0s autopkgtest [15:09:08]: starting date and time: 2025-03-15 15:09:08+0000
  0s autopkgtest [15:09:08]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [15:09:08]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dzg1aaj5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-bioc-pwalign --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-43.secgroup --name adt-plucky-arm64-r-bioc-pwalign-20250315-150908-juju-7f2275-prod-proposed-migration-environment-15-01affd72-5eb2-47d2-84d7-86975c9127d7 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,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/
184s autopkgtest [15:12:12]: testbed dpkg architecture: arm64
184s autopkgtest [15:12:12]: testbed apt version: 2.9.33
184s autopkgtest [15:12:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup
185s autopkgtest [15:12:13]: testbed release detected to be: None
186s autopkgtest [15:12:14]: updating testbed package index (apt update)
186s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
186s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
186s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
186s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
187s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
187s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB]
187s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
187s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB]
187s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B]
187s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B]
187s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB]
187s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB]
187s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B]
187s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B]
188s Fetched 1094 kB in 2s (633 kB/s)
189s Reading package lists...
189s + lsb_release --codename --short
189s + RELEASE=plucky
189s + cat
189s + [ plucky != trusty ]
189s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade
189s Reading package lists...
190s Building dependency tree...
190s Reading state information...
190s Calculating upgrade...
190s Calculating upgrade...
191s The following packages will be upgraded:
191s   python3-jinja2 strace
191s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
191s Need to get 608 kB of archives.
191s After this operation, 11.3 kB of additional disk space will be used.
191s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB]
192s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
192s Fetched 608 kB in 1s (699 kB/s)
192s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
192s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ...
192s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
193s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
193s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
193s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
193s Setting up strace (6.13+ds-1ubuntu1) ...
193s Processing triggers for man-db (2.13.0-1) ...
194s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref
194s + /usr/lib/apt/apt-helper analyze-pattern ?true
194s + uname -r
194s + sed s/\./\\./g
194s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.*
194s + apt list ?obsolete
194s + tail -n+2
194s + cut -d/ -f1
194s + grep -v ^linux-.*6\.14\.0-10-generic.*
194s + obsolete_pkgs=linux-headers-6.11.0-8-generic
194s linux-headers-6.11.0-8
194s linux-image-6.11.0-8-generic
194s linux-modules-6.11.0-8-generic
194s linux-tools-6.11.0-8-generic
194s linux-tools-6.11.0-8
194s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8
194s Reading package lists...
194s Building dependency tree...
194s Reading state information...
195s Solving dependencies...
195s The following packages will be REMOVED:
195s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
195s   libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
195s   linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic*
195s   linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic*
195s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded.
195s After this operation, 267 MB disk space will be freed.
195s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
195s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
195s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
195s Removing libpython3.12t64:arm64 (3.12.9-1) ...
195s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ...
196s Removing libnsl2:arm64 (1.3.0-3build3) ...
196s Removing libpython3.12-minimal:arm64 (3.12.9-1) ...
196s Removing libunwind8:arm64 (1.6.2-3.1) ...
196s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
196s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
198s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
198s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic
198s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic
198s /etc/kernel/postrm.d/initramfs-tools:
198s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
198s /etc/kernel/postrm.d/zz-flash-kernel:
198s flash-kernel: Kernel 6.11.0-8-generic has been removed.
198s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required.
198s /etc/kernel/postrm.d/zz-update-grub:
198s Sourcing file `/etc/default/grub'
198s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
198s Generating grub configuration file ...
199s Found linux image: /boot/vmlinuz-6.14.0-10-generic
199s Found initrd image: /boot/initrd.img-6.14.0-10-generic
199s Warning: os-prober will not be executed to detect other bootable partitions.
199s Systems on them will not be added to the GRUB boot configuration.
199s Check GRUB_DISABLE_OS_PROBER documentation entry.
199s Adding boot menu entry for UEFI Firmware Settings ...
199s done
199s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
199s Processing triggers for libc-bin (2.41-1ubuntu1) ...
199s (Reading database ... 
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(Reading database ... 81650 files and directories currently installed.)
199s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
199s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ...
199s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
200s + grep -q trusty /etc/lsb-release
200s + [ ! -d /usr/share/doc/unattended-upgrades ]
200s + [ ! -d /usr/share/doc/lxd ]
200s + [ ! -d /usr/share/doc/lxd-client ]
200s + [ ! -d /usr/share/doc/snapd ]
200s + type iptables
200s + cat
200s + chmod 755 /etc/rc.local
200s + . /etc/rc.local
200s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu
200s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP
200s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP
200s + uname -m
200s + [ aarch64 = ppc64le ]
200s + [ -d /run/systemd/system ]
200s + systemd-detect-virt --quiet --vm
200s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/
200s + cat
200s + grep -q lz4 /etc/initramfs-tools/initramfs.conf
200s + echo COMPRESS=lz4
200s autopkgtest [15:12:28]: upgrading testbed (apt dist-upgrade and autopurge)
200s Reading package lists...
200s Building dependency tree...
200s Reading state information...
201s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
201s Starting 2 pkgProblemResolver with broken count: 0
201s Done
202s Entering ResolveByKeep
202s 
202s Calculating upgrade...
202s The following packages will be upgraded:
202s   libc-bin libc-dev-bin libc6 libc6-dev locales
203s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
203s Need to get 9530 kB of archives.
203s After this operation, 0 B of additional disk space will be used.
203s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB]
205s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB]
205s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB]
207s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB]
208s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB]
212s Preconfiguring packages ...
212s Fetched 9530 kB in 9s (1109 kB/s)
212s (Reading database ... 
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(Reading database ... 81647 files and directories currently installed.)
212s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ...
212s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
212s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ...
212s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
212s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ...
212s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
212s Setting up libc6:arm64 (2.41-1ubuntu2) ...
213s (Reading database ... 
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(Reading database ... 81647 files and directories currently installed.)
213s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ...
213s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
213s Setting up libc-bin (2.41-1ubuntu2) ...
213s (Reading database ... 
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(Reading database ... 95%
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(Reading database ... 81647 files and directories currently installed.)
213s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
213s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
213s Setting up locales (2.41-1ubuntu2) ...
214s Generating locales (this might take a while)...
216s   en_US.UTF-8... done
216s Generation complete.
216s Setting up libc-dev-bin (2.41-1ubuntu2) ...
216s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ...
216s Processing triggers for man-db (2.13.0-1) ...
217s Processing triggers for systemd (257.3-1ubuntu3) ...
218s Reading package lists...
218s Building dependency tree...
218s Reading state information...
218s Starting pkgProblemResolver with broken count: 0
218s Starting 2 pkgProblemResolver with broken count: 0
218s Done
219s Solving dependencies...
219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
219s autopkgtest [15:12:47]: rebooting testbed after setup commands that affected boot
244s autopkgtest [15:13:12]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025
247s autopkgtest [15:13:15]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-pwalign
249s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-pwalign 1.2.0-2 (dsc) [2182 B]
249s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-pwalign 1.2.0-2 (tar) [327 kB]
249s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-pwalign 1.2.0-2 (diff) [5492 B]
250s gpgv: Signature made Sun Jan 12 19:21:49 2025 UTC
250s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
250s gpgv:                issuer "crusoe@debian.org"
250s gpgv: Can't check signature: No public key
250s dpkg-source: warning: cannot verify inline signature for ./r-bioc-pwalign_1.2.0-2.dsc: no acceptable signature found
250s autopkgtest [15:13:18]: testing package r-bioc-pwalign version 1.2.0-2
252s autopkgtest [15:13:20]: build not needed
259s autopkgtest [15:13:27]: test pkg-r-autopkgtest: preparing testbed
259s Reading package lists...
260s Building dependency tree...
260s Reading state information...
260s Starting pkgProblemResolver with broken count: 0
260s Starting 2 pkgProblemResolver with broken count: 0
260s Done
261s The following NEW packages will be installed:
261s   build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
261s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
261s   g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
261s   gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14
261s   gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools
261s   libasan8 libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 libdatrie1
261s   libdeflate-dev libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev
261s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6
261s   libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8
261s   libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblerc4
261s   liblsan0 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0
261s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0
261s   libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3
261s   libpng-dev libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6
261s   libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1
261s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
261s   pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev
261s   r-bioc-biocgenerics r-bioc-biostrings r-bioc-genomeinfodb
261s   r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-pwalign r-bioc-s4vectors
261s   r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-askpass
261s   r-cran-crayon r-cran-curl r-cran-httr r-cran-jsonlite r-cran-mime
261s   r-cran-openssl r-cran-r6 r-cran-runit r-cran-sys unzip x11-common xdg-utils
261s   zip zlib1g-dev
262s 0 upgraded, 118 newly installed, 0 to remove and 0 not upgraded.
262s Need to get 170 MB of archives.
262s After this operation, 460 MB of additional disk space will be used.
262s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB]
262s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB]
262s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB]
271s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B]
271s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B]
271s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB]
271s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB]
271s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB]
271s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB]
271s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB]
273s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB]
275s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB]
277s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB]
278s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB]
280s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB]
282s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB]
300s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB]
300s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B]
300s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B]
300s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB]
303s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB]
312s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB]
312s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B]
312s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B]
312s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B]
313s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB]
313s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
313s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
314s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB]
314s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB]
314s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB]
314s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB]
314s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB]
315s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB]
326s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB]
326s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B]
326s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B]
326s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB]
326s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB]
326s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB]
326s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB]
326s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
326s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
326s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
326s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
326s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
326s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
326s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB]
326s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB]
326s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
326s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB]
326s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
326s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB]
326s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB]
335s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
335s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB]
335s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
335s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B]
344s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B]
344s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB]
344s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB]
344s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
344s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB]
344s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
344s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
344s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB]
344s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB]
344s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB]
344s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB]
344s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB]
344s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB]
344s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB]
344s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B]
344s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB]
344s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB]
344s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
344s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB]
344s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB]
344s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
344s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB]
344s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB]
345s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
345s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
345s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
345s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
345s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
345s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB]
346s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB]
346s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB]
346s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB]
346s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
346s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB]
371s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB]
372s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB]
372s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB]
372s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB]
372s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B]
372s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
372s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
372s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-s4vectors arm64 0.44.0+dfsg-2 [2054 kB]
374s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-iranges arm64 2.40.1-2 [2303 kB]
376s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
376s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-xvector arm64 0.46.0-2 [618 kB]
376s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-curl arm64 6.2.1+dfsg-1ubuntu1 [196 kB]
377s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB]
377s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mime arm64 0.12-2 [35.8 kB]
377s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sys arm64 3.4.3-1 [45.2 kB]
377s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-askpass arm64 1.2.1-1 [24.8 kB]
377s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-openssl arm64 2.3.2+dfsg-1 [406 kB]
378s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB]
378s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
378s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
378s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
390s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
398s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-crayon all 1.5.3-1 [165 kB]
398s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biostrings arm64 2.74.1+dfsg-2 [13.3 MB]
407s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-pwalign arm64 1.2.0-2 [752 kB]
407s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-runit all 0.4.33-1 [377 kB]
416s Preconfiguring packages ...
425s Fetched 170 MB in 2min 27s (1154 kB/s)
425s Selecting previously unselected package libisl23:arm64.
425s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81647 files and directories currently installed.)
425s Preparing to unpack .../000-libisl23_0.27-1_arm64.deb ...
425s Unpacking libisl23:arm64 (0.27-1) ...
425s Selecting previously unselected package libmpc3:arm64.
425s Preparing to unpack .../001-libmpc3_1.3.1-1build2_arm64.deb ...
425s Unpacking libmpc3:arm64 (1.3.1-1build2) ...
425s Selecting previously unselected package cpp-14-aarch64-linux-gnu.
425s Preparing to unpack .../002-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package cpp-14.
425s Preparing to unpack .../003-cpp-14_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking cpp-14 (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package cpp-aarch64-linux-gnu.
425s Preparing to unpack .../004-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
425s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
425s Selecting previously unselected package cpp.
425s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ...
425s Unpacking cpp (4:14.2.0-1ubuntu1) ...
425s Selecting previously unselected package libcc1-0:arm64.
425s Preparing to unpack .../006-libcc1-0_15-20250222-0ubuntu1_arm64.deb ...
425s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ...
425s Selecting previously unselected package libgomp1:arm64.
425s Preparing to unpack .../007-libgomp1_15-20250222-0ubuntu1_arm64.deb ...
425s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ...
425s Selecting previously unselected package libitm1:arm64.
425s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_arm64.deb ...
425s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ...
425s Selecting previously unselected package libasan8:arm64.
425s Preparing to unpack .../009-libasan8_15-20250222-0ubuntu1_arm64.deb ...
425s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ...
425s Selecting previously unselected package liblsan0:arm64.
425s Preparing to unpack .../010-liblsan0_15-20250222-0ubuntu1_arm64.deb ...
425s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ...
425s Selecting previously unselected package libtsan2:arm64.
425s Preparing to unpack .../011-libtsan2_15-20250222-0ubuntu1_arm64.deb ...
425s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ...
425s Selecting previously unselected package libubsan1:arm64.
425s Preparing to unpack .../012-libubsan1_15-20250222-0ubuntu1_arm64.deb ...
425s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ...
425s Selecting previously unselected package libhwasan0:arm64.
425s Preparing to unpack .../013-libhwasan0_15-20250222-0ubuntu1_arm64.deb ...
425s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ...
425s Selecting previously unselected package libgcc-14-dev:arm64.
425s Preparing to unpack .../014-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package gcc-14-aarch64-linux-gnu.
425s Preparing to unpack .../015-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package gcc-14.
425s Preparing to unpack .../016-gcc-14_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking gcc-14 (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package gcc-aarch64-linux-gnu.
425s Preparing to unpack .../017-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
425s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
425s Selecting previously unselected package gcc.
425s Preparing to unpack .../018-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ...
425s Unpacking gcc (4:14.2.0-1ubuntu1) ...
425s Selecting previously unselected package libstdc++-14-dev:arm64.
425s Preparing to unpack .../019-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package g++-14-aarch64-linux-gnu.
425s Preparing to unpack .../020-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package g++-14.
425s Preparing to unpack .../021-g++-14_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking g++-14 (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package g++-aarch64-linux-gnu.
425s Preparing to unpack .../022-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
425s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
425s Selecting previously unselected package g++.
425s Preparing to unpack .../023-g++_4%3a14.2.0-1ubuntu1_arm64.deb ...
425s Unpacking g++ (4:14.2.0-1ubuntu1) ...
425s Selecting previously unselected package build-essential.
425s Preparing to unpack .../024-build-essential_12.10ubuntu1_arm64.deb ...
425s Unpacking build-essential (12.10ubuntu1) ...
425s Selecting previously unselected package dctrl-tools.
425s Preparing to unpack .../025-dctrl-tools_2.24-3build3_arm64.deb ...
425s Unpacking dctrl-tools (2.24-3build3) ...
425s Selecting previously unselected package fonts-dejavu-mono.
425s Preparing to unpack .../026-fonts-dejavu-mono_2.37-8_all.deb ...
425s Unpacking fonts-dejavu-mono (2.37-8) ...
425s Selecting previously unselected package fonts-dejavu-core.
425s Preparing to unpack .../027-fonts-dejavu-core_2.37-8_all.deb ...
425s Unpacking fonts-dejavu-core (2.37-8) ...
425s Selecting previously unselected package fontconfig-config.
425s Preparing to unpack .../028-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ...
425s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
425s Selecting previously unselected package libfontconfig1:arm64.
425s Preparing to unpack .../029-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ...
425s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
425s Selecting previously unselected package fontconfig.
425s Preparing to unpack .../030-fontconfig_2.15.0-2ubuntu1_arm64.deb ...
425s Unpacking fontconfig (2.15.0-2ubuntu1) ...
425s Selecting previously unselected package libgfortran5:arm64.
425s Preparing to unpack .../031-libgfortran5_15-20250222-0ubuntu1_arm64.deb ...
425s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ...
425s Selecting previously unselected package libgfortran-14-dev:arm64.
425s Preparing to unpack .../032-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package gfortran-14-aarch64-linux-gnu.
425s Preparing to unpack .../033-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package gfortran-14.
425s Preparing to unpack .../034-gfortran-14_14.2.0-17ubuntu3_arm64.deb ...
425s Unpacking gfortran-14 (14.2.0-17ubuntu3) ...
425s Selecting previously unselected package gfortran-aarch64-linux-gnu.
425s Preparing to unpack .../035-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
425s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
425s Selecting previously unselected package gfortran.
425s Preparing to unpack .../036-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ...
425s Unpacking gfortran (4:14.2.0-1ubuntu1) ...
425s Selecting previously unselected package icu-devtools.
425s Preparing to unpack .../037-icu-devtools_76.1-1ubuntu2_arm64.deb ...
425s Unpacking icu-devtools (76.1-1ubuntu2) ...
425s Selecting previously unselected package libblas3:arm64.
425s Preparing to unpack .../038-libblas3_3.12.1-2_arm64.deb ...
425s Unpacking libblas3:arm64 (3.12.1-2) ...
425s Selecting previously unselected package libblas-dev:arm64.
425s Preparing to unpack .../039-libblas-dev_3.12.1-2_arm64.deb ...
425s Unpacking libblas-dev:arm64 (3.12.1-2) ...
425s Selecting previously unselected package libbz2-dev:arm64.
425s Preparing to unpack .../040-libbz2-dev_1.0.8-6_arm64.deb ...
425s Unpacking libbz2-dev:arm64 (1.0.8-6) ...
425s Selecting previously unselected package libpixman-1-0:arm64.
425s Preparing to unpack .../041-libpixman-1-0_0.44.0-3_arm64.deb ...
425s Unpacking libpixman-1-0:arm64 (0.44.0-3) ...
425s Selecting previously unselected package libxcb-render0:arm64.
425s Preparing to unpack .../042-libxcb-render0_1.17.0-2_arm64.deb ...
425s Unpacking libxcb-render0:arm64 (1.17.0-2) ...
425s Selecting previously unselected package libxcb-shm0:arm64.
425s Preparing to unpack .../043-libxcb-shm0_1.17.0-2_arm64.deb ...
425s Unpacking libxcb-shm0:arm64 (1.17.0-2) ...
425s Selecting previously unselected package libxrender1:arm64.
425s Preparing to unpack .../044-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
425s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
425s Selecting previously unselected package libcairo2:arm64.
425s Preparing to unpack .../045-libcairo2_1.18.2-2_arm64.deb ...
425s Unpacking libcairo2:arm64 (1.18.2-2) ...
425s Selecting previously unselected package libdatrie1:arm64.
425s Preparing to unpack .../046-libdatrie1_0.2.13-3build1_arm64.deb ...
425s Unpacking libdatrie1:arm64 (0.2.13-3build1) ...
425s Selecting previously unselected package libdeflate0:arm64.
425s Preparing to unpack .../047-libdeflate0_1.23-1_arm64.deb ...
425s Unpacking libdeflate0:arm64 (1.23-1) ...
425s Selecting previously unselected package libdeflate-dev:arm64.
425s Preparing to unpack .../048-libdeflate-dev_1.23-1_arm64.deb ...
425s Unpacking libdeflate-dev:arm64 (1.23-1) ...
425s Selecting previously unselected package libgraphite2-3:arm64.
425s Preparing to unpack .../049-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
425s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
425s Selecting previously unselected package libharfbuzz0b:arm64.
425s Preparing to unpack .../050-libharfbuzz0b_10.2.0-1_arm64.deb ...
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425s Selecting previously unselected package x11-common.
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425s Selecting previously unselected package libice6:arm64.
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425s Selecting previously unselected package libicu-dev:arm64.
425s Preparing to unpack .../053-libicu-dev_76.1-1ubuntu2_arm64.deb ...
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425s Selecting previously unselected package libjpeg-turbo8:arm64.
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425s Selecting previously unselected package liblapack3:arm64.
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425s Selecting previously unselected package liblerc4:arm64.
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425s Selecting previously unselected package libncurses-dev:arm64.
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425s Selecting previously unselected package libthai-data.
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425s Selecting previously unselected package libpango-1.0-0:arm64.
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425s Selecting previously unselected package libpangoft2-1.0-0:arm64.
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425s Selecting previously unselected package libpangocairo-1.0-0:arm64.
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425s Selecting previously unselected package libpaper2:arm64.
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425s Selecting previously unselected package libpaper-utils.
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425s Selecting previously unselected package libpcre2-16-0:arm64.
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425s Selecting previously unselected package libpcre2-posix3:arm64.
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425s Selecting previously unselected package libpcre2-dev:arm64.
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425s Selecting previously unselected package libpkgconf3:arm64.
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425s Selecting previously unselected package zlib1g-dev:arm64.
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425s Selecting previously unselected package libpng-dev:arm64.
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425s Selecting previously unselected package libreadline-dev:arm64.
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425s Selecting previously unselected package libsharpyuv0:arm64.
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425s Selecting previously unselected package libsm6:arm64.
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425s Selecting previously unselected package libtcl8.6:arm64.
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425s Selecting previously unselected package libjbig0:arm64.
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425s Selecting previously unselected package libwebp7:arm64.
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425s Selecting previously unselected package libtiff6:arm64.
425s Preparing to unpack .../083-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ...
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425s Selecting previously unselected package libxft2:arm64.
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425s Selecting previously unselected package libxss1:arm64.
425s Preparing to unpack .../085-libxss1_1%3a1.2.3-1build3_arm64.deb ...
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425s Selecting previously unselected package libtk8.6:arm64.
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425s Preparing to unpack .../088-zip_3.0-14ubuntu2_arm64.deb ...
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425s Preparing to unpack .../089-unzip_6.0-28ubuntu6_arm64.deb ...
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425s Selecting previously unselected package liblzma-dev:arm64.
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425s Selecting previously unselected package pkgconf-bin.
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425s Selecting previously unselected package libtirpc-dev:arm64.
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425s Selecting previously unselected package r-bioc-biocgenerics.
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425s Selecting previously unselected package r-bioc-s4vectors.
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425s Selecting previously unselected package r-bioc-iranges.
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425s Selecting previously unselected package r-bioc-zlibbioc.
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425s Selecting previously unselected package r-bioc-xvector.
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425s Selecting previously unselected package r-cran-curl.
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425s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
425s Setting up libpixman-1-0:arm64 (0.44.0-3) ...
425s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ...
425s Setting up libncurses-dev:arm64 (6.5+20250216-2) ...
425s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
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425s Setting up libdatrie1:arm64 (0.2.13-3build1) ...
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425s Setting up unzip (6.0-28ubuntu6) ...
425s Setting up x11-common (1:7.7+23ubuntu3) ...
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425s Setting up libreadline-dev:arm64 (8.2-6) ...
425s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ...
425s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
425s Setting up libpcre2-16-0:arm64 (10.45-1) ...
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425s Setting up libblas3:arm64 (3.12.1-2) ...
425s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
425s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ...
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425s Setting up icu-devtools (76.1-1ubuntu2) ...
425s Setting up fonts-dejavu-core (2.37-8) ...
425s Setting up pkgconf-bin (1.8.1-4) ...
425s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
425s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ...
425s Setting up libwebp7:arm64 (1.5.0-0.1) ...
425s Setting up liblzma-dev:arm64 (5.6.4-1) ...
425s Setting up libubsan1:arm64 (15-20250222-0ubuntu1) ...
425s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
425s Setting up libpcre2-posix3:arm64 (10.45-1) ...
425s Setting up libhwasan0:arm64 (15-20250222-0ubuntu1) ...
425s Setting up libasan8:arm64 (15-20250222-0ubuntu1) ...
425s Setting up libharfbuzz0b:arm64 (10.2.0-1) ...
425s Setting up libthai-data (0.1.29-2build1) ...
425s Setting up libxss1:arm64 (1:1.2.3-1build3) ...
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425s Setting up libtsan2:arm64 (15-20250222-0ubuntu1) ...
425s Setting up libisl23:arm64 (0.27-1) ...
425s Setting up libdeflate-dev:arm64 (1.23-1) ...
425s Setting up libicu-dev:arm64 (76.1-1ubuntu2) ...
425s Setting up xdg-utils (1.2.1-2ubuntu1) ...
425s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
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425s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode
425s Setting up dctrl-tools (2.24-3build3) ...
425s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ...
425s Setting up libbz2-dev:arm64 (1.0.8-6) ...
425s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
425s Setting up libice6:arm64 (2:1.1.1-1) ...
425s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ...
425s Setting up liblapack3:arm64 (3.12.1-2) ...
425s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
425s Setting up libpcre2-dev:arm64 (10.45-1) ...
425s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
425s Setting up libpng-dev:arm64 (1.6.47-1) ...
425s Setting up libpaper-utils (2.2.5-0.3) ...
425s Setting up pkgconf:arm64 (1.8.1-4) ...
425s Setting up libthai0:arm64 (0.1.29-2build1) ...
425s Setting up liblapack-dev:arm64 (3.12.1-2) ...
425s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode
425s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
425s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
425s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
425s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
425s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ...
425s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ...
425s Setting up libsm6:arm64 (2:1.2.4-1) ...
425s Setting up libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ...
425s Setting up fontconfig (2.15.0-2ubuntu1) ...
425s Regenerating fonts cache... done.
425s Setting up libxft2:arm64 (2.3.6-1build1) ...
425s Setting up libtk8.6:arm64 (8.6.16-1) ...
425s Setting up libpango-1.0-0:arm64 (1.56.2-1) ...
425s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ...
425s Setting up libcairo2:arm64 (1.18.2-2) ...
425s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
425s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ...
425s Setting up cpp-14 (14.2.0-17ubuntu3) ...
425s Setting up cpp (4:14.2.0-1ubuntu1) ...
425s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
425s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ...
425s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ...
425s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
425s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
425s Setting up gcc-14 (14.2.0-17ubuntu3) ...
425s Setting up r-base-core (4.4.3-1) ...
425s Creating config file /etc/R/Renviron with new version
425s Setting up r-cran-crayon (1.5.3-1) ...
425s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
425s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
425s Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
425s Setting up g++-14 (14.2.0-17ubuntu3) ...
425s Setting up r-cran-r6 (2.6.1-1) ...
425s Setting up gfortran-14 (14.2.0-17ubuntu3) ...
425s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
425s Setting up r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
425s Setting up r-bioc-biocgenerics (0.52.0-2) ...
425s Setting up r-cran-sys (3.4.3-1) ...
425s Setting up r-cran-mime (0.12-2) ...
425s Setting up gcc (4:14.2.0-1ubuntu1) ...
425s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
425s Setting up r-cran-askpass (1.2.1-1) ...
425s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
425s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
425s Setting up r-cran-runit (0.4.33-1) ...
425s Setting up g++ (4:14.2.0-1ubuntu1) ...
425s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
425s Setting up build-essential (12.10ubuntu1) ...
425s Setting up r-bioc-iranges (2.40.1-2) ...
425s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
425s Setting up gfortran (4:14.2.0-1ubuntu1) ...
425s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
425s 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
425s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
425s 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
425s Setting up r-cran-httr (1.4.7+dfsg-1) ...
425s Setting up r-bioc-xvector (0.46.0-2) ...
425s Setting up r-base-dev (4.4.3-1) ...
425s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
425s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
425s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
425s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
425s Setting up r-bioc-pwalign (1.2.0-2) ...
425s Processing triggers for man-db (2.13.0-1) ...
425s Processing triggers for install-info (7.1.1-1) ...
425s Processing triggers for libc-bin (2.41-1ubuntu2) ...
594s autopkgtest [15:19:02]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
594s autopkgtest [15:19:02]: test pkg-r-autopkgtest: [-----------------------
600s Test: Try to load the R library pwalign
601s 
601s R version 4.4.3 (2025-02-28) -- "Trophy Case"
601s Copyright (C) 2025 The R Foundation for Statistical Computing
601s Platform: aarch64-unknown-linux-gnu
601s 
601s R is free software and comes with ABSOLUTELY NO WARRANTY.
601s You are welcome to redistribute it under certain conditions.
601s Type 'license()' or 'licence()' for distribution details.
601s 
601s R is a collaborative project with many contributors.
601s Type 'contributors()' for more information and
601s 'citation()' on how to cite R or R packages in publications.
601s 
601s Type 'demo()' for some demos, 'help()' for on-line help, or
601s 'help.start()' for an HTML browser interface to help.
601s Type 'q()' to quit R.
601s 
601s > library('pwalign')
601s Loading required package: BiocGenerics
601s 
601s Attaching package: ‘BiocGenerics’
601s 
601s The following objects are masked from ‘package:stats’:
601s 
601s     IQR, mad, sd, var, xtabs
601s 
601s The following objects are masked from ‘package:base’:
601s 
601s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
601s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
601s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
601s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
601s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
601s     table, tapply, union, unique, unsplit, which.max, which.min
601s 
601s Loading required package: S4Vectors
601s Loading required package: stats4
601s 
601s Attaching package: ‘S4Vectors’
601s 
601s The following object is masked from ‘package:utils’:
601s 
601s     findMatches
601s 
601s The following objects are masked from ‘package:base’:
601s 
601s     expand.grid, I, unname
601s 
601s Loading required package: IRanges
602s Loading required package: Biostrings
602s Loading required package: XVector
602s Loading required package: GenomeInfoDb
603s 
603s Attaching package: ‘Biostrings’
603s 
603s The following object is masked from ‘package:base’:
603s 
603s     strsplit
603s 
603s 
603s Attaching package: ‘pwalign’
603s 
603s The following objects are masked from ‘package:Biostrings’:
603s 
603s     aligned, alignedPattern, alignedSubject, compareStrings, deletion,
603s     errorSubstitutionMatrices, indel, insertion, mismatchSummary,
603s     mismatchTable, nedit, nindel, nucleotideSubstitutionMatrix,
603s     pairwiseAlignment, PairwiseAlignments,
603s     PairwiseAlignmentsSingleSubject, pid, qualitySubstitutionMatrices,
603s     stringDist, unaligned, writePairwiseAlignments
603s 
603s > 
603s > 
603s Other tests are currently unsupported!
603s They will be progressively added.
604s autopkgtest [15:19:12]: test pkg-r-autopkgtest: -----------------------]
743s pkg-r-autopkgtest    PASS
744s autopkgtest [15:21:31]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
751s autopkgtest [15:21:39]: @@@@@@@@@@@@@@@@@@@@ summary
751s pkg-r-autopkgtest    PASS
869s nova [W] Using flock in prodstack6-arm64
869s Creating nova instance adt-plucky-arm64-r-bioc-pwalign-20250315-150908-juju-7f2275-prod-proposed-migration-environment-15-01affd72-5eb2-47d2-84d7-86975c9127d7 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)...
869s nova [W] Timed out waiting for deb9f7c1-db29-4ab1-94e3-7ed5de2e44f0 to get deleted.