0s autopkgtest [20:44:34]: starting date and time: 2025-02-15 20:44:34+0000
  0s autopkgtest [20:44:34]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [20:44:34]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.q6sm_0_4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:iproute2,src:php-twig,src:postgresql-17,src:postgresql-common,src:roundcube --apt-upgrade libvcflib --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu1 iproute2/6.13.0-1ubuntu1 php-twig/3.19.0-1 postgresql-17/17.3-2 postgresql-common/273 roundcube/1.6.10+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-14.secgroup --name adt-plucky-amd64-libvcflib-20250215-204434-juju-7f2275-prod-proposed-migration-environment-15-99f288ae-4be1-410c-b87c-e09b2f177cca --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
108s autopkgtest [20:46:22]: testbed dpkg architecture: amd64
110s autopkgtest [20:46:22]: testbed apt version: 2.9.28
110s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB]
110s autopkgtest [20:46:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup
110s autopkgtest [20:46:22]: testbed release detected to be: None
110s autopkgtest [20:46:23]: updating testbed package index (apt update)
110s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
110s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
110s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
110s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [62.8 kB]
110s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB]
110s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B]
110s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [820 kB]
110s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.0 kB]
110s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [82.9 kB]
110s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B]
110s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B]
110s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [303 kB]
110s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [844 kB]
111s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [10.3 kB]
111s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3520 B]
111s Fetched 2329 kB in 1s (1900 kB/s)
111s Reading package lists...
112s + lsb_release --codename --short
112s + RELEASE=plucky
112s + cat
112s + [ plucky != trusty ]
112s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade
112s Reading package lists...
112s Building dependency tree...
112s Reading state information...
112s Calculating upgrade...
113s The following packages will be upgraded:
113s   libtasn1-6
113s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
113s Need to get 51.2 kB of archives.
113s After this operation, 22.5 kB of additional disk space will be used.
113s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6 amd64 4.20.0-2 [51.2 kB]
113s Fetched 51.2 kB in 0s (170 kB/s)
113s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 108914 files and directories currently installed.)
113s Preparing to unpack .../libtasn1-6_4.20.0-2_amd64.deb ...
113s Unpacking libtasn1-6:amd64 (4.20.0-2) over (4.19.0-3build1) ...
114s Setting up libtasn1-6:amd64 (4.20.0-2) ...
114s Processing triggers for libc-bin (2.40-4ubuntu1) ...
114s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref
114s + /usr/lib/apt/apt-helper analyze-pattern ?true
114s + uname -r
114s + sed s/\./\\./g
114s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.*
114s + apt list ?obsolete
114s + tail -n+2
114s + cut -d/ -f1
114s + grep -v ^linux-.*6\.12\.0-15-generic.*
114s + true
114s + obsolete_pkgs=
114s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove
114s Reading package lists...
114s Building dependency tree...
114s Reading state information...
114s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
114s + grep -q trusty /etc/lsb-release
114s + [ ! -d /usr/share/doc/unattended-upgrades ]
114s + [ ! -d /usr/share/doc/lxd ]
114s + [ ! -d /usr/share/doc/lxd-client ]
114s + [ ! -d /usr/share/doc/snapd ]
114s + type iptables
114s + cat
114s + chmod 755 /etc/rc.local
114s + . /etc/rc.local
114s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu
114s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP
114s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP
114s + uname -m
114s + [ x86_64 = ppc64le ]
114s + [ -d /run/systemd/system ]
114s + systemd-detect-virt --quiet --vm
114s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/
114s + cat
114s + grep -q lz4 /etc/initramfs-tools/initramfs.conf
114s + echo COMPRESS=lz4
114s autopkgtest [20:46:28]: upgrading testbed (apt dist-upgrade and autopurge)
115s Reading package lists...
115s Building dependency tree...
115s Reading state information...
115s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
115s Starting 2 pkgProblemResolver with broken count: 0
115s Done
116s Entering ResolveByKeep
116s 
116s The following packages will be upgraded:
116s   iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales
116s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
116s Need to get 11.8 MB of archives.
116s After this operation, 746 kB of additional disk space will be used.
116s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB]
116s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB]
117s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu1 [4246 kB]
118s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB]
119s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB]
119s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB]
119s Preconfiguring packages ...
119s Fetched 11.8 MB in 3s (4153 kB/s)
119s (Reading database ... 
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(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 ... 108914 files and directories currently installed.)
119s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ...
119s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
119s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ...
119s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
119s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ...
119s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
120s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ...
120s Checking for services that may need to be restarted...
120s Checking init scripts...
120s Checking for services that may need to be restarted...
120s Checking init scripts...
120s Stopping some services possibly affected by the upgrade (will be restarted later):
120s   cron: stopping...done.
120s 
120s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
120s Setting up libc6:amd64 (2.41-1ubuntu1) ...
120s Checking for services that may need to be restarted...
120s Checking init scripts...
120s Restarting services possibly affected by the upgrade:
120s   cron: restarting...done.
120s 
120s Services restarted successfully.
120s (Reading database ... 
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(Reading database ... 60%
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 108915 files and directories currently installed.)
120s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ...
120s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
120s Setting up libc-bin (2.41-1ubuntu1) ...
120s (Reading database ... 
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(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 ... 108915 files and directories currently installed.)
120s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_amd64.deb ...
121s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ...
121s Setting up iproute2 (6.13.0-1ubuntu1) ...
121s Setting up locales (2.41-1ubuntu1) ...
121s Installing new version of config file /etc/locale.alias ...
121s Generating locales (this might take a while)...
123s   en_US.UTF-8... done
123s Generation complete.
123s Setting up libc-dev-bin (2.41-1ubuntu1) ...
123s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ...
123s Processing triggers for man-db (2.13.0-1) ...
124s Processing triggers for systemd (257.2-3ubuntu1) ...
125s Reading package lists...
125s Building dependency tree...
125s Reading state information...
125s Starting pkgProblemResolver with broken count: 0
125s Starting 2 pkgProblemResolver with broken count: 0
125s Done
125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
128s autopkgtest [20:46:42]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb  4 16:02:16 UTC 2025
128s autopkgtest [20:46:42]: @@@@@@@@@@@@@@@@@@@@ apt-source libvcflib
134s Get:1 http://ftpmaster.internal/ubuntu plucky/universe libvcflib 1.0.9+dfsg1-3build1 (dsc) [2651 B]
134s Get:2 http://ftpmaster.internal/ubuntu plucky/universe libvcflib 1.0.9+dfsg1-3build1 (tar) [9044 kB]
134s Get:3 http://ftpmaster.internal/ubuntu plucky/universe libvcflib 1.0.9+dfsg1-3build1 (diff) [74.2 kB]
134s gpgv: Signature made Sun Apr 14 18:02:06 2024 UTC
134s gpgv:                using RSA key AC0A4FF12611B6FCCF01C111393587D97D86500B
134s gpgv: Can't check signature: No public key
134s dpkg-source: warning: cannot verify inline signature for ./libvcflib_1.0.9+dfsg1-3build1.dsc: no acceptable signature found
135s autopkgtest [20:46:49]: testing package libvcflib version 1.0.9+dfsg1-3build1
135s autopkgtest [20:46:49]: build not needed
138s autopkgtest [20:46:52]: test command1: preparing testbed
139s Reading package lists...
139s Building dependency tree...
139s Reading state information...
139s Starting pkgProblemResolver with broken count: 0
139s Starting 2 pkgProblemResolver with broken count: 0
139s Done
139s The following NEW packages will be installed:
139s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3
139s   libcairo2 libdatrie1 libdeflate0 libdisorder0 libfastahack0 libfontconfig1
139s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2
139s   libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
139s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0
139s   libsharpyuv0 libsm6 libsmithwaterman0 libtabixpp0t64 libtcl8.6 libthai-data
139s   libthai0 libtiff6 libtk8.6 libvcflib-tools libvcflib2 libwebp7 libwfa2-0
139s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler
139s   r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver
139s   r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband
139s   r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler
139s   r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell
139s   r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr
139s   r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-scales
139s   r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr unzip
139s   x11-common xdg-utils zip
140s 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded.
140s Need to get 75.8 MB of archives.
140s After this operation, 151 MB of additional disk space will be used.
140s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
141s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
141s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
141s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
141s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB]
141s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB]
141s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
141s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
141s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
141s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
141s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
142s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
142s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB]
142s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4build1 [4738 B]
142s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfastahack0 amd64 1.0.0+dfsg-11 [29.0 kB]
142s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-17ubuntu1 [910 kB]
142s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-17ubuntu1 [148 kB]
142s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
142s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB]
142s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB]
142s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB]
142s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
142s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB]
142s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB]
142s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
142s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB]
143s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
143s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
143s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
143s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.1-1 [255 kB]
143s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [52.6 kB]
143s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [29.1 kB]
143s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB]
143s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB]
143s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB]
143s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB]
143s Get:37 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12 [37.6 kB]
143s Get:38 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtabixpp0t64 amd64 1.1.2-2.1build1 [10.8 kB]
143s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB]
144s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
144s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB]
144s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
144s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
144s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
144s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB]
144s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwfa2-0 amd64 2.3.3-4 [62.8 kB]
144s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 libvcflib2 amd64 1.0.9+dfsg1-3build1 [200 kB]
144s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB]
144s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB]
144s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
144s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
144s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.2-1build1 [28.9 MB]
150s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB]
150s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-2 [2554 B]
150s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
150s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB]
151s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
151s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.3-1 [1348 kB]
151s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
151s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB]
151s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
151s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
151s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB]
152s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB]
152s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB]
152s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB]
152s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-2-1 [4456 kB]
153s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB]
153s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB]
153s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB]
153s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB]
153s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB]
153s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB]
153s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
153s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB]
153s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-scales all 1.3.0-1 [603 kB]
153s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB]
153s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
153s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB]
153s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
153s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
153s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
153s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB]
153s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
153s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
154s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gridbase all 0.4-7-5build1 [163 kB]
154s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 libvcflib-tools amd64 1.0.9+dfsg1-3build1 [670 kB]
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158s Unpacking r-cran-tibble (3.2.1+dfsg-3) ...
158s Selecting previously unselected package r-cran-withr.
158s Preparing to unpack .../83-r-cran-withr_3.0.2+dfsg-1_all.deb ...
158s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
158s Selecting previously unselected package r-cran-ggplot2.
158s Preparing to unpack .../84-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ...
158s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
158s Selecting previously unselected package r-cran-gridbase.
158s Preparing to unpack .../85-r-cran-gridbase_0.4-7-5build1_all.deb ...
158s Unpacking r-cran-gridbase (0.4-7-5build1) ...
158s Selecting previously unselected package libvcflib-tools.
158s Preparing to unpack .../86-libvcflib-tools_1.0.9+dfsg1-3build1_amd64.deb ...
158s Unpacking libvcflib-tools (1.0.9+dfsg1-3build1) ...
158s Setting up libhtscodecs2:amd64 (1.6.1-1) ...
158s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
158s Setting up libdisorder0:amd64 (0.0.2+git20130809.8062ee1-4build1) ...
158s Setting up libpixman-1-0:amd64 (0.44.0-3) ...
158s Setting up libwfa2-0:amd64 (2.3.3-4) ...
158s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ...
158s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
158s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
158s Setting up libdatrie1:amd64 (0.2.13-3build1) ...
158s Setting up libxcb-render0:amd64 (1.17.0-2) ...
158s Setting up unzip (6.0-28ubuntu6) ...
158s Setting up x11-common (1:7.7+23ubuntu3) ...
158s Setting up libsmithwaterman0:amd64 (0.0+git20160702.2610e25-12) ...
158s Setting up libdeflate0:amd64 (1.23-1) ...
158s Setting up libxcb-shm0:amd64 (1.17.0-2) ...
158s Setting up libgomp1:amd64 (14.2.0-17ubuntu1) ...
158s Setting up libfastahack0:amd64 (1.0.0+dfsg-11) ...
158s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ...
158s Setting up zip (3.0-14ubuntu2) ...
158s Setting up libblas3:amd64 (3.12.1-2) ...
158s 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
158s Setting up fonts-dejavu-mono (2.37-8) ...
158s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ...
158s Setting up fonts-dejavu-core (2.37-8) ...
158s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ...
158s Setting up libgfortran5:amd64 (14.2.0-17ubuntu1) ...
158s Setting up libwebp7:amd64 (1.5.0-0.1) ...
158s Setting up libhts3t64:amd64 (1.21+ds-1) ...
158s Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
158s Setting up libthai-data (0.1.29-2build1) ...
158s Setting up libxss1:amd64 (1:1.2.3-1build3) ...
158s Setting up libpaper2:amd64 (2.2.5-0.3) ...
158s Setting up xdg-utils (1.2.1-2ubuntu1) ...
158s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
158s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
158s Setting up libice6:amd64 (2:1.1.1-1) ...
158s Setting up liblapack3:amd64 (3.12.1-2) ...
158s 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
158s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
159s Setting up libpaper-utils (2.2.5-0.3) ...
159s Setting up libthai0:amd64 (0.1.29-2build1) ...
159s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
159s Setting up libtabixpp0t64:amd64 (1.1.2-2.1build1) ...
159s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
159s Setting up libsm6:amd64 (2:1.2.4-1) ...
159s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
161s Regenerating fonts cache... done.
161s Setting up libxft2:amd64 (2.3.6-1build1) ...
161s Setting up libtk8.6:amd64 (8.6.16-1) ...
161s Setting up libpango-1.0-0:amd64 (1.56.1-1) ...
161s Setting up libcairo2:amd64 (1.18.2-2) ...
161s Setting up libvcflib2:amd64 (1.0.9+dfsg1-3build1) ...
161s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ...
161s Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ...
161s Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ...
161s Setting up r-base-core (4.4.2-1build1) ...
161s Creating config file /etc/R/Renviron with new version
161s Setting up r-cran-labeling (0.4.3-1) ...
161s Setting up r-cran-lattice (0.22-6-1) ...
161s Setting up r-cran-nlme (3.1.167-1) ...
161s Setting up r-cran-farver (2.1.2-1) ...
161s Setting up r-cran-viridislite (0.4.2-2) ...
161s Setting up r-cran-r6 (2.5.1-1) ...
161s Setting up r-cran-pkgkitten (0.2.4-1) ...
161s Setting up r-cran-magrittr (2.0.3-1) ...
161s Setting up r-cran-littler (0.3.20-2) ...
161s Setting up r-cran-rcpp (1.0.14-1) ...
161s Setting up r-cran-rlang (1.1.5-1) ...
161s Setting up r-cran-gridbase (0.4-7-5build1) ...
161s Setting up littler (0.3.20-2) ...
161s Setting up r-cran-withr (3.0.2+dfsg-1) ...
161s Setting up r-cran-fansi (1.0.5-1) ...
161s Setting up r-cran-mass (7.3-64-1) ...
161s Setting up r-cran-glue (1.8.0-1) ...
161s Setting up r-cran-cli (3.6.3-1) ...
161s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
161s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
161s Setting up r-cran-utf8 (1.2.4-1) ...
161s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
161s Setting up r-cran-plyr (1.8.9-1) ...
161s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
161s Setting up r-cran-isoband (0.2.7-1) ...
161s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
161s Setting up r-cran-matrix (1.7-2-1) ...
161s Setting up r-cran-mgcv (1.9-1-1) ...
161s Setting up r-cran-vctrs (0.6.5-1) ...
161s Setting up r-cran-pillar (1.10.1+dfsg-1) ...
161s Setting up r-cran-munsell (0.5.1-1) ...
161s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
161s Setting up r-cran-scales (1.3.0-1) ...
161s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
161s Setting up libvcflib-tools (1.0.9+dfsg1-3build1) ...
161s Processing triggers for install-info (7.1.1-1) ...
161s Processing triggers for libc-bin (2.41-1ubuntu1) ...
161s Processing triggers for man-db (2.13.0-1) ...
162s autopkgtest [20:47:16]: test command1: vcffilter -f 'AC > 10' samples/1kg-phaseIII-v5a.20130502.genotypes.chr22-16-16.5mb.vcf.gz | wc -l | grep 1471
162s autopkgtest [20:47:16]: test command1: [-----------------------
168s 1471
168s autopkgtest [20:47:22]: test command1: -----------------------]
168s autopkgtest [20:47:22]: test command1:  - - - - - - - - - - results - - - - - - - - - -
168s command1             PASS
169s autopkgtest [20:47:23]: test command2: preparing testbed
169s Reading package lists...
169s Building dependency tree...
169s Reading state information...
169s Starting pkgProblemResolver with broken count: 0
169s Starting 2 pkgProblemResolver with broken count: 0
169s Done
170s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
171s autopkgtest [20:47:25]: test command2: vcffilter -f 'AC > 100' samples/1kg-phaseIII-v5a.20130502.genotypes.chr22-16-16.5mb.vcf.gz | wc -l | grep 748
171s autopkgtest [20:47:25]: test command2: [-----------------------
175s 748
176s autopkgtest [20:47:30]: test command2: -----------------------]
176s autopkgtest [20:47:30]: test command2:  - - - - - - - - - - results - - - - - - - - - -
176s command2             PASS
176s autopkgtest [20:47:30]: @@@@@@@@@@@@@@@@@@@@ summary
176s command1             PASS
176s command2             PASS
193s nova [W] Skipping flock for amd64
193s Creating nova instance adt-plucky-amd64-libvcflib-20250215-204434-juju-7f2275-prod-proposed-migration-environment-15-99f288ae-4be1-410c-b87c-e09b2f177cca from image adt/ubuntu-plucky-amd64-server-20250215.img (UUID d1f7bb98-7df8-4026-816e-9f6798166d8b)...
193s nova [W] Timed out waiting for bcdc0c77-6bb5-405e-88a1-24b6dff70c79 to get deleted.