0s autopkgtest [17:38:51]: starting date and time: 2024-03-16 17:38:51+0000
  0s autopkgtest [17:38:51]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [17:38:51]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r_qnzm5u/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-bioc-pcamethods --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-22.secgroup --name adt-noble-arm64-r-bioc-pcamethods-20240316-173851-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
121s autopkgtest [17:40:52]: testbed dpkg architecture: arm64
121s autopkgtest [17:40:52]: testbed apt version: 2.7.12
121s autopkgtest [17:40:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup
121s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
122s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [473 kB]
122s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
122s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
122s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3670 kB]
122s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB]
122s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
122s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
122s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
122s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3995 kB]
122s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
122s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB]
122s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
124s Fetched 9060 kB in 2s (5422 kB/s)
124s Reading package lists...
128s Reading package lists...
129s Building dependency tree...
129s Reading state information...
129s Calculating upgrade...
130s The following packages will be REMOVED:
130s   libglib2.0-0 libssl3
130s The following NEW packages will be installed:
130s   libglib2.0-0t64 libssl3t64 xdg-user-dirs
130s The following packages have been kept back:
130s   curl
130s The following packages will be upgraded:
130s   gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common
130s   ubuntu-minimal ubuntu-standard
130s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded.
130s Need to get 4613 kB of archives.
130s After this operation, 211 kB of additional disk space will be used.
130s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB]
130s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB]
130s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
131s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
131s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB]
131s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B]
131s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB]
131s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB]
131s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB]
131s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB]
131s Fetched 4613 kB in 1s (5654 kB/s)
131s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
131s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ...
131s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
131s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested:
131s  udisks2 depends on libglib2.0-0 (>= 2.77.0).
131s  shared-mime-info depends on libglib2.0-0 (>= 2.75.3).
131s  python3-gi depends on libglib2.0-0 (>= 2.77.0).
131s  python3-dbus depends on libglib2.0-0 (>= 2.16.0).
131s  netplan.io depends on libglib2.0-0 (>= 2.70.0).
131s  netplan-generator depends on libglib2.0-0 (>= 2.70.0).
131s  libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0).
131s  libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0).
131s  libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3).
131s  libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56).
131s  libqmi-proxy depends on libglib2.0-0 (>= 2.30.0).
131s  libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0).
131s  libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
131s  libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
131s  libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3).
131s  libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0).
131s  libmbim-proxy depends on libglib2.0-0 (>= 2.56).
131s  libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56).
131s  libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3).
131s  libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3).
131s  libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3).
131s  libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
131s  libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0).
131s  libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0).
131s  libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2).
131s  libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3).
131s  libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2).
131s  libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2).
131s  libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2).
131s  libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2).
131s  libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2).
131s  libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2).
131s  libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2).
131s  fwupd depends on libglib2.0-0 (>= 2.79.0).
131s  bolt depends on libglib2.0-0 (>= 2.56.0).
131s 
132s (Reading database ... 
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132s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ...
132s Selecting previously unselected package libglib2.0-0t64:arm64.
132s (Reading database ... 
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132s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ...
132s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled...
132s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm'
132s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ...
132s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
132s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
132s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
132s  wget depends on libssl3 (>= 3.0.0).
132s  u-boot-tools depends on libssl3 (>= 3.0.0).
132s  tnftp depends on libssl3 (>= 3.0.0).
132s  tcpdump depends on libssl3 (>= 3.0.0).
132s  systemd-resolved depends on libssl3 (>= 3.0.0).
132s  systemd depends on libssl3 (>= 3.0.0).
132s  sudo depends on libssl3 (>= 3.0.0).
132s  sbsigntool depends on libssl3 (>= 3.0.0).
132s  rsync depends on libssl3 (>= 3.0.0).
132s  python3-cryptography depends on libssl3 (>= 3.0.0).
132s  openssh-server depends on libssl3 (>= 3.0.10).
132s  openssh-client depends on libssl3 (>= 3.0.10).
132s  mtd-utils depends on libssl3 (>= 3.0.0).
132s  mokutil depends on libssl3 (>= 3.0.0).
132s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
132s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
132s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
132s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
132s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
132s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
132s  libnvme1 depends on libssl3 (>= 3.0.0).
132s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
132s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
132s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
132s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
132s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
132s  kmod depends on libssl3 (>= 3.0.0).
132s  dhcpcd-base depends on libssl3 (>= 3.0.0).
132s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
132s 
132s (Reading database ... 
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132s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
132s Selecting previously unselected package libssl3t64:arm64.
132s (Reading database ... 
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(Reading database ... 74747 files and directories currently installed.)
132s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
132s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
132s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ...
132s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
132s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ...
132s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ...
132s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ...
132s Unpacking readline-common (8.2-3.1) over (8.2-3) ...
132s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ...
132s Unpacking ubuntu-minimal (1.536) over (1.535) ...
132s Selecting previously unselected package xdg-user-dirs.
132s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ...
132s Unpacking xdg-user-dirs (0.18-1) ...
132s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ...
132s Unpacking ubuntu-standard (1.536) over (1.535) ...
132s Setting up ubuntu-minimal (1.536) ...
132s Setting up xdg-user-dirs (0.18-1) ...
132s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
132s Setting up libtirpc-common (1.3.4+ds-1.1) ...
132s Setting up ubuntu-standard (1.536) ...
132s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ...
132s No schema files found: doing nothing.
132s Setting up libglib2.0-data (2.79.3-3ubuntu5) ...
132s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ...
132s Setting up openssl (3.0.13-0ubuntu1) ...
132s Setting up readline-common (8.2-3.1) ...
132s Processing triggers for man-db (2.12.0-3) ...
133s Processing triggers for install-info (7.1-3) ...
133s Processing triggers for libc-bin (2.39-0ubuntu2) ...
134s Reading package lists...
134s Building dependency tree...
134s Reading state information...
135s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
135s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
135s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
135s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
136s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
137s Reading package lists...
137s Reading package lists...
137s Building dependency tree...
137s Reading state information...
139s Calculating upgrade...
140s The following packages have been kept back:
140s   curl
140s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
140s Reading package lists...
141s Building dependency tree...
141s Reading state information...
142s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
145s autopkgtest [17:41:16]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
145s autopkgtest [17:41:16]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-pcamethods
147s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-bioc-pcamethods 1.94.0-1 (dsc) [2159 B]
147s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-bioc-pcamethods 1.94.0-1 (tar) [612 kB]
147s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-bioc-pcamethods 1.94.0-1 (diff) [3072 B]
148s gpgv: Signature made Thu Nov 30 07:59:29 2023 UTC
148s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
148s gpgv:                issuer "tille@debian.org"
148s gpgv: Can't check signature: No public key
148s dpkg-source: warning: cannot verify inline signature for ./r-bioc-pcamethods_1.94.0-1.dsc: no acceptable signature found
148s autopkgtest [17:41:19]: testing package r-bioc-pcamethods version 1.94.0-1
148s autopkgtest [17:41:19]: build not needed
150s autopkgtest [17:41:21]: test pkg-r-autopkgtest: preparing testbed
155s Reading package lists...
155s Building dependency tree...
155s Reading state information...
155s Starting pkgProblemResolver with broken count: 0
155s Starting 2 pkgProblemResolver with broken count: 0
156s Done
156s The following additional packages will be installed:
156s   build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu
156s   curl dctrl-tools fontconfig fontconfig-config fonts-dejavu-core
156s   fonts-dejavu-mono g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu
156s   gcc gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran
156s   gfortran-13 gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu
156s   icu-devtools libasan8 libatomic1 libblas-dev libblas3 libbz2-dev
156s   libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libcurl4t64
156s   libdatrie1 libdeflate0 libfontconfig1 libgcc-13-dev libgfortran-13-dev
156s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6
156s   libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8
156s   libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblerc4
156s   liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev libpango-1.0-0
156s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0
156s   libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3
156s   libpng-dev libpng16-16t64 libpsl5t64 libreadline-dev libreadline8t64
156s   libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6 libthai-data libthai0
156s   libtiff6 libtirpc-dev libtirpc3t64 libtk8.6 libtsan2 libubsan1 libwebp7
156s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
156s   linux-libc-dev littler pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin
156s   r-base-core r-base-dev r-bioc-biobase r-bioc-biocgenerics r-bioc-pcamethods
156s   r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2
156s   r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice
156s   r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix
156s   r-cran-matrixstats r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar
156s   r-cran-pkgconfig r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
156s   r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs
156s   r-cran-viridislite r-cran-withr rpcsvc-proto unzip x11-common xdg-utils zip
156s   zlib1g-dev
156s Suggested packages:
156s   cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib
156s   manpages-dev autoconf automake libtool flex bison gdb gcc-doc
156s   gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev
156s   liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc
156s   libstdc++-13-doc tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib
156s   r-base-html texlive-base texlive-latex-base texlive-plain-generic
156s   texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
156s   texlive-latex-recommended texlive-latex-extra texinfo r-bioc-all
156s   r-cran-runit r-bioc-biocstyle r-cran-knitr r-bioc-s4vectors r-bioc-iranges
156s   r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools
156s   r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate
156s   r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny
156s   r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-rmarkdown
156s   r-cran-viridis r-cran-covr r-cran-magick r-cran-sf r-cran-getopt
156s   r-cran-bit64 r-cran-dbi r-cran-formattable r-cran-nanotime
156s   r-cran-palmerpenguins r-cran-stringi r-cran-survival r-cran-units
156s   r-cran-vdiffr r-cran-testthat r-cran-inline r-cran-bench r-cran-blob
156s   r-cran-brio r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here
156s   r-cran-hms r-cran-htmltools r-cran-pkgbuild r-cran-pkgload r-cran-purrr
156s   r-cran-tidyr
156s Recommended packages:
156s   bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-recommended
156s   r-doc-html r-cran-callr r-cran-covr r-cran-crayon r-cran-digest
156s   r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockery
156s   r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot
156s   r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-unitizer r-cran-dplyr
156s   r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps r-cran-multcomp
156s   r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-rpart r-cran-sf
156s   r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-dbi r-cran-rsqlite
156s   r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-base64enc r-cran-markdown
156s   r-cran-r.devices r-cran-r.rsp r-cran-lubridate r-cran-fs r-cran-usethis
156s   r-cran-bit64 r-cran-dichromat r-cran-hms r-cran-stringi r-cran-data.table
156s   r-cran-mockr r-cran-formattable r-cran-generics r-cran-pkgdown
156s   r-cran-zeallot libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl
156s   x11-utils x11-xserver-utils
156s The following packages will be REMOVED:
156s   libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3
156s The following NEW packages will be installed:
156s   autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu
156s   cpp-aarch64-linux-gnu dctrl-tools fontconfig fontconfig-config
156s   fonts-dejavu-core fonts-dejavu-mono g++ g++-13 g++-13-aarch64-linux-gnu
156s   g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu
156s   gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu
156s   gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev
156s   libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev
156s   libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 libgcc-13-dev
156s   libgfortran-13-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
156s   libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev
156s   libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev
156s   liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev
156s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
156s   libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
156s   libpixman-1-0 libpkgconf3 libpng-dev libpng16-16t64 libpsl5t64
156s   libreadline-dev libreadline8t64 libsharpyuv0 libsm6 libstdc++-13-dev
156s   libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev libtirpc3t64 libtk8.6
156s   libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1
156s   libxss1 libxt6t64 linux-libc-dev littler pkg-config pkg-r-autopkgtest
156s   pkgconf pkgconf-bin r-base-core r-base-dev r-bioc-biobase
156s   r-bioc-biocgenerics r-bioc-pcamethods r-cran-cli r-cran-colorspace
156s   r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable
156s   r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle
156s   r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats
156s   r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig
156s   r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang
156s   r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite
156s   r-cran-withr rpcsvc-proto unzip x11-common xdg-utils zip zlib1g-dev
156s The following packages will be upgraded:
156s   curl
156s 1 upgraded, 147 newly installed, 5 to remove and 0 not upgraded.
156s Need to get 165 MB/165 MB of archives.
156s After this operation, 480 MB of additional disk space will be used.
156s Get:1 /tmp/autopkgtest.Zy9Krm/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [756 B]
156s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB]
157s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB]
157s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB]
157s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB]
157s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB]
157s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB]
157s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB]
157s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB]
157s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB]
157s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB]
157s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB]
157s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB]
157s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB]
157s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB]
157s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB]
157s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB]
157s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B]
157s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B]
157s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB]
157s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB]
157s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
157s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB]
157s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB]
157s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB]
157s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB]
157s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB]
158s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB]
158s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB]
158s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB]
158s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB]
158s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB]
158s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B]
158s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B]
158s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB]
158s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB]
159s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB]
159s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B]
159s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B]
159s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B]
159s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB]
159s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
159s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
159s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
159s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
159s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB]
159s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
159s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB]
159s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB]
159s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB]
159s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B]
159s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B]
159s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB]
159s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
159s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB]
159s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB]
159s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
159s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
159s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
159s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
159s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
159s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB]
159s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
159s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
159s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
159s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
159s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB]
159s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB]
159s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
159s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB]
159s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
159s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B]
159s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B]
159s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
160s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB]
160s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
160s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB]
160s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB]
160s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB]
160s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB]
160s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB]
160s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB]
160s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB]
160s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B]
160s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB]
160s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB]
160s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B]
160s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB]
160s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB]
160s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB]
160s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB]
160s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB]
160s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
160s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB]
160s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB]
160s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
160s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
160s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
160s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB]
160s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B]
160s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB]
160s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB]
160s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB]
160s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB]
160s Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
160s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB]
161s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB]
161s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B]
161s Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB]
161s Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB]
161s Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B]
161s Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB]
161s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B]
161s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
161s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocgenerics all 0.48.1-2 [595 kB]
162s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biobase arm64 2.62.0-1 [2136 kB]
162s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB]
162s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB]
162s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB]
162s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-pcamethods arm64 1.94.0-1 [961 kB]
162s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB]
162s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB]
162s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB]
162s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB]
162s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB]
162s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB]
162s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
162s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB]
162s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB]
162s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB]
162s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB]
162s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB]
162s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB]
162s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB]
162s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB]
162s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB]
162s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
162s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB]
162s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB]
163s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB]
163s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB]
163s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB]
163s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB]
163s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
163s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB]
163s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB]
163s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB]
163s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrixstats arm64 1.2.0-1 [475 kB]
165s Preconfiguring packages ...
165s Fetched 165 MB in 7s (25.4 MB/s)
165s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested:
165s  wget depends on libpsl5 (>= 0.16.0).
165s  libcurl4:arm64 depends on libpsl5 (>= 0.16.0).
165s  libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0).
165s 
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165s Removing libpsl5:arm64 (0.21.2-1build1) ...
165s Selecting previously unselected package libpsl5t64:arm64.
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165s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ...
165s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ...
165s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ...
165s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ...
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165s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ...
165s Selecting previously unselected package libcurl4t64:arm64.
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165s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ...
165s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ...
165s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested:
165s  libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2).
165s  libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1).
165s 
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165s Removing libpng16-16:arm64 (1.6.43-1) ...
166s Selecting previously unselected package libpng16-16t64:arm64.
166s (Reading database ... 
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166s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ...
166s Unpacking libpng16-16t64:arm64 (1.6.43-3) ...
166s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested:
166s  parted depends on libreadline8 (>= 6.0).
166s  libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta).
166s  gpgsm depends on libreadline8 (>= 6.0).
166s  gpgconf depends on libreadline8 (>= 6.0).
166s  gpg depends on libreadline8 (>= 6.0).
166s  gawk depends on libreadline8 (>= 6.0).
166s  fdisk depends on libreadline8 (>= 6.0).
166s 
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166s Removing libreadline8:arm64 (8.2-3) ...
166s Selecting previously unselected package libreadline8t64:arm64.
166s (Reading database ... 
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166s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ...
166s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
166s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
166s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
166s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
166s Unpacking libreadline8t64:arm64 (8.2-3.1) ...
166s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested:
166s  lsof depends on libtirpc3 (>= 1.0.2).
166s  libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2).
166s  libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2).
166s  libnsl2:arm64 depends on libtirpc3 (>= 1.0.2).
166s  iproute2 depends on libtirpc3 (>= 1.0.2).
166s 
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166s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ...
166s Selecting previously unselected package libtirpc3t64:arm64.
166s (Reading database ... 
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166s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ...
166s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
166s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
166s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ...
166s Selecting previously unselected package libc-dev-bin.
166s Preparing to unpack .../001-libc-dev-bin_2.39-0ubuntu2_arm64.deb ...
166s Unpacking libc-dev-bin (2.39-0ubuntu2) ...
166s Selecting previously unselected package linux-libc-dev:arm64.
166s Preparing to unpack .../002-linux-libc-dev_6.8.0-11.11_arm64.deb ...
166s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ...
166s Selecting previously unselected package libcrypt-dev:arm64.
166s Preparing to unpack .../003-libcrypt-dev_1%3a4.4.36-4_arm64.deb ...
166s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ...
166s Selecting previously unselected package libtirpc-dev:arm64.
166s Preparing to unpack .../004-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ...
166s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ...
166s Selecting previously unselected package libnsl-dev:arm64.
166s Preparing to unpack .../005-libnsl-dev_1.3.0-3_arm64.deb ...
166s Unpacking libnsl-dev:arm64 (1.3.0-3) ...
166s Selecting previously unselected package rpcsvc-proto.
166s Preparing to unpack .../006-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ...
166s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
166s Selecting previously unselected package libc6-dev:arm64.
166s Preparing to unpack .../007-libc6-dev_2.39-0ubuntu2_arm64.deb ...
166s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ...
166s Selecting previously unselected package libisl23:arm64.
166s Preparing to unpack .../008-libisl23_0.26-3_arm64.deb ...
166s Unpacking libisl23:arm64 (0.26-3) ...
167s Selecting previously unselected package libmpc3:arm64.
167s Preparing to unpack .../009-libmpc3_1.3.1-1_arm64.deb ...
167s Unpacking libmpc3:arm64 (1.3.1-1) ...
167s Selecting previously unselected package cpp-13-aarch64-linux-gnu.
167s Preparing to unpack .../010-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ...
167s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
167s Selecting previously unselected package cpp-13.
167s Preparing to unpack .../011-cpp-13_13.2.0-17ubuntu2_arm64.deb ...
167s Unpacking cpp-13 (13.2.0-17ubuntu2) ...
167s Selecting previously unselected package cpp-aarch64-linux-gnu.
167s Preparing to unpack .../012-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ...
167s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
167s Selecting previously unselected package cpp.
167s Preparing to unpack .../013-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ...
167s Unpacking cpp (4:13.2.0-7ubuntu1) ...
167s Selecting previously unselected package libcc1-0:arm64.
167s Preparing to unpack .../014-libcc1-0_14-20240303-1ubuntu1_arm64.deb ...
167s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ...
167s Selecting previously unselected package libgomp1:arm64.
167s Preparing to unpack .../015-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
167s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
167s Selecting previously unselected package libitm1:arm64.
167s Preparing to unpack .../016-libitm1_14-20240303-1ubuntu1_arm64.deb ...
167s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ...
167s Selecting previously unselected package libatomic1:arm64.
167s Preparing to unpack .../017-libatomic1_14-20240303-1ubuntu1_arm64.deb ...
167s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ...
167s Selecting previously unselected package libasan8:arm64.
167s Preparing to unpack .../018-libasan8_14-20240303-1ubuntu1_arm64.deb ...
167s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ...
167s Selecting previously unselected package liblsan0:arm64.
167s Preparing to unpack .../019-liblsan0_14-20240303-1ubuntu1_arm64.deb ...
167s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ...
168s Selecting previously unselected package libtsan2:arm64.
168s Preparing to unpack .../020-libtsan2_14-20240303-1ubuntu1_arm64.deb ...
168s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ...
168s Selecting previously unselected package libubsan1:arm64.
168s Preparing to unpack .../021-libubsan1_14-20240303-1ubuntu1_arm64.deb ...
168s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ...
168s Selecting previously unselected package libhwasan0:arm64.
168s Preparing to unpack .../022-libhwasan0_14-20240303-1ubuntu1_arm64.deb ...
168s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ...
168s Selecting previously unselected package libgcc-13-dev:arm64.
168s Preparing to unpack .../023-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ...
168s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ...
168s Selecting previously unselected package gcc-13-aarch64-linux-gnu.
168s Preparing to unpack .../024-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ...
168s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
168s Selecting previously unselected package gcc-13.
168s Preparing to unpack .../025-gcc-13_13.2.0-17ubuntu2_arm64.deb ...
168s Unpacking gcc-13 (13.2.0-17ubuntu2) ...
168s Selecting previously unselected package gcc-aarch64-linux-gnu.
168s Preparing to unpack .../026-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ...
168s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
168s Selecting previously unselected package gcc.
168s Preparing to unpack .../027-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ...
168s Unpacking gcc (4:13.2.0-7ubuntu1) ...
168s Selecting previously unselected package libstdc++-13-dev:arm64.
168s Preparing to unpack .../028-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ...
168s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ...
169s Selecting previously unselected package g++-13-aarch64-linux-gnu.
169s Preparing to unpack .../029-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ...
169s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
169s Selecting previously unselected package g++-13.
169s Preparing to unpack .../030-g++-13_13.2.0-17ubuntu2_arm64.deb ...
169s Unpacking g++-13 (13.2.0-17ubuntu2) ...
169s Selecting previously unselected package g++-aarch64-linux-gnu.
169s Preparing to unpack .../031-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ...
169s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
169s Selecting previously unselected package g++.
169s Preparing to unpack .../032-g++_4%3a13.2.0-7ubuntu1_arm64.deb ...
169s Unpacking g++ (4:13.2.0-7ubuntu1) ...
169s Selecting previously unselected package build-essential.
169s Preparing to unpack .../033-build-essential_12.10ubuntu1_arm64.deb ...
169s Unpacking build-essential (12.10ubuntu1) ...
169s Selecting previously unselected package dctrl-tools.
169s Preparing to unpack .../034-dctrl-tools_2.24-3build2_arm64.deb ...
169s Unpacking dctrl-tools (2.24-3build2) ...
169s Selecting previously unselected package fonts-dejavu-mono.
169s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ...
169s Unpacking fonts-dejavu-mono (2.37-8) ...
169s Selecting previously unselected package fonts-dejavu-core.
170s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ...
170s Unpacking fonts-dejavu-core (2.37-8) ...
170s Selecting previously unselected package fontconfig-config.
170s Preparing to unpack .../037-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
170s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
170s Selecting previously unselected package libfontconfig1:arm64.
170s Preparing to unpack .../038-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
170s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
170s Selecting previously unselected package fontconfig.
170s Preparing to unpack .../039-fontconfig_2.15.0-1ubuntu1_arm64.deb ...
170s Unpacking fontconfig (2.15.0-1ubuntu1) ...
170s Selecting previously unselected package libgfortran5:arm64.
170s Preparing to unpack .../040-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
170s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
170s Selecting previously unselected package libgfortran-13-dev:arm64.
170s Preparing to unpack .../041-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ...
170s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ...
170s Selecting previously unselected package gfortran-13-aarch64-linux-gnu.
170s Preparing to unpack .../042-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ...
170s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
171s Selecting previously unselected package gfortran-13.
171s Preparing to unpack .../043-gfortran-13_13.2.0-17ubuntu2_arm64.deb ...
171s Unpacking gfortran-13 (13.2.0-17ubuntu2) ...
171s Selecting previously unselected package gfortran-aarch64-linux-gnu.
171s Preparing to unpack .../044-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ...
171s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
171s Selecting previously unselected package gfortran.
171s Preparing to unpack .../045-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ...
171s Unpacking gfortran (4:13.2.0-7ubuntu1) ...
171s Selecting previously unselected package icu-devtools.
171s Preparing to unpack .../046-icu-devtools_74.2-1ubuntu1_arm64.deb ...
171s Unpacking icu-devtools (74.2-1ubuntu1) ...
171s Selecting previously unselected package libblas3:arm64.
171s Preparing to unpack .../047-libblas3_3.12.0-3_arm64.deb ...
171s Unpacking libblas3:arm64 (3.12.0-3) ...
171s Selecting previously unselected package libblas-dev:arm64.
171s Preparing to unpack .../048-libblas-dev_3.12.0-3_arm64.deb ...
171s Unpacking libblas-dev:arm64 (3.12.0-3) ...
171s Selecting previously unselected package libbz2-dev:arm64.
171s Preparing to unpack .../049-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ...
171s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ...
171s Selecting previously unselected package libpixman-1-0:arm64.
171s Preparing to unpack .../050-libpixman-1-0_0.42.2-1_arm64.deb ...
171s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
171s Selecting previously unselected package libxcb-render0:arm64.
171s Preparing to unpack .../051-libxcb-render0_1.15-1_arm64.deb ...
171s Unpacking libxcb-render0:arm64 (1.15-1) ...
171s Selecting previously unselected package libxcb-shm0:arm64.
171s Preparing to unpack .../052-libxcb-shm0_1.15-1_arm64.deb ...
171s Unpacking libxcb-shm0:arm64 (1.15-1) ...
171s Selecting previously unselected package libxrender1:arm64.
171s Preparing to unpack .../053-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
171s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
171s Selecting previously unselected package libcairo2:arm64.
171s Preparing to unpack .../054-libcairo2_1.18.0-1_arm64.deb ...
171s Unpacking libcairo2:arm64 (1.18.0-1) ...
171s Selecting previously unselected package libdatrie1:arm64.
171s Preparing to unpack .../055-libdatrie1_0.2.13-3_arm64.deb ...
171s Unpacking libdatrie1:arm64 (0.2.13-3) ...
171s Selecting previously unselected package libdeflate0:arm64.
171s Preparing to unpack .../056-libdeflate0_1.19-1_arm64.deb ...
171s Unpacking libdeflate0:arm64 (1.19-1) ...
171s Selecting previously unselected package libgraphite2-3:arm64.
171s Preparing to unpack .../057-libgraphite2-3_1.3.14-2_arm64.deb ...
171s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
171s Selecting previously unselected package libharfbuzz0b:arm64.
171s Preparing to unpack .../058-libharfbuzz0b_8.3.0-2_arm64.deb ...
171s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
171s Selecting previously unselected package x11-common.
171s Preparing to unpack .../059-x11-common_1%3a7.7+23ubuntu2_all.deb ...
171s Unpacking x11-common (1:7.7+23ubuntu2) ...
171s Selecting previously unselected package libice6:arm64.
171s Preparing to unpack .../060-libice6_2%3a1.0.10-1build2_arm64.deb ...
171s Unpacking libice6:arm64 (2:1.0.10-1build2) ...
171s Selecting previously unselected package libicu-dev:arm64.
172s Preparing to unpack .../061-libicu-dev_74.2-1ubuntu1_arm64.deb ...
172s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ...
172s Selecting previously unselected package libjpeg-turbo8:arm64.
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172s Selecting previously unselected package libjpeg-turbo8-dev:arm64.
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172s Selecting previously unselected package libjpeg8:arm64.
172s Preparing to unpack .../064-libjpeg8_8c-2ubuntu11_arm64.deb ...
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172s Selecting previously unselected package libjpeg8-dev:arm64.
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172s Selecting previously unselected package libjpeg-dev:arm64.
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172s Selecting previously unselected package liblapack3:arm64.
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172s Selecting previously unselected package liblerc4:arm64.
173s Preparing to unpack .../069-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
173s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
173s Selecting previously unselected package libncurses-dev:arm64.
173s Preparing to unpack .../070-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ...
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173s Selecting previously unselected package libthai-data.
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173s Selecting previously unselected package libthai0:arm64.
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173s Selecting previously unselected package libpango-1.0-0:arm64.
174s Preparing to unpack .../073-libpango-1.0-0_1.51.0+ds-4_arm64.deb ...
174s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ...
174s Selecting previously unselected package libpangoft2-1.0-0:arm64.
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175s Selecting previously unselected package libpangocairo-1.0-0:arm64.
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175s Selecting previously unselected package libpaper1:arm64.
175s Preparing to unpack .../076-libpaper1_1.1.29_arm64.deb ...
175s Unpacking libpaper1:arm64 (1.1.29) ...
175s Selecting previously unselected package libpaper-utils.
175s Preparing to unpack .../077-libpaper-utils_1.1.29_arm64.deb ...
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175s Selecting previously unselected package libpcre2-16-0:arm64.
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175s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ...
175s Selecting previously unselected package libpcre2-32-0:arm64.
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175s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ...
175s Selecting previously unselected package libpcre2-posix3:arm64.
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176s Selecting previously unselected package libpkgconf3:arm64.
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176s Selecting previously unselected package zlib1g-dev:arm64.
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176s Selecting previously unselected package libpng-dev:arm64.
176s Preparing to unpack .../084-libpng-dev_1.6.43-3_arm64.deb ...
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176s Selecting previously unselected package libreadline-dev:arm64.
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176s Selecting previously unselected package libsharpyuv0:arm64.
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176s Selecting previously unselected package libsm6:arm64.
176s Preparing to unpack .../087-libsm6_2%3a1.2.3-1build2_arm64.deb ...
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176s Selecting previously unselected package libtcl8.6:arm64.
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176s Selecting previously unselected package libjbig0:arm64.
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176s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
176s Selecting previously unselected package libwebp7:arm64.
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176s Preparing to unpack .../091-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
176s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
176s Selecting previously unselected package libxft2:arm64.
176s Preparing to unpack .../092-libxft2_2.3.6-1_arm64.deb ...
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176s Selecting previously unselected package libxss1:arm64.
176s Preparing to unpack .../093-libxss1_1%3a1.2.3-1build2_arm64.deb ...
176s Unpacking libxss1:arm64 (1:1.2.3-1build2) ...
176s Selecting previously unselected package libtk8.6:arm64.
177s Preparing to unpack .../094-libtk8.6_8.6.13-2_arm64.deb ...
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177s Selecting previously unselected package libxt6t64:arm64.
177s Preparing to unpack .../095-libxt6t64_1%3a1.2.1-1.2_arm64.deb ...
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177s Selecting previously unselected package zip.
177s Preparing to unpack .../096-zip_3.0-13_arm64.deb ...
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177s Preparing to unpack .../097-unzip_6.0-28ubuntu3_arm64.deb ...
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177s Selecting previously unselected package xdg-utils.
177s Preparing to unpack .../098-xdg-utils_1.1.3-4.1ubuntu3_all.deb ...
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177s Selecting previously unselected package r-base-core.
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178s Selecting previously unselected package r-cran-littler.
178s Preparing to unpack .../100-r-cran-littler_0.3.19-1_arm64.deb ...
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178s Selecting previously unselected package littler.
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178s Selecting previously unselected package pkgconf:arm64.
178s Preparing to unpack .../103-pkgconf_1.8.1-2_arm64.deb ...
178s Unpacking pkgconf:arm64 (1.8.1-2) ...
178s Selecting previously unselected package pkg-config:arm64.
178s Preparing to unpack .../104-pkg-config_1.8.1-2_arm64.deb ...
178s Unpacking pkg-config:arm64 (1.8.1-2) ...
178s Selecting previously unselected package liblzma-dev:arm64.
178s Preparing to unpack .../105-liblzma-dev_5.4.5-0.3_arm64.deb ...
178s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ...
178s Selecting previously unselected package r-base-dev.
178s Preparing to unpack .../106-r-base-dev_4.3.3-2build1_all.deb ...
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178s Selecting previously unselected package pkg-r-autopkgtest.
178s Preparing to unpack .../107-pkg-r-autopkgtest_20231212ubuntu1_all.deb ...
178s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ...
178s Selecting previously unselected package r-bioc-biocgenerics.
178s Preparing to unpack .../108-r-bioc-biocgenerics_0.48.1-2_all.deb ...
178s Unpacking r-bioc-biocgenerics (0.48.1-2) ...
178s Selecting previously unselected package r-bioc-biobase.
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178s Unpacking r-bioc-biobase (2.62.0-1) ...
178s Selecting previously unselected package r-cran-pkgkitten.
179s Preparing to unpack .../110-r-cran-pkgkitten_0.2.3-1_all.deb ...
179s Unpacking r-cran-pkgkitten (0.2.3-1) ...
179s Selecting previously unselected package r-cran-rcpp.
179s Preparing to unpack .../111-r-cran-rcpp_1.0.12-1_arm64.deb ...
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179s Selecting previously unselected package r-cran-mass.
179s Preparing to unpack .../112-r-cran-mass_7.3-60.0.1-1_arm64.deb ...
179s Unpacking r-cran-mass (7.3-60.0.1-1) ...
179s Selecting previously unselected package r-bioc-pcamethods.
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179s Unpacking r-bioc-pcamethods (1.94.0-1) ...
179s Selecting previously unselected package r-cran-cli.
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179s Selecting previously unselected package r-cran-colorspace.
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179s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ...
179s Selecting previously unselected package r-cran-fansi.
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179s Selecting previously unselected package r-cran-farver.
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180s Selecting previously unselected package r-cran-gtable.
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180s Selecting previously unselected package r-cran-isoband.
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180s Selecting previously unselected package r-cran-lattice.
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181s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
181s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
181s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
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181s 
181s Creating config file /etc/papersize with new version
181s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
181s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
181s Setting up libdatrie1:arm64 (0.2.13-3) ...
181s Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1) ...
181s Setting up libxcb-render0:arm64 (1.15-1) ...
181s Setting up unzip (6.0-28ubuntu3) ...
181s Setting up x11-common (1:7.7+23ubuntu2) ...
182s Setting up libpsl5t64:arm64 (0.21.2-1.1) ...
182s Setting up libdeflate0:arm64 (1.19-1) ...
182s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ...
182s Setting up libxcb-shm0:arm64 (1.15-1) ...
182s Setting up libpaper-utils (1.1.29) ...
182s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
182s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
182s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ...
182s Setting up zip (3.0-13) ...
182s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ...
182s Setting up libblas3:arm64 (3.12.0-3) ...
182s 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
182s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1) ...
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182s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
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182s Setting up libmpc3:arm64 (1.3.1-1) ...
182s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ...
182s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ...
182s Setting up icu-devtools (74.2-1ubuntu1) ...
182s Setting up fonts-dejavu-core (2.37-8) ...
182s Setting up pkgconf-bin (1.8.1-2) ...
182s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
182s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
182s Setting up libwebp7:arm64 (1.3.2-0.4) ...
182s Setting up libreadline8t64:arm64 (8.2-3.1) ...
182s Setting up liblzma-dev:arm64 (5.4.5-0.3) ...
182s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ...
182s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ...
182s Setting up libnsl-dev:arm64 (1.3.0-3) ...
182s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ...
182s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ...
182s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ...
182s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
182s Setting up libthai-data (0.1.29-2) ...
182s Setting up libxss1:arm64 (1:1.2.3-1build2) ...
182s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ...
182s Setting up libisl23:arm64 (0.26-3) ...
182s Setting up libc-dev-bin (2.39-0ubuntu2) ...
182s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
182s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
182s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ...
182s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ...
182s Setting up libblas-dev:arm64 (3.12.0-3) ...
182s 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
182s Setting up dctrl-tools (2.24-3build2) ...
182s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ...
182s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
182s Setting up libice6:arm64 (2:1.0.10-1build2) ...
182s Setting up liblapack3:arm64 (3.12.0-3) ...
182s 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
182s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
182s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ...
182s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
183s Setting up pkgconf:arm64 (1.8.1-2) ...
183s Setting up libthai0:arm64 (0.1.29-2) ...
183s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
183s Setting up liblapack-dev:arm64 (3.12.0-3) ...
183s 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
183s Setting up pkg-config:arm64 (1.8.1-2) ...
183s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ...
183s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
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183s Setting up curl (8.5.0-2ubuntu7) ...
183s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
183s Setting up libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ...
183s Setting up libsm6:arm64 (2:1.2.3-1build2) ...
183s Setting up libicu-dev:arm64 (74.2-1ubuntu1) ...
183s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ...
183s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ...
183s Setting up fontconfig (2.15.0-1ubuntu1) ...
185s Regenerating fonts cache... done.
185s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ...
185s Setting up libxft2:arm64 (2.3.6-1) ...
185s Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ...
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185s Setting up cpp-13 (13.2.0-17ubuntu2) ...
185s Setting up libtk8.6:arm64 (8.6.13-2) ...
185s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ...
185s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
185s Setting up libreadline-dev:arm64 (8.2-3.1) ...
185s Setting up libcairo2:arm64 (1.18.0-1) ...
185s Setting up libxt6t64:arm64 (1:1.2.1-1.2) ...
185s Setting up gcc-13 (13.2.0-17ubuntu2) ...
185s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ...
185s Setting up cpp (4:13.2.0-7ubuntu1) ...
185s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
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185s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
185s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
185s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
185s Setting up g++-13 (13.2.0-17ubuntu2) ...
185s Setting up libpng-dev:arm64 (1.6.43-3) ...
185s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ...
185s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
185s Setting up gcc (4:13.2.0-7ubuntu1) ...
185s Setting up gfortran-13 (13.2.0-17ubuntu2) ...
185s Setting up r-base-core (4.3.3-2build1) ...
185s 
185s Creating config file /etc/R/Renviron with new version
185s Setting up r-cran-labeling (0.4.3-1) ...
185s Setting up r-cran-lattice (0.22-5-1) ...
185s Setting up r-cran-nlme (3.1.164-1) ...
185s Setting up r-cran-farver (2.1.1-1) ...
185s Setting up r-cran-viridislite (0.4.2-2) ...
185s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
185s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
185s Setting up r-cran-r6 (2.5.1-1) ...
185s Setting up r-cran-pkgkitten (0.2.3-1) ...
185s Setting up r-cran-magrittr (2.0.3-1) ...
185s Setting up r-cran-littler (0.3.19-1) ...
185s Setting up r-cran-rcpp (1.0.12-1) ...
185s Setting up r-bioc-biocgenerics (0.48.1-2) ...
185s Setting up r-cran-rlang (1.1.3-1) ...
185s Setting up r-cran-matrixstats (1.2.0-1) ...
185s Setting up littler (0.3.19-1) ...
185s Setting up r-cran-withr (2.5.0-1) ...
185s Setting up r-cran-fansi (1.0.5-1) ...
185s Setting up r-cran-mass (7.3-60.0.1-1) ...
185s Setting up r-cran-glue (1.7.0-1) ...
185s Setting up r-cran-cli (3.6.2-1) ...
185s Setting up gfortran (4:13.2.0-7ubuntu1) ...
185s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
185s 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
185s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
185s 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
185s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
185s Setting up r-bioc-biobase (2.62.0-1) ...
185s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
185s Setting up r-cran-utf8 (1.2.4-1) ...
185s Setting up r-cran-colorspace (2.1-0+dfsg-1) ...
185s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
185s Setting up r-cran-isoband (0.2.7-1) ...
185s Setting up r-cran-gtable (0.3.4+dfsg-1) ...
185s Setting up r-cran-matrix (1.6-5-1) ...
185s Setting up r-cran-mgcv (1.9-1-1) ...
185s Setting up g++ (4:13.2.0-7ubuntu1) ...
185s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
185s Setting up build-essential (12.10ubuntu1) ...
185s Setting up r-cran-vctrs (0.6.5-1) ...
185s Setting up r-cran-pillar (1.9.0+dfsg-1) ...
185s Setting up r-base-dev (4.3.3-2build1) ...
185s Setting up r-cran-munsell (0.5.0-2build1) ...
185s Setting up r-cran-tibble (3.2.1+dfsg-2) ...
185s Setting up r-bioc-pcamethods (1.94.0-1) ...
185s Setting up r-cran-scales (1.3.0-1) ...
185s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
185s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ...
185s Setting up autopkgtest-satdep (0) ...
185s Processing triggers for man-db (2.12.0-3) ...
186s Processing triggers for install-info (7.1-3) ...
186s Processing triggers for libc-bin (2.39-0ubuntu2) ...
195s (Reading database ... 84648 files and directories currently installed.)
195s Removing autopkgtest-satdep (0) ...
196s autopkgtest [17:42:07]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
196s autopkgtest [17:42:07]: test pkg-r-autopkgtest: [-----------------------
196s Test: Try to load the R library pcaMethods
197s 
197s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
197s Copyright (C) 2024 The R Foundation for Statistical Computing
197s Platform: aarch64-unknown-linux-gnu (64-bit)
197s 
197s R is free software and comes with ABSOLUTELY NO WARRANTY.
197s You are welcome to redistribute it under certain conditions.
197s Type 'license()' or 'licence()' for distribution details.
197s 
197s R is a collaborative project with many contributors.
197s Type 'contributors()' for more information and
197s 'citation()' on how to cite R or R packages in publications.
197s 
197s Type 'demo()' for some demos, 'help()' for on-line help, or
197s 'help.start()' for an HTML browser interface to help.
197s Type 'q()' to quit R.
197s 
197s > library('pcaMethods')
197s Loading required package: Biobase
197s Loading required package: BiocGenerics
197s 
197s Attaching package: ‘BiocGenerics’
197s 
197s The following objects are masked from ‘package:stats’:
197s 
197s     IQR, mad, sd, var, xtabs
197s 
197s The following objects are masked from ‘package:base’:
197s 
197s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
197s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
197s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
197s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
197s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
197s     table, tapply, union, unique, unsplit, which.max, which.min
197s 
197s Welcome to Bioconductor
197s 
197s     Vignettes contain introductory material; view with
197s     'browseVignettes()'. To cite Bioconductor, see
197s     'citation("Biobase")', and for packages 'citation("pkgname")'.
197s 
197s > 
197s > 
197s 
197s Attaching package: ‘pcaMethods’
197s 
197s The following object is masked from ‘package:stats’:
197s 
197s     loadings
197s 
197s Other tests are currently unsupported!
197s They will be progressively added.
198s autopkgtest [17:42:09]: test pkg-r-autopkgtest: -----------------------]
198s pkg-r-autopkgtest    PASS
198s autopkgtest [17:42:09]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
199s autopkgtest [17:42:10]: @@@@@@@@@@@@@@@@@@@@ summary
199s pkg-r-autopkgtest    PASS
212s Creating nova instance adt-noble-arm64-r-bioc-pcamethods-20240316-173851-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...