help.start()' for an HTML browser interface to help.
1164s Type 'q()' to quit R.
1164s 
1164s > library('Epi')
1165s > 
1165s > 
1165s Other tests are currently unsupported!
1165s They will be progressively added.
1166s autopkgtest [02:07:45]: test pkg-r-autopkgtest: -----------------------]
1166s pkg-r-autopkgtest    PASS
1166s autopkgtest [02:07:45]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
1166s autopkgtest [02:07:45]: @@@@@@@@@@@@@@@@@@@@ summary
1166s vignette             PASS
1166s pkg-r-autopkgtest    PASS
1171s nova [W] Skipping flock for amd64
1171s Creating nova instance adt-questing-amd64-r-cran-epi-20250504-014819-juju-7f2275-prod-proposed-migration-environment-15-7a6becfc-9143-4a93-bcab-315ca8db87c8 from image adt/ubuntu-questing-amd64-server-20250503.img (UUID 57b7c1b6-ad80-4bdb-b031-36f045f7f3b3)...
1171s nova [W] nova quota exceeded (attempt #0)
1171s nova [W] Timed out waiting for a29363b5-d75a-44cb-a6c2-3127f521fea5 to get deleted.