0s autopkgtest [23:21:30]: starting date and time: 2026-02-09 23:21:30+0000 0s autopkgtest [23:21:30]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:21:30]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qbzsyhtm/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-bioc-purecn --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-21.secgroup --name adt-resolute-arm64-r-bioc-purecn-20260209-232130-juju-7f2275-prod-proposed-migration-environment-15-9e558101-8020-42cd-9199-aab795190ee0 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-r-bioc-purecn-20260209-232130-juju-7f2275-prod-proposed-migration-environment-15-9e558101-8020-42cd-9199-aab795190ee0 from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 123s autopkgtest [23:23:33]: testbed dpkg architecture: arm64 123s autopkgtest [23:23:33]: testbed apt version: 3.1.15 123s autopkgtest [23:23:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 123s autopkgtest [23:23:33]: testbed release detected to be: None 124s autopkgtest [23:23:34]: updating testbed package index (apt update) 124s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 124s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 124s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 124s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 124s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 125s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 125s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 127s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 127s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 127s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 127s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 130s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 130s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 130s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 132s Fetched 3862 kB in 6s (679 kB/s) 132s Reading package lists... 133s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 133s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 133s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 133s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 134s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Calculating upgrade... 135s The following packages will be upgraded: 135s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 135s libip6tc2 libxtables12 wget 135s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Need to get 2534 kB of archives. 135s After this operation, 18.4 kB of additional disk space will be used. 135s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 135s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 135s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 135s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 135s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 137s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 137s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 137s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 137s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 137s dpkg-preconfigure: unable to re-open stdin: No such file or directory 137s Fetched 2534 kB in 2s (1301 kB/s) 137s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 136597 files and directories currently installed.) 137s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 137s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 137s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 137s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 137s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 138s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 138s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 138s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 138s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 138s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 138s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 138s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 138s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.deb ... 138s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 138s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_arm64.deb ... 138s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 138s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 138s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 138s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 138s Setting up wget (1.25.0-2ubuntu4) ... 138s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 138s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 138s Setting up dracut-install (109-11ubuntu1) ... 138s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 138s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 138s Setting up iptables (1.8.11-2ubuntu3) ... 138s Setting up iproute2 (6.18.0-1ubuntu1) ... 139s Processing triggers for man-db (2.13.1-1build1) ... 140s Processing triggers for install-info (7.2-5) ... 140s Processing triggers for libc-bin (2.42-2ubuntu4) ... 140s autopkgtest [23:23:50]: upgrading testbed (apt dist-upgrade and autopurge) 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Calculating upgrade... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s Solving dependencies... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s autopkgtest [23:23:54]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 144s autopkgtest [23:23:54]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-purecn 154s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-purecn 2.12.0+dfsg-2 (dsc) [2504 B] 154s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-purecn 2.12.0+dfsg-2 (tar) [5496 kB] 154s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-purecn 2.12.0+dfsg-2 (diff) [6696 B] 154s gpgv: Signature made Tue Jan 14 08:02:30 2025 UTC 154s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 154s gpgv: issuer "crusoe@debian.org" 154s gpgv: Can't check signature: No public key 154s dpkg-source: warning: cannot verify inline signature for ./r-bioc-purecn_2.12.0+dfsg-2.dsc: no acceptable signature found 155s autopkgtest [23:24:05]: testing package r-bioc-purecn version 2.12.0+dfsg-2 156s autopkgtest [23:24:06]: build not needed 158s autopkgtest [23:24:08]: test pkg-r-autopkgtest: preparing testbed 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s Solving dependencies... 159s The following NEW packages will be installed: 159s build-essential comerr-dev cpp cpp-15 cpp-15-aarch64-linux-gnu 159s cpp-aarch64-linux-gnu dctrl-tools fontconfig fontconfig-config 159s fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 159s fonts-glyphicons-halflings fonts-lmodern fonts-mathjax g++ g++-15 159s g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-15 159s gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-15 159s gfortran-15-aarch64-linux-gnu gfortran-aarch64-linux-gnu hdf5-helpers 159s icu-devtools javascript-common krb5-multidev libaec-dev libaec0 libasan8 159s libbibtex-parser-perl libblas-dev libblas3 libblosc1 libboost-dev 159s libboost1.90-dev libbrotli-dev libbz2-dev libc-dev-bin libc6-dev libcairo2 159s libcc1-0 libcrypt-dev libcurl4-openssl-dev libdatrie1 libdeflate-dev 159s libdeflate0 libevent-2.1-7t64 libfontconfig1 libgcc-15-dev 159s libgfortran-15-dev libgfortran5 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 159s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libgraphite2-3 libgssrpc4t64 159s libharfbuzz0b libhdf5-310 libhdf5-cpp-310 libhdf5-dev libhdf5-fortran-310 159s libhdf5-hl-310 libhdf5-hl-cpp-310 libhdf5-hl-fortran-310 libhwasan0 libice6 159s libicu-dev libidn2-dev libio-string-perl libisl23 libitm1 libjbig0 159s libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 159s libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js 159s libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js 159s libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js 159s libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js 159s libjs-twitter-bootstrap-datepicker libkadm5clnt-mit12 libkadm5srv-mit12 159s libkdb5-10t64 libkpathsea6 libkrb5-dev liblapack-dev liblapack3 159s liblatex-tounicode-perl libldap-dev liblerc4 liblsan0 liblua5.4-0 159s liblzma-dev libmpc3 libmpfi0 libncurses-dev libnghttp2-dev libp11-kit-dev 159s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 159s libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 159s libpixman-1-0 libpkgconf3 libpng-dev libpotrace0 libpsl-dev libptexenc1 159s libreadline-dev librtmp-dev libsharpyuv0 libsm6 libsnappy1v5 libssh2-1-dev 159s libssl-dev libstdc++-15-dev libsynctex2 libsz2 libtasn1-6-dev libtcl8.6 159s libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-dev 159s libtk8.6 libtsan2 libubsan1 libunbound8 libwebp7 libxaw7 libxcb-render0 159s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 159s libzstd-dev libzzip-0-13t64 linux-libc-dev nettle-dev node-bootstrap-sass 159s node-html5shiv node-normalize.css pandoc pandoc-data pkg-r-autopkgtest 159s pkgconf pkgconf-bin r-base-core r-base-dev r-bioc-annotationdbi 159s r-bioc-aroma.light r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio 159s r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biostrings 159s r-bioc-bsgenome r-bioc-delayedarray r-bioc-dnacopy r-bioc-genomeinfodb 159s r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures 159s r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics 159s r-bioc-org.hs.eg.db r-bioc-purecn r-bioc-rhdf5 r-bioc-rhdf5filters 159s r-bioc-rhdf5lib r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer 159s r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray 159s r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation 159s r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-base64enc 159s r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops 159s r-cran-blob r-cran-bookdown r-cran-brio r-cran-bslib r-cran-cachem 159s r-cran-callr r-cran-cli r-cran-codetools r-cran-commonmark r-cran-covr 159s r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi 159s r-cran-desc r-cran-diffobj r-cran-digest r-cran-evaluate r-cran-farver 159s r-cran-fastmap r-cran-fontawesome r-cran-formatr r-cran-fs 159s r-cran-futile.logger r-cran-futile.options r-cran-future r-cran-getopt 159s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gridextra r-cran-gtable 159s r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-isoband 159s r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling 159s r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle 159s r-cran-listenv r-cran-littler r-cran-magrittr r-cran-markdown r-cran-matrix 159s r-cran-matrixstats r-cran-mclust r-cran-memoise r-cran-mime r-cran-openssl 159s r-cran-optparse r-cran-parallelly r-cran-pkgbuild r-cran-pkgconfig 159s r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-png r-cran-praise 159s r-cran-processx r-cran-promises r-cran-ps r-cran-pscbs r-cran-r.cache 159s r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs 159s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rex 159s r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rprojroot r-cran-rsqlite 159s r-cran-s7 r-cran-sass r-cran-scales r-cran-shiny r-cran-snow 159s r-cran-sourcetools r-cran-sys r-cran-testthat r-cran-tinytex r-cran-vctrs 159s r-cran-vgam r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xfun 159s r-cran-xml r-cran-xtable r-cran-yaml rpcsvc-proto t1utils tex-common 159s texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base unzip 159s x11-common xdg-utils zip zlib1g-dev 159s 0 upgraded, 343 newly installed, 0 to remove and 0 not upgraded. 159s Need to get 553 MB of archives. 159s After this operation, 1887 MB of additional disk space will be used. 159s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libc-dev-bin arm64 2.42-2ubuntu4 [22.5 kB] 159s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 linux-libc-dev arm64 6.19.0-3.3 [1819 kB] 163s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libcrypt-dev arm64 1:4.5.1-1 [123 kB] 163s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 rpcsvc-proto arm64 1.4.3-1build1 [65.6 kB] 163s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libc6-dev arm64 2.42-2ubuntu4 [1765 kB] 166s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 167s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 167s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 185s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 185s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 185s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 185s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 185s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 185s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 185s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 193s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 195s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 204s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 206s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 209s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 213s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 253s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 253s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 253s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 253s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 257s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 279s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 279s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 279s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 279s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 279s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 dctrl-tools arm64 2.24-3build4 [102 kB] 279s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 279s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 281s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 281s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 281s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 281s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 283s Get:38 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 283s Get:39 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-lmodern all 2.005-1build1 [4788 kB] 296s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 300s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 300s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran-15-dev arm64 15.2.0-12ubuntu1 [490 kB] 300s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [12.5 MB] 333s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15 arm64 15.2.0-12ubuntu1 [18.1 kB] 333s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1022 B] 333s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran arm64 4:15.2.0-4ubuntu1 [1160 B] 333s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 hdf5-helpers arm64 1.14.6+repack-2 [17.3 kB] 333s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 icu-devtools arm64 78.2-1ubuntu1 [207 kB] 333s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 javascript-common all 12+nmu1build1 [4864 B] 333s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 comerr-dev arm64 2.1-1.47.2-3ubuntu2 [45.6 kB] 333s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libgssrpc4t64 arm64 1.22.1-2 [57.9 kB] 333s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libkadm5clnt-mit12 arm64 1.22.1-2 [39.9 kB] 333s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libkdb5-10t64 arm64 1.22.1-2 [41.4 kB] 333s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libkadm5srv-mit12 arm64 1.22.1-2 [54.8 kB] 333s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 krb5-multidev arm64 1.22.1-2 [126 kB] 333s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 libaec0 arm64 1.1.5-1 [21.8 kB] 333s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libio-string-perl all 1.08-4 [11.1 kB] 333s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblatex-tounicode-perl all 1.93-1 [29.2 kB] 333s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 libbibtex-parser-perl all 1.93+dfsg-1 [17.4 kB] 333s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 333s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas-dev arm64 3.12.1-7ubuntu1 [160 kB] 333s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libsnappy1v5 arm64 1.2.2-2 [30.1 kB] 333s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 libblosc1 arm64 1.21.5+ds-2 [25.9 kB] 334s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost1.90-dev arm64 1.90.0-2ubuntu1 [11.5 MB] 357s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-dev arm64 1.90.0.0ubuntu3 [4764 B] 357s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli-dev arm64 1.1.0-2build6 [355 kB] 357s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 libbz2-dev arm64 1.0.8-6build2 [34.9 kB] 357s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 357s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 357s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 357s Get:71 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 357s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 359s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 libidn2-dev arm64 2.3.8-4build1 [121 kB] 359s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 libkrb5-dev arm64 1.22.1-2 [11.9 kB] 359s Get:75 http://ftpmaster.internal/ubuntu resolute/main arm64 libldap-dev arm64 2.6.10+dfsg-1ubuntu5 [317 kB] 359s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 libpkgconf3 arm64 1.8.1-4build1 [33.7 kB] 359s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf-bin arm64 1.8.1-4build1 [21.7 kB] 359s Get:78 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf arm64 1.8.1-4build1 [16.8 kB] 359s Get:79 http://ftpmaster.internal/ubuntu resolute/main arm64 libnghttp2-dev arm64 1.64.0-1.1ubuntu1 [119 kB] 359s Get:80 http://ftpmaster.internal/ubuntu resolute/main arm64 libpsl-dev arm64 0.21.2-1.1build2 [79.1 kB] 359s Get:81 http://ftpmaster.internal/ubuntu resolute/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-5ubuntu1 [9944 B] 359s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-5ubuntu1 [348 kB] 359s Get:83 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10build2 [140 kB] 359s Get:84 http://ftpmaster.internal/ubuntu resolute/main arm64 libunbound8 arm64 1.24.2-1ubuntu1 [436 kB] 359s Get:85 http://ftpmaster.internal/ubuntu resolute/main arm64 libgnutls-dane0t64 arm64 3.8.10-3ubuntu1 [24.5 kB] 359s Get:86 http://ftpmaster.internal/ubuntu resolute/main arm64 libgnutls-openssl27t64 arm64 3.8.10-3ubuntu1 [24.4 kB] 359s Get:87 http://ftpmaster.internal/ubuntu resolute/main arm64 libp11-kit-dev arm64 0.25.10-1 [29.3 kB] 359s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 libtasn1-6-dev arm64 4.21.0-2 [91.3 kB] 359s Get:89 http://ftpmaster.internal/ubuntu resolute/main arm64 nettle-dev arm64 3.10.2-1 [1183 kB] 362s Get:90 http://ftpmaster.internal/ubuntu resolute/main arm64 libgnutls28-dev arm64 3.8.10-3ubuntu1 [1126 kB] 365s Get:91 http://ftpmaster.internal/ubuntu resolute/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu2 [899 kB] 368s Get:92 http://ftpmaster.internal/ubuntu resolute/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-3 [70.6 kB] 368s Get:93 http://ftpmaster.internal/ubuntu resolute/main arm64 libssl-dev arm64 3.5.3-1ubuntu2 [3448 kB] 378s Get:94 http://ftpmaster.internal/ubuntu resolute/main arm64 libssh2-1-dev arm64 1.11.1-1build1 [292 kB] 378s Get:95 http://ftpmaster.internal/ubuntu resolute/main arm64 libzstd-dev arm64 1.5.7+dfsg-3 [349 kB] 378s Get:96 http://ftpmaster.internal/ubuntu resolute/main arm64 libcurl4-openssl-dev arm64 8.18.0-1ubuntu1 [548 kB] 379s Get:97 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 379s Get:98 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 379s Get:99 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate-dev arm64 1.23-2build1 [54.3 kB] 379s Get:100 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 379s Get:101 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 379s Get:102 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsz2 arm64 1.1.5-1 [17.0 kB] 379s Get:103 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-310 arm64 1.14.6+repack-2 [1287 kB] 382s Get:104 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-cpp-310 arm64 1.14.6+repack-2 [117 kB] 382s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-fortran-310 arm64 1.14.6+repack-2 [104 kB] 382s Get:106 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-hl-310 arm64 1.14.6+repack-2 [59.1 kB] 382s Get:107 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-hl-fortran-310 arm64 1.14.6+repack-2 [31.1 kB] 382s Get:108 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-hl-cpp-310 arm64 1.14.6+repack-2 [11.7 kB] 382s Get:109 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 382s Get:110 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8-dev arm64 2.1.5-4ubuntu3 [301 kB] 382s Get:111 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 382s Get:112 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 382s Get:113 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 382s Get:114 http://ftpmaster.internal/ubuntu resolute/universe arm64 libaec-dev arm64 1.1.5-1 [22.7 kB] 382s Get:115 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhdf5-dev arm64 1.14.6+repack-2 [3483 kB] 388s Get:116 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 388s Get:117 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 388s Get:118 http://ftpmaster.internal/ubuntu resolute/main arm64 libicu-dev arm64 78.2-1ubuntu1 [12.5 MB] 409s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 409s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-popper.js all 1.16.1+ds-6build1 [53.8 kB] 409s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB] 410s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-d3 all 3.5.17-4build1 [136 kB] 410s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-es5-shim all 4.6.7-2 [39.8 kB] 410s Get:124 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 410s Get:125 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 410s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 410s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 410s Get:128 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-microplugin.js all 0.0.3+dfsg-2 [3946 B] 410s Get:129 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 410s Get:130 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1build1 [251 kB] 410s Get:131 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-json all 0~20221030+~1.0.8-1build1 [20.6 kB] 410s Get:132 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB] 410s Get:133 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-prettify all 2015.12.04+dfsg-3 [41.4 kB] 410s Get:134 http://ftpmaster.internal/ubuntu resolute/universe arm64 libkpathsea6 arm64 2025.20250727.75242+ds-5build1 [65.4 kB] 410s Get:135 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 415s Get:136 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack-dev arm64 3.12.1-7ubuntu1 [4456 kB] 423s Get:137 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 423s Get:138 http://ftpmaster.internal/ubuntu resolute/main arm64 liblua5.4-0 arm64 5.4.8-1 [171 kB] 423s Get:139 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmpfi0 arm64 1.5.4+ds-4build1 [36.4 kB] 423s Get:140 http://ftpmaster.internal/ubuntu resolute/main arm64 libncurses-dev arm64 6.6+20251231-1 [391 kB] 423s Get:141 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 423s Get:142 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 423s Get:143 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 423s Get:144 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 423s Get:145 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 423s Get:146 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 423s Get:147 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 423s Get:148 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-16-0 arm64 10.46-1 [225 kB] 423s Get:149 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-32-0 arm64 10.46-1 [213 kB] 423s Get:150 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-posix3 arm64 10.46-1 [7300 B] 423s Get:151 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-dev arm64 10.46-1 [772 kB] 425s Get:152 http://ftpmaster.internal/ubuntu resolute/main arm64 libpng-dev arm64 1.6.54-1 [268 kB] 425s Get:153 http://ftpmaster.internal/ubuntu resolute/universe arm64 libpotrace0 arm64 1.16-2build2 [16.3 kB] 425s Get:154 http://ftpmaster.internal/ubuntu resolute/universe arm64 libptexenc1 arm64 2025.20250727.75242+ds-5build1 [46.2 kB] 425s Get:155 http://ftpmaster.internal/ubuntu resolute/main arm64 libreadline-dev arm64 8.3-3 [199 kB] 425s Get:156 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 425s Get:157 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 425s Get:158 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsynctex2 arm64 2025.20250727.75242+ds-5build1 [61.4 kB] 425s Get:159 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 426s Get:160 http://ftpmaster.internal/ubuntu resolute/universe arm64 libteckit0 arm64 2.5.13+ds-1 [393 kB] 426s Get:161 http://ftpmaster.internal/ubuntu resolute/universe arm64 libtexlua53-5 arm64 2025.20250727.75242+ds-5build1 [122 kB] 426s Get:162 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 426s Get:163 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 426s Get:164 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 426s Get:165 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 426s Get:166 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 426s Get:167 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 427s Get:168 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 427s Get:169 http://ftpmaster.internal/ubuntu resolute/main arm64 libxmu6 arm64 2:1.1.3-4 [47.6 kB] 427s Get:170 http://ftpmaster.internal/ubuntu resolute/main arm64 libxpm4 arm64 1:3.5.17-1build3 [35.5 kB] 427s Get:171 http://ftpmaster.internal/ubuntu resolute/main arm64 libxaw7 arm64 2:1.0.16-1build1 [183 kB] 427s Get:172 http://ftpmaster.internal/ubuntu resolute/main arm64 libxi6 arm64 2:1.8.2-2 [32.4 kB] 427s Get:173 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.2 [30.7 kB] 427s Get:174 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-bootstrap-sass all 3.4.3-2 [187 kB] 427s Get:175 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 427s Get:176 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 427s Get:177 http://ftpmaster.internal/ubuntu resolute/universe arm64 pandoc-data all 3.1.11.1-3build1 [78.8 kB] 427s Get:178 http://ftpmaster.internal/ubuntu resolute/universe arm64 pandoc arm64 3.1.11.1+ds-4 [28.0 MB] 482s Get:179 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 482s Get:180 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 482s Get:181 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 482s Get:182 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 536s Get:183 http://ftpmaster.internal/ubuntu resolute/main arm64 liblzma-dev arm64 5.8.2-2 [180 kB] 536s Get:184 http://ftpmaster.internal/ubuntu resolute/main arm64 libtirpc-dev arm64 1.3.6+ds-1 [202 kB] 536s Get:185 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 536s Get:186 http://ftpmaster.internal/ubuntu resolute/universe arm64 pkg-r-autopkgtest all 20250812 [6158 B] 536s Get:187 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 538s Get:188 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biobase arm64 2.66.0-2 [2331 kB] 543s Get:189 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-s4vectors arm64 0.44.0+dfsg-2 [2054 kB] 546s Get:190 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-iranges arm64 2.40.1-3 [2301 kB] 550s Get:191 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dbi all 1.2.3-1build1 [855 kB] 552s Get:192 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bit arm64 4.6.0+dfsg-1 [450 kB] 552s Get:193 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bit64 arm64 4.6.0-1-4 [495 kB] 553s Get:194 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 556s Get:195 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 558s Get:196 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 558s Get:197 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 558s Get:198 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 561s Get:199 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-blob all 1.3.0-1 [54.1 kB] 561s Get:200 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fastmap arm64 1.2.0-1 [70.6 kB] 561s Get:201 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cachem arm64 1.1.0-1 [74.1 kB] 561s Get:202 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-memoise all 2.0.1-1build1 [54.5 kB] 561s Get:203 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 561s Get:204 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-plogr all 0.2.0-3build2 [15.8 kB] 561s Get:205 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cpp11 all 0.5.3-1 [242 kB] 561s Get:206 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rsqlite arm64 2.3.9-1 [1247 kB] 564s Get:207 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-curl arm64 7.0.0+dfsg-1 [202 kB] 564s Get:208 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB] 564s Get:209 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mime arm64 0.12-2 [35.8 kB] 564s Get:210 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sys arm64 3.4.3-1 [45.2 kB] 564s Get:211 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-askpass arm64 1.2.1-1 [24.8 kB] 564s Get:212 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-openssl arm64 2.3.2+dfsg-1 [406 kB] 564s Get:213 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 564s Get:214 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] 564s Get:215 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-png arm64 0.1-8-1build2 [40.1 kB] 564s Get:216 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB] 564s Get:217 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-xvector arm64 0.46.0-2 [618 kB] 565s Get:218 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB] 566s Get:219 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB] 594s Get:220 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB] 602s Get:221 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-crayon all 1.5.3-1 [165 kB] 602s Get:222 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biostrings arm64 2.74.1+dfsg-2 [13.3 MB] 628s Get:223 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-keggrest all 1.46.0+dfsg-3 [183 kB] 628s Get:224 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB] 637s Get:225 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 638s Get:226 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r.oo all 1.27.1-1 [978 kB] 639s Get:227 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r.utils all 2.13.0-1 [1423 kB] 642s Get:228 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrixstats arm64 1.5.0-1 [496 kB] 642s Get:229 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-aroma.light all 3.36.0-2 [583 kB] 643s Get:230 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biocio all 1.16.0+dfsg-2 [209 kB] 643s Get:231 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-formatr all 1.14-2 [152 kB] 643s Get:232 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lambda.r all 1.2.4-2build2 [118 kB] 643s Get:233 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-futile.options all 1.0.1-3build2 [20.5 kB] 643s Get:234 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-futile.logger all 1.4.3-4build2 [98.4 kB] 644s Get:235 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-snow all 1:0.4.4-2build1 [98.7 kB] 644s Get:236 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-codetools all 0.2-20-1build1 [91.1 kB] 644s Get:237 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bh all 1.84.0-1 [5962 B] 644s Get:238 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biocparallel arm64 1.40.0-2 [1333 kB] 646s Get:239 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-base64enc arm64 0.1-3-3build1 [28.5 kB] 646s Get:240 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-digest arm64 0.6.39-1 [196 kB] 646s Get:241 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-htmltools arm64 0.5.8.1-1 [373 kB] 646s Get:242 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-evaluate all 1.0.5-1 [117 kB] 646s Get:243 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xfun arm64 0.55+dfsg-1 [587 kB] 647s Get:244 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 647s Get:245 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 647s Get:246 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 658s Get:247 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 660s Get:248 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-jquerylib all 0.1.4+dfsg-5 [13.7 kB] 660s Get:249 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fs arm64 1.6.5+dfsg-1 [244 kB] 660s Get:250 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rappdirs arm64 0.3.3-1build1 [49.5 kB] 660s Get:251 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sass arm64 0.4.9+dfsg-1 [957 kB] 662s Get:252 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB] 671s Get:253 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fontawesome all 0.5.3-1 [1331 kB] 675s Get:254 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tinytex all 0.58-1 [148 kB] 675s Get:255 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-modernizr all 3.13.0-0.1build1 [100 kB] 675s Get:256 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.22-1 [85.1 kB] 675s Get:257 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 675s Get:258 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 681s Get:259 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-later arm64 1.4.1+dfsg-1 [141 kB] 681s Get:260 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 681s Get:261 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-promises arm64 1.3.2+dfsg-1 [290 kB] 681s Get:262 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-httpuv arm64 1.6.15+dfsg-1 [489 kB] 681s Get:263 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xtable all 1:1.8-4-2build1 [691 kB] 682s Get:264 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sourcetools arm64 0.1.7-1-1 [47.2 kB] 682s Get:265 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 682s Get:266 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-commonmark arm64 1.9.5-1 [130 kB] 682s Get:267 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 682s Get:268 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB] 688s Get:269 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rmarkdown all 2.30+dfsg-1 [1501 kB] 692s Get:270 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bookdown all 0.42+dfsg-1 [1409 kB] 696s Get:271 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB] 696s Get:272 http://ftpmaster.internal/ubuntu resolute/universe arm64 tex-common all 6.20 [30.0 kB] 696s Get:273 http://ftpmaster.internal/ubuntu resolute/main arm64 t1utils arm64 1.41-4build4 [59.8 kB] 696s Get:274 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-binaries arm64 2025.20250727.75242+ds-5build1 [8302 kB] 718s Get:275 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-base all 2025.20260124-1 [22.8 MB] 775s Get:276 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-latex-base all 2025.20260124-1 [1321 kB] 780s Get:277 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-bibtex-extra all 2025.20260124-1 [80.6 MB] 961s Get:278 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biocversion all 3.20.0-2 [11.1 kB] 961s Get:279 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biocstyle all 2.34.0+dfsg-1 [451 kB] 961s Get:280 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomicranges arm64 1.58.0+dfsg-2 [2083 kB] 965s Get:281 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xml arm64 3.99-0.20-1 [1749 kB] 969s Get:282 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bitops arm64 1.0-9-1 [30.2 kB] 969s Get:283 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-rhtslib arm64 3.2.0+dfsg-2 [1429 kB] 972s Get:284 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-rsamtools arm64 2.22.0+dfsg-2 [3668 kB] 979s Get:285 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB] 979s Get:286 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lattice arm64 0.22-7-1 [1365 kB] 981s Get:287 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 988s Get:288 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-abind all 1.4-8-1build1 [67.0 kB] 988s Get:289 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-s4arrays arm64 1.6.0+dfsg-2 [698 kB] 989s Get:290 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-sparsearray arm64 1.6.2+dfsg-2 [1369 kB] 991s Get:291 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-delayedarray arm64 0.32.0+dfsg-2 [2064 kB] 995s Get:292 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB] 997s Get:293 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomicalignments arm64 1.42.0-2 [2164 kB] 1000s Get:294 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcurl arm64 1.98-1.16+dfsg-1 [806 kB] 1002s Get:295 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rjson arm64 0.2.23-1 [104 kB] 1002s Get:296 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-restfulr arm64 0.0.15-1 [380 kB] 1002s Get:297 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-rtracklayer arm64 1.66.0-3 [5216 kB] 1010s Get:298 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-bsgenome all 1.74.0-2 [7001 kB] 1023s Get:299 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-dnacopy arm64 1.80.0-2 [497 kB] 1024s Get:300 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomicfeatures all 1.58.0+dfsg-2 [937 kB] 1025s Get:301 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-org.hs.eg.db all 3.20.0-3 [63.1 MB] 1146s Get:302 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-variantannotation arm64 1.52.0-2 [3592 kB] 1154s Get:303 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 1154s Get:304 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-data.table arm64 1.17.0+dfsg-1 [2129 kB] 1158s Get:305 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 1158s Get:306 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 1160s Get:307 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-s7 arm64 0.2.0-1 [329 kB] 1161s Get:308 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 1163s Get:309 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 1163s Get:310 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.3-1 [1088 kB] 1166s Get:311 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.4.0-1 [725 kB] 1168s Get:312 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 1178s Get:313 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gridextra all 2.3-3build2 [1032 kB] 1181s Get:314 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vgam arm64 1.1-13-1 [7758 kB] 1204s Get:315 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mclust arm64 6.1.1-1 [3939 kB] 1211s Get:316 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-rhdf5lib arm64 1.28.0+dfsg-3 [97.1 kB] 1211s Get:317 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-rhdf5filters arm64 1.18.1+dfsg-1 [135 kB] 1211s Get:318 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-rhdf5 arm64 2.50.2+dfsg-1build1 [819 kB] 1213s Get:319 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-purecn all 2.12.0+dfsg-2 [6054 kB] 1224s Get:320 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-brio arm64 1.1.5-1 [39.1 kB] 1224s Get:321 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ps arm64 1.9.0-1 [407 kB] 1224s Get:322 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-processx arm64 3.8.6-1 [363 kB] 1224s Get:323 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-callr all 3.7.6-1 [458 kB] 1224s Get:324 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lazyeval arm64 0.2.2-1build2 [145 kB] 1224s Get:325 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rex all 1.2.1-1build1 [126 kB] 1224s Get:326 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-covr arm64 3.6.4+dfsg-1 [302 kB] 1224s Get:327 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-desc all 1.4.3-1 [359 kB] 1224s Get:328 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-diffobj arm64 0.3.5-1build1 [1154 kB] 1226s Get:329 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-globals all 0.19.0-1 [160 kB] 1226s Get:330 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-listenv all 0.10.0+dfsg-1 [113 kB] 1226s Get:331 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-parallelly arm64 1.42.0-1 [540 kB] 1227s Get:332 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 1229s Get:333 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-getopt all 1.20.4-1 [38.4 kB] 1229s Get:334 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-markdown all 1.13-1 [162 kB] 1229s Get:335 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-optparse all 1.7.5-1 [83.6 kB] 1229s Get:336 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgbuild all 1.4.8-1 [219 kB] 1229s Get:337 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rprojroot all 2.1.1-1 [131 kB] 1229s Get:338 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgload all 1.4.1-1 [252 kB] 1229s Get:339 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-praise all 1.0.0-4build2 [20.9 kB] 1229s Get:340 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r.cache all 0.17.0-1 [117 kB] 1229s Get:341 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pscbs all 0.68.0-1 [4234 kB] 1238s Get:342 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-waldo all 0.6.2-1 [153 kB] 1238s Get:343 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-testthat arm64 3.2.3-1 [1644 kB] 1242s Preconfiguring packages ... 1242s Fetched 553 MB in 18min 3s (511 kB/s) 1242s Selecting previously unselected package libc-dev-bin. 1242s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 136600 files and directories currently installed.) 1242s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_arm64.deb ... 1242s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 1242s Selecting previously unselected package linux-libc-dev:arm64. 1243s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_arm64.deb ... 1243s Unpacking linux-libc-dev:arm64 (6.19.0-3.3) ... 1243s Selecting previously unselected package libcrypt-dev:arm64. 1243s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_arm64.deb ... 1243s Unpacking libcrypt-dev:arm64 (1:4.5.1-1) ... 1243s Selecting previously unselected package rpcsvc-proto. 1243s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_arm64.deb ... 1243s Unpacking rpcsvc-proto (1.4.3-1build1) ... 1243s Selecting previously unselected package libc6-dev:arm64. 1243s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_arm64.deb ... 1243s Unpacking libc6-dev:arm64 (2.42-2ubuntu4) ... 1243s Selecting previously unselected package libisl23:arm64. 1243s Preparing to unpack .../005-libisl23_0.27-1build1_arm64.deb ... 1243s Unpacking libisl23:arm64 (0.27-1build1) ... 1243s Selecting previously unselected package libmpc3:arm64. 1243s Preparing to unpack .../006-libmpc3_1.3.1-2_arm64.deb ... 1243s Unpacking libmpc3:arm64 (1.3.1-2) ... 1243s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 1243s Preparing to unpack .../007-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1243s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1243s Selecting previously unselected package cpp-15. 1243s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 1243s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 1243s Selecting previously unselected package cpp-aarch64-linux-gnu. 1243s Preparing to unpack .../009-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1243s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1243s Selecting previously unselected package cpp. 1243s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 1243s Unpacking cpp (4:15.2.0-4ubuntu1) ... 1243s Selecting previously unselected package libcc1-0:arm64. 1243s Preparing to unpack .../011-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 1243s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 1243s Selecting previously unselected package libgomp1:arm64. 1243s Preparing to unpack .../012-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 1243s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 1243s Selecting previously unselected package libitm1:arm64. 1243s Preparing to unpack .../013-libitm1_15.2.0-12ubuntu1_arm64.deb ... 1243s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 1243s Selecting previously unselected package libasan8:arm64. 1243s Preparing to unpack .../014-libasan8_15.2.0-12ubuntu1_arm64.deb ... 1243s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 1243s Selecting previously unselected package liblsan0:arm64. 1244s Preparing to unpack .../015-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 1244s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 1244s Selecting previously unselected package libtsan2:arm64. 1244s Preparing to unpack .../016-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 1244s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 1244s Selecting previously unselected package libubsan1:arm64. 1244s Preparing to unpack .../017-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 1244s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 1244s Selecting previously unselected package libhwasan0:arm64. 1244s Preparing to unpack .../018-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 1244s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 1244s Selecting previously unselected package libgcc-15-dev:arm64. 1244s Preparing to unpack .../019-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 1244s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 1244s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 1244s Preparing to unpack .../020-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1244s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1244s Selecting previously unselected package gcc-15. 1244s Preparing to unpack .../021-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 1244s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 1244s Selecting previously unselected package gcc-aarch64-linux-gnu. 1244s Preparing to unpack .../022-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1244s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1245s Selecting previously unselected package gcc. 1245s Preparing to unpack .../023-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 1245s Unpacking gcc (4:15.2.0-4ubuntu1) ... 1245s Selecting previously unselected package libstdc++-15-dev:arm64. 1245s Preparing to unpack .../024-libstdc++-15-dev_15.2.0-12ubuntu1_arm64.deb ... 1245s Unpacking libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 1245s Selecting previously unselected package g++-15-aarch64-linux-gnu. 1245s Preparing to unpack .../025-g++-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1245s Unpacking g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1245s Selecting previously unselected package g++-15. 1245s Preparing to unpack .../026-g++-15_15.2.0-12ubuntu1_arm64.deb ... 1245s Unpacking g++-15 (15.2.0-12ubuntu1) ... 1245s Selecting previously unselected package g++-aarch64-linux-gnu. 1245s Preparing to unpack .../027-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1245s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1245s Selecting previously unselected package g++. 1245s Preparing to unpack .../028-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 1245s Unpacking g++ (4:15.2.0-4ubuntu1) ... 1245s Selecting previously unselected package build-essential. 1245s Preparing to unpack .../029-build-essential_12.12ubuntu2_arm64.deb ... 1245s Unpacking build-essential (12.12ubuntu2) ... 1245s Selecting previously unselected package dctrl-tools. 1245s Preparing to unpack .../030-dctrl-tools_2.24-3build4_arm64.deb ... 1245s Unpacking dctrl-tools (2.24-3build4) ... 1245s Selecting previously unselected package fonts-dejavu-mono. 1245s Preparing to unpack .../031-fonts-dejavu-mono_2.37-8build1_all.deb ... 1245s Unpacking fonts-dejavu-mono (2.37-8build1) ... 1245s Selecting previously unselected package fonts-dejavu-core. 1245s Preparing to unpack .../032-fonts-dejavu-core_2.37-8build1_all.deb ... 1245s Unpacking fonts-dejavu-core (2.37-8build1) ... 1245s Selecting previously unselected package fontconfig-config. 1245s Preparing to unpack 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unselected package fonts-lmodern. 1246s Preparing to unpack .../038-fonts-lmodern_2.005-1build1_all.deb ... 1246s Unpacking fonts-lmodern (2.005-1build1) ... 1246s Selecting previously unselected package fonts-mathjax. 1246s Preparing to unpack .../039-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 1246s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 1246s Selecting previously unselected package libgfortran5:arm64. 1246s Preparing to unpack .../040-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 1246s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 1246s Selecting previously unselected package libgfortran-15-dev:arm64. 1246s Preparing to unpack .../041-libgfortran-15-dev_15.2.0-12ubuntu1_arm64.deb ... 1246s Unpacking libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 1246s Selecting previously unselected package gfortran-15-aarch64-linux-gnu. 1246s Preparing to unpack .../042-gfortran-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1246s Unpacking gfortran-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1246s Selecting previously unselected package gfortran-15. 1246s Preparing to unpack .../043-gfortran-15_15.2.0-12ubuntu1_arm64.deb ... 1246s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 1246s Selecting previously unselected package gfortran-aarch64-linux-gnu. 1246s Preparing to unpack .../044-gfortran-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1246s Unpacking gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1246s Selecting previously unselected package gfortran. 1246s Preparing to unpack .../045-gfortran_4%3a15.2.0-4ubuntu1_arm64.deb ... 1246s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 1246s Selecting previously unselected package hdf5-helpers. 1246s Preparing to unpack .../046-hdf5-helpers_1.14.6+repack-2_arm64.deb ... 1246s Unpacking hdf5-helpers (1.14.6+repack-2) ... 1246s Selecting previously unselected package icu-devtools. 1247s Preparing to unpack .../047-icu-devtools_78.2-1ubuntu1_arm64.deb ... 1247s Unpacking icu-devtools (78.2-1ubuntu1) ... 1247s Selecting previously unselected package javascript-common. 1247s Preparing to unpack .../048-javascript-common_12+nmu1build1_all.deb ... 1247s Unpacking javascript-common (12+nmu1build1) ... 1247s Selecting previously unselected package comerr-dev:arm64. 1247s Preparing to unpack .../049-comerr-dev_2.1-1.47.2-3ubuntu2_arm64.deb ... 1247s Unpacking comerr-dev:arm64 (2.1-1.47.2-3ubuntu2) ... 1247s Selecting previously unselected package libgssrpc4t64:arm64. 1247s Preparing to unpack .../050-libgssrpc4t64_1.22.1-2_arm64.deb ... 1247s Unpacking libgssrpc4t64:arm64 (1.22.1-2) ... 1247s Selecting previously unselected package libkadm5clnt-mit12:arm64. 1247s Preparing to unpack .../051-libkadm5clnt-mit12_1.22.1-2_arm64.deb ... 1247s Unpacking libkadm5clnt-mit12:arm64 (1.22.1-2) ... 1247s Selecting previously unselected package libkdb5-10t64:arm64. 1247s Preparing to unpack .../052-libkdb5-10t64_1.22.1-2_arm64.deb ... 1247s Unpacking libkdb5-10t64:arm64 (1.22.1-2) ... 1247s Selecting previously unselected package libkadm5srv-mit12:arm64. 1247s Preparing to unpack .../053-libkadm5srv-mit12_1.22.1-2_arm64.deb ... 1247s Unpacking libkadm5srv-mit12:arm64 (1.22.1-2) ... 1247s Selecting previously unselected package krb5-multidev:arm64. 1247s Preparing to unpack .../054-krb5-multidev_1.22.1-2_arm64.deb ... 1247s Unpacking krb5-multidev:arm64 (1.22.1-2) ... 1247s Selecting previously unselected package libaec0:arm64. 1247s Preparing to unpack .../055-libaec0_1.1.5-1_arm64.deb ... 1247s Unpacking libaec0:arm64 (1.1.5-1) ... 1247s Selecting previously unselected package libio-string-perl. 1247s Preparing to unpack .../056-libio-string-perl_1.08-4_all.deb ... 1247s Unpacking libio-string-perl (1.08-4) ... 1247s Selecting previously unselected package liblatex-tounicode-perl. 1247s Preparing to unpack .../057-liblatex-tounicode-perl_1.93-1_all.deb ... 1247s Unpacking liblatex-tounicode-perl (1.93-1) ... 1247s Selecting previously unselected package libbibtex-parser-perl. 1247s Preparing to unpack .../058-libbibtex-parser-perl_1.93+dfsg-1_all.deb ... 1247s Unpacking libbibtex-parser-perl (1.93+dfsg-1) ... 1247s Selecting previously unselected package libblas3:arm64. 1247s Preparing to unpack .../059-libblas3_3.12.1-7ubuntu1_arm64.deb ... 1247s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 1247s Selecting previously unselected package libblas-dev:arm64. 1247s Preparing to unpack .../060-libblas-dev_3.12.1-7ubuntu1_arm64.deb ... 1247s Unpacking libblas-dev:arm64 (3.12.1-7ubuntu1) ... 1247s Selecting previously unselected package libsnappy1v5:arm64. 1247s Preparing to unpack .../061-libsnappy1v5_1.2.2-2_arm64.deb ... 1247s Unpacking libsnappy1v5:arm64 (1.2.2-2) ... 1247s Selecting previously unselected package libblosc1:arm64. 1247s Preparing to unpack .../062-libblosc1_1.21.5+ds-2_arm64.deb ... 1247s Unpacking libblosc1:arm64 (1.21.5+ds-2) ... 1247s Selecting previously unselected package libboost1.90-dev:arm64. 1247s Preparing to unpack .../063-libboost1.90-dev_1.90.0-2ubuntu1_arm64.deb ... 1247s Unpacking libboost1.90-dev:arm64 (1.90.0-2ubuntu1) ... 1249s Selecting previously unselected package libboost-dev:arm64. 1249s Preparing to unpack .../064-libboost-dev_1.90.0.0ubuntu3_arm64.deb ... 1249s Unpacking libboost-dev:arm64 (1.90.0.0ubuntu3) ... 1249s Selecting previously unselected package libbrotli-dev:arm64. 1249s Preparing to unpack .../065-libbrotli-dev_1.1.0-2build6_arm64.deb ... 1249s Unpacking libbrotli-dev:arm64 (1.1.0-2build6) ... 1249s Selecting previously unselected package libbz2-dev:arm64. 1249s Preparing to unpack .../066-libbz2-dev_1.0.8-6build2_arm64.deb ... 1249s Unpacking libbz2-dev:arm64 (1.0.8-6build2) ... 1249s Selecting previously unselected package libpixman-1-0:arm64. 1249s Preparing to unpack .../067-libpixman-1-0_0.46.4-1_arm64.deb ... 1249s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 1249s Selecting previously unselected package libxcb-render0:arm64. 1249s Preparing to unpack .../068-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 1249s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 1249s Selecting previously unselected package libxcb-shm0:arm64. 1249s Preparing to unpack .../069-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 1249s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 1249s Selecting previously unselected package libxrender1:arm64. 1249s Preparing to unpack .../070-libxrender1_1%3a0.9.12-1_arm64.deb ... 1249s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 1249s Selecting previously unselected package libcairo2:arm64. 1249s Preparing to unpack .../071-libcairo2_1.18.4-3_arm64.deb ... 1249s Unpacking libcairo2:arm64 (1.18.4-3) ... 1249s Selecting previously unselected package libidn2-dev:arm64. 1249s Preparing to unpack .../072-libidn2-dev_2.3.8-4build1_arm64.deb ... 1249s Unpacking libidn2-dev:arm64 (2.3.8-4build1) ... 1249s Selecting previously unselected package libkrb5-dev:arm64. 1249s Preparing to unpack .../073-libkrb5-dev_1.22.1-2_arm64.deb ... 1249s Unpacking libkrb5-dev:arm64 (1.22.1-2) ... 1249s Selecting previously unselected package libldap-dev:arm64. 1249s Preparing to unpack .../074-libldap-dev_2.6.10+dfsg-1ubuntu5_arm64.deb ... 1249s Unpacking libldap-dev:arm64 (2.6.10+dfsg-1ubuntu5) ... 1249s Selecting previously unselected package libpkgconf3:arm64. 1249s Preparing to unpack .../075-libpkgconf3_1.8.1-4build1_arm64.deb ... 1249s Unpacking libpkgconf3:arm64 (1.8.1-4build1) ... 1249s Selecting previously unselected package pkgconf-bin. 1249s Preparing to unpack .../076-pkgconf-bin_1.8.1-4build1_arm64.deb ... 1249s Unpacking pkgconf-bin (1.8.1-4build1) ... 1249s Selecting previously unselected package pkgconf:arm64. 1249s Preparing to unpack .../077-pkgconf_1.8.1-4build1_arm64.deb ... 1249s Unpacking pkgconf:arm64 (1.8.1-4build1) ... 1249s Selecting previously unselected package libnghttp2-dev:arm64. 1249s Preparing to unpack .../078-libnghttp2-dev_1.64.0-1.1ubuntu1_arm64.deb ... 1249s Unpacking libnghttp2-dev:arm64 (1.64.0-1.1ubuntu1) ... 1249s Selecting previously unselected package libpsl-dev:arm64. 1249s Preparing to unpack .../079-libpsl-dev_0.21.2-1.1build2_arm64.deb ... 1249s Unpacking libpsl-dev:arm64 (0.21.2-1.1build2) ... 1249s Selecting previously unselected package libgmpxx4ldbl:arm64. 1250s Preparing to unpack .../080-libgmpxx4ldbl_2%3a6.3.0+dfsg-5ubuntu1_arm64.deb ... 1250s Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-5ubuntu1) ... 1250s Selecting previously unselected package libgmp-dev:arm64. 1250s Preparing to unpack .../081-libgmp-dev_2%3a6.3.0+dfsg-5ubuntu1_arm64.deb ... 1250s Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-5ubuntu1) ... 1250s Selecting previously unselected package libevent-2.1-7t64:arm64. 1250s Preparing to unpack .../082-libevent-2.1-7t64_2.1.12-stable-10build2_arm64.deb ... 1250s Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10build2) ... 1250s Selecting previously unselected package libunbound8:arm64. 1250s Preparing to unpack .../083-libunbound8_1.24.2-1ubuntu1_arm64.deb ... 1250s Unpacking libunbound8:arm64 (1.24.2-1ubuntu1) ... 1250s Selecting previously unselected package libgnutls-dane0t64:arm64. 1250s Preparing to unpack .../084-libgnutls-dane0t64_3.8.10-3ubuntu1_arm64.deb ... 1250s Unpacking libgnutls-dane0t64:arm64 (3.8.10-3ubuntu1) ... 1250s Selecting previously unselected package libgnutls-openssl27t64:arm64. 1250s Preparing to unpack .../085-libgnutls-openssl27t64_3.8.10-3ubuntu1_arm64.deb ... 1250s Unpacking libgnutls-openssl27t64:arm64 (3.8.10-3ubuntu1) ... 1250s Selecting previously unselected package libp11-kit-dev:arm64. 1250s Preparing to unpack .../086-libp11-kit-dev_0.25.10-1_arm64.deb ... 1250s Unpacking libp11-kit-dev:arm64 (0.25.10-1) ... 1250s Selecting previously unselected package libtasn1-6-dev:arm64. 1250s Preparing to unpack .../087-libtasn1-6-dev_4.21.0-2_arm64.deb ... 1250s Unpacking libtasn1-6-dev:arm64 (4.21.0-2) ... 1250s Selecting previously unselected package nettle-dev:arm64. 1250s Preparing to unpack .../088-nettle-dev_3.10.2-1_arm64.deb ... 1250s Unpacking nettle-dev:arm64 (3.10.2-1) ... 1250s Selecting previously unselected package libgnutls28-dev:arm64. 1250s Preparing to unpack .../089-libgnutls28-dev_3.8.10-3ubuntu1_arm64.deb ... 1250s Unpacking libgnutls28-dev:arm64 (3.8.10-3ubuntu1) ... 1250s Selecting previously unselected package zlib1g-dev:arm64. 1250s Preparing to unpack .../090-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_arm64.deb ... 1250s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 1250s Selecting previously unselected package librtmp-dev:arm64. 1250s Preparing to unpack .../091-librtmp-dev_2.4+20151223.gitfa8646d.1-3_arm64.deb ... 1250s Unpacking librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-3) ... 1250s Selecting previously unselected package libssl-dev:arm64. 1250s Preparing to unpack .../092-libssl-dev_3.5.3-1ubuntu2_arm64.deb ... 1250s Unpacking libssl-dev:arm64 (3.5.3-1ubuntu2) ... 1250s Selecting previously unselected package libssh2-1-dev:arm64. 1250s Preparing to unpack .../093-libssh2-1-dev_1.11.1-1build1_arm64.deb ... 1250s Unpacking libssh2-1-dev:arm64 (1.11.1-1build1) ... 1250s Selecting previously unselected package libzstd-dev:arm64. 1250s Preparing to unpack .../094-libzstd-dev_1.5.7+dfsg-3_arm64.deb ... 1250s Unpacking libzstd-dev:arm64 (1.5.7+dfsg-3) ... 1250s Selecting previously unselected package libcurl4-openssl-dev:arm64. 1250s Preparing to unpack .../095-libcurl4-openssl-dev_8.18.0-1ubuntu1_arm64.deb ... 1250s Unpacking libcurl4-openssl-dev:arm64 (8.18.0-1ubuntu1) ... 1250s Selecting previously unselected package libdatrie1:arm64. 1250s Preparing to unpack .../096-libdatrie1_0.2.14-1_arm64.deb ... 1250s Unpacking libdatrie1:arm64 (0.2.14-1) ... 1250s Selecting previously unselected package libdeflate0:arm64. 1250s Preparing to unpack .../097-libdeflate0_1.23-2build1_arm64.deb ... 1250s Unpacking libdeflate0:arm64 (1.23-2build1) ... 1250s Selecting previously unselected package libdeflate-dev:arm64. 1250s Preparing to unpack .../098-libdeflate-dev_1.23-2build1_arm64.deb ... 1250s Unpacking libdeflate-dev:arm64 (1.23-2build1) ... 1250s Selecting previously unselected package libgraphite2-3:arm64. 1251s Preparing to unpack .../099-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 1251s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 1251s Selecting previously unselected package libharfbuzz0b:arm64. 1251s Preparing to unpack .../100-libharfbuzz0b_12.3.2-1_arm64.deb ... 1251s Unpacking libharfbuzz0b:arm64 (12.3.2-1) ... 1251s Selecting previously unselected package libsz2:arm64. 1251s Preparing to unpack .../101-libsz2_1.1.5-1_arm64.deb ... 1251s Unpacking libsz2:arm64 (1.1.5-1) ... 1251s Selecting previously unselected package libhdf5-310:arm64. 1251s Preparing to unpack .../102-libhdf5-310_1.14.6+repack-2_arm64.deb ... 1251s Unpacking libhdf5-310:arm64 (1.14.6+repack-2) ... 1251s Selecting previously unselected package libhdf5-cpp-310:arm64. 1251s Preparing to unpack .../103-libhdf5-cpp-310_1.14.6+repack-2_arm64.deb ... 1251s Unpacking libhdf5-cpp-310:arm64 (1.14.6+repack-2) ... 1251s Selecting previously unselected package libhdf5-fortran-310:arm64. 1251s Preparing to unpack .../104-libhdf5-fortran-310_1.14.6+repack-2_arm64.deb ... 1251s Unpacking libhdf5-fortran-310:arm64 (1.14.6+repack-2) ... 1251s Selecting previously unselected package libhdf5-hl-310:arm64. 1251s Preparing to unpack .../105-libhdf5-hl-310_1.14.6+repack-2_arm64.deb ... 1251s Unpacking libhdf5-hl-310:arm64 (1.14.6+repack-2) ... 1251s Selecting previously unselected package libhdf5-hl-fortran-310:arm64. 1251s Preparing to unpack .../106-libhdf5-hl-fortran-310_1.14.6+repack-2_arm64.deb ... 1251s Unpacking libhdf5-hl-fortran-310:arm64 (1.14.6+repack-2) ... 1251s Selecting previously unselected package libhdf5-hl-cpp-310:arm64. 1251s Preparing to unpack .../107-libhdf5-hl-cpp-310_1.14.6+repack-2_arm64.deb ... 1251s Unpacking libhdf5-hl-cpp-310:arm64 (1.14.6+repack-2) ... 1251s Selecting previously unselected package libjpeg-turbo8:arm64. 1251s Preparing to unpack .../108-libjpeg-turbo8_2.1.5-4ubuntu3_arm64.deb ... 1251s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu3) ... 1251s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 1251s Preparing to unpack .../109-libjpeg-turbo8-dev_2.1.5-4ubuntu3_arm64.deb ... 1251s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-4ubuntu3) ... 1251s Selecting previously unselected package libjpeg8:arm64. 1251s Preparing to unpack .../110-libjpeg8_8c-2ubuntu11_arm64.deb ... 1251s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 1251s Selecting previously unselected package libjpeg8-dev:arm64. 1251s Preparing to unpack .../111-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 1251s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 1251s Selecting previously unselected package libjpeg-dev:arm64. 1251s Preparing to unpack .../112-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 1251s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 1251s Selecting previously unselected package libaec-dev:arm64. 1251s Preparing to unpack .../113-libaec-dev_1.1.5-1_arm64.deb ... 1251s Unpacking libaec-dev:arm64 (1.1.5-1) ... 1251s Selecting previously unselected package libhdf5-dev. 1251s Preparing to unpack .../114-libhdf5-dev_1.14.6+repack-2_arm64.deb ... 1251s Unpacking libhdf5-dev (1.14.6+repack-2) ... 1251s Selecting previously unselected package x11-common. 1251s Preparing to unpack .../115-x11-common_1%3a7.7+24ubuntu1_all.deb ... 1251s Unpacking x11-common (1:7.7+24ubuntu1) ... 1251s Selecting previously unselected package libice6:arm64. 1251s Preparing to unpack .../116-libice6_2%3a1.1.1-1build1_arm64.deb ... 1251s Unpacking libice6:arm64 (2:1.1.1-1build1) ... 1251s Selecting previously unselected package libicu-dev:arm64. 1251s Preparing to unpack .../117-libicu-dev_78.2-1ubuntu1_arm64.deb ... 1251s Unpacking libicu-dev:arm64 (78.2-1ubuntu1) ... 1252s Selecting previously unselected package libjs-bootstrap. 1252s Preparing to unpack .../118-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 1252s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 1252s Selecting previously unselected package libjs-popper.js. 1252s Preparing to unpack .../119-libjs-popper.js_1.16.1+ds-6build1_all.deb ... 1252s Unpacking libjs-popper.js (1.16.1+ds-6build1) ... 1252s Selecting previously unselected package libjs-bootstrap4. 1252s Preparing to unpack .../120-libjs-bootstrap4_4.6.2+dfsg-1_all.deb ... 1252s Unpacking libjs-bootstrap4 (4.6.2+dfsg-1) ... 1252s Selecting previously unselected package libjs-d3. 1252s Preparing to unpack .../121-libjs-d3_3.5.17-4build1_all.deb ... 1252s Unpacking libjs-d3 (3.5.17-4build1) ... 1252s Selecting previously unselected package libjs-es5-shim. 1252s Preparing to unpack .../122-libjs-es5-shim_4.6.7-2_all.deb ... 1252s Unpacking libjs-es5-shim (4.6.7-2) ... 1252s Selecting previously unselected package libjs-highlight.js. 1252s Preparing to unpack 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libkpathsea6:arm64. 1253s Preparing to unpack .../133-libkpathsea6_2025.20250727.75242+ds-5build1_arm64.deb ... 1253s Unpacking libkpathsea6:arm64 (2025.20250727.75242+ds-5build1) ... 1253s Selecting previously unselected package liblapack3:arm64. 1253s Preparing to unpack .../134-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 1253s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 1253s Selecting previously unselected package liblapack-dev:arm64. 1253s Preparing to unpack .../135-liblapack-dev_3.12.1-7ubuntu1_arm64.deb ... 1253s Unpacking liblapack-dev:arm64 (3.12.1-7ubuntu1) ... 1253s Selecting previously unselected package liblerc4:arm64. 1253s Preparing to unpack .../136-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb ... 1253s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 1253s Selecting previously unselected package liblua5.4-0:arm64. 1253s Preparing to unpack .../137-liblua5.4-0_5.4.8-1_arm64.deb ... 1253s Unpacking liblua5.4-0:arm64 (5.4.8-1) ... 1253s Selecting previously unselected package libmpfi0:arm64. 1253s Preparing to unpack .../138-libmpfi0_1.5.4+ds-4build1_arm64.deb ... 1253s Unpacking libmpfi0:arm64 (1.5.4+ds-4build1) ... 1253s Selecting previously unselected package libncurses-dev:arm64. 1253s Preparing to unpack .../139-libncurses-dev_6.6+20251231-1_arm64.deb ... 1253s Unpacking libncurses-dev:arm64 (6.6+20251231-1) ... 1253s Selecting previously unselected package libthai-data. 1253s Preparing to unpack .../140-libthai-data_0.1.30-1_all.deb ... 1253s Unpacking libthai-data (0.1.30-1) ... 1253s Selecting previously unselected package libthai0:arm64. 1253s Preparing to unpack .../141-libthai0_0.1.30-1_arm64.deb ... 1253s Unpacking libthai0:arm64 (0.1.30-1) ... 1253s Selecting previously unselected package libpango-1.0-0:arm64. 1253s Preparing to unpack .../142-libpango-1.0-0_1.57.0-1_arm64.deb ... 1253s Unpacking libpango-1.0-0:arm64 (1.57.0-1) ... 1253s Selecting previously unselected package libpangoft2-1.0-0:arm64. 1253s Preparing to unpack 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1254s Unpacking libptexenc1:arm64 (2025.20250727.75242+ds-5build1) ... 1254s Selecting previously unselected package libreadline-dev:arm64. 1254s Preparing to unpack .../154-libreadline-dev_8.3-3_arm64.deb ... 1254s Unpacking libreadline-dev:arm64 (8.3-3) ... 1254s Selecting previously unselected package libsharpyuv0:arm64. 1254s Preparing to unpack .../155-libsharpyuv0_1.5.0-0.1build1_arm64.deb ... 1254s Unpacking libsharpyuv0:arm64 (1.5.0-0.1build1) ... 1254s Selecting previously unselected package libsm6:arm64. 1254s Preparing to unpack .../156-libsm6_2%3a1.2.6-1build1_arm64.deb ... 1254s Unpacking libsm6:arm64 (2:1.2.6-1build1) ... 1254s Selecting previously unselected package libsynctex2:arm64. 1254s Preparing to unpack .../157-libsynctex2_2025.20250727.75242+ds-5build1_arm64.deb ... 1254s Unpacking libsynctex2:arm64 (2025.20250727.75242+ds-5build1) ... 1254s Selecting previously unselected package libtcl8.6:arm64. 1254s Preparing to unpack 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1255s Selecting previously unselected package libxpm4:arm64. 1255s Preparing to unpack .../169-libxpm4_1%3a3.5.17-1build3_arm64.deb ... 1255s Unpacking libxpm4:arm64 (1:3.5.17-1build3) ... 1255s Selecting previously unselected package libxaw7:arm64. 1255s Preparing to unpack .../170-libxaw7_2%3a1.0.16-1build1_arm64.deb ... 1255s Unpacking libxaw7:arm64 (2:1.0.16-1build1) ... 1255s Selecting previously unselected package libxi6:arm64. 1255s Preparing to unpack .../171-libxi6_2%3a1.8.2-2_arm64.deb ... 1255s Unpacking libxi6:arm64 (2:1.8.2-2) ... 1255s Selecting previously unselected package libzzip-0-13t64:arm64. 1255s Preparing to unpack .../172-libzzip-0-13t64_0.13.78+dfsg.1-0.2_arm64.deb ... 1255s Unpacking libzzip-0-13t64:arm64 (0.13.78+dfsg.1-0.2) ... 1255s Selecting previously unselected package node-bootstrap-sass. 1255s Preparing to unpack .../173-node-bootstrap-sass_3.4.3-2_all.deb ... 1255s Unpacking node-bootstrap-sass (3.4.3-2) ... 1255s Selecting previously unselected package node-html5shiv. 1255s Preparing to unpack .../174-node-html5shiv_3.7.3+dfsg-5_all.deb ... 1255s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 1255s Selecting previously unselected package node-normalize.css. 1255s Preparing to unpack .../175-node-normalize.css_8.0.1-5.1_all.deb ... 1255s Unpacking node-normalize.css (8.0.1-5.1) ... 1255s Selecting previously unselected package pandoc-data. 1255s Preparing to unpack .../176-pandoc-data_3.1.11.1-3build1_all.deb ... 1255s Unpacking pandoc-data (3.1.11.1-3build1) ... 1255s Selecting previously unselected package pandoc. 1255s Preparing to unpack .../177-pandoc_3.1.11.1+ds-4_arm64.deb ... 1255s Unpacking pandoc (3.1.11.1+ds-4) ... 1256s Selecting previously unselected package zip. 1256s Preparing to unpack .../178-zip_3.0-15ubuntu3_arm64.deb ... 1256s Unpacking zip (3.0-15ubuntu3) ... 1256s Selecting previously unselected package unzip. 1256s Preparing to unpack .../179-unzip_6.0-29ubuntu1_arm64.deb ... 1256s Unpacking unzip 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Preparing to unpack .../185-pkg-r-autopkgtest_20250812_all.deb ... 1257s Unpacking pkg-r-autopkgtest (20250812) ... 1257s Selecting previously unselected package r-bioc-biocgenerics. 1257s Preparing to unpack .../186-r-bioc-biocgenerics_0.52.0-2_all.deb ... 1257s Unpacking r-bioc-biocgenerics (0.52.0-2) ... 1257s Selecting previously unselected package r-bioc-biobase. 1257s Preparing to unpack .../187-r-bioc-biobase_2.66.0-2_arm64.deb ... 1257s Unpacking r-bioc-biobase (2.66.0-2) ... 1257s Selecting previously unselected package r-bioc-s4vectors. 1257s Preparing to unpack .../188-r-bioc-s4vectors_0.44.0+dfsg-2_arm64.deb ... 1257s Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) ... 1257s Selecting previously unselected package r-bioc-iranges. 1257s Preparing to unpack .../189-r-bioc-iranges_2.40.1-3_arm64.deb ... 1257s Unpacking r-bioc-iranges (2.40.1-3) ... 1257s Selecting previously unselected package r-cran-dbi. 1257s Preparing to unpack .../190-r-cran-dbi_1.2.3-1build1_all.deb ... 1257s Unpacking r-cran-dbi (1.2.3-1build1) ... 1257s Selecting previously unselected package r-cran-bit. 1257s Preparing to unpack .../191-r-cran-bit_4.6.0+dfsg-1_arm64.deb ... 1257s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 1257s Selecting previously unselected package r-cran-bit64. 1257s Preparing to unpack .../192-r-cran-bit64_4.6.0-1-4_arm64.deb ... 1257s Unpacking r-cran-bit64 (4.6.0-1-4) ... 1257s Selecting previously unselected package r-cran-rlang. 1257s Preparing to unpack .../193-r-cran-rlang_1.1.5-3_arm64.deb ... 1257s Unpacking r-cran-rlang (1.1.5-3) ... 1257s Selecting previously unselected package r-cran-cli. 1257s Preparing to unpack .../194-r-cran-cli_3.6.4-1_arm64.deb ... 1257s Unpacking r-cran-cli (3.6.4-1) ... 1257s Selecting previously unselected package r-cran-glue. 1257s Preparing to unpack .../195-r-cran-glue_1.8.0-1_arm64.deb ... 1257s Unpacking r-cran-glue (1.8.0-1) ... 1257s Selecting previously unselected package r-cran-lifecycle. 1257s Preparing to unpack .../196-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 1257s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 1257s Selecting previously unselected package r-cran-vctrs. 1257s Preparing to unpack .../197-r-cran-vctrs_0.6.5-1_arm64.deb ... 1257s Unpacking r-cran-vctrs (0.6.5-1) ... 1257s Selecting previously unselected package r-cran-blob. 1257s Preparing to unpack .../198-r-cran-blob_1.3.0-1_all.deb ... 1257s Unpacking r-cran-blob (1.3.0-1) ... 1257s Selecting previously unselected package r-cran-fastmap. 1257s Preparing to unpack .../199-r-cran-fastmap_1.2.0-1_arm64.deb ... 1257s Unpacking r-cran-fastmap (1.2.0-1) ... 1257s Selecting previously unselected package r-cran-cachem. 1257s Preparing to unpack .../200-r-cran-cachem_1.1.0-1_arm64.deb ... 1257s Unpacking r-cran-cachem (1.1.0-1) ... 1257s Selecting previously unselected package r-cran-memoise. 1257s Preparing to unpack .../201-r-cran-memoise_2.0.1-1build1_all.deb ... 1257s Unpacking r-cran-memoise (2.0.1-1build1) ... 1258s Selecting previously unselected package r-cran-pkgconfig. 1258s Preparing to unpack .../202-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 1258s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 1258s Selecting previously unselected package r-cran-plogr. 1258s Preparing to unpack .../203-r-cran-plogr_0.2.0-3build2_all.deb ... 1258s Unpacking r-cran-plogr (0.2.0-3build2) ... 1258s Selecting previously unselected package r-cran-cpp11. 1258s Preparing to unpack .../204-r-cran-cpp11_0.5.3-1_all.deb ... 1258s Unpacking r-cran-cpp11 (0.5.3-1) ... 1258s Selecting previously unselected package r-cran-rsqlite. 1258s Preparing to unpack .../205-r-cran-rsqlite_2.3.9-1_arm64.deb ... 1258s Unpacking r-cran-rsqlite (2.3.9-1) ... 1258s Selecting previously unselected package r-cran-curl. 1258s Preparing to unpack .../206-r-cran-curl_7.0.0+dfsg-1_arm64.deb ... 1258s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 1258s Selecting previously unselected package r-cran-jsonlite. 1258s Preparing to unpack .../207-r-cran-jsonlite_1.9.1+dfsg-1_arm64.deb ... 1258s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 1258s Selecting previously unselected package r-cran-mime. 1258s Preparing to unpack .../208-r-cran-mime_0.12-2_arm64.deb ... 1258s Unpacking r-cran-mime (0.12-2) ... 1258s Selecting previously unselected package r-cran-sys. 1258s Preparing to unpack .../209-r-cran-sys_3.4.3-1_arm64.deb ... 1258s Unpacking r-cran-sys (3.4.3-1) ... 1258s Selecting previously unselected package r-cran-askpass. 1258s Preparing to unpack .../210-r-cran-askpass_1.2.1-1_arm64.deb ... 1258s Unpacking r-cran-askpass (1.2.1-1) ... 1258s Selecting previously unselected package r-cran-openssl. 1258s Preparing to unpack .../211-r-cran-openssl_2.3.2+dfsg-1_arm64.deb ... 1258s Unpacking r-cran-openssl (2.3.2+dfsg-1) ... 1258s Selecting previously unselected package r-cran-r6. 1258s Preparing to unpack .../212-r-cran-r6_2.6.1-1_all.deb ... 1258s Unpacking r-cran-r6 (2.6.1-1) ... 1258s Selecting previously unselected package r-cran-httr. 1258s Preparing to unpack .../213-r-cran-httr_1.4.7+dfsg-1_all.deb ... 1258s Unpacking r-cran-httr (1.4.7+dfsg-1) ... 1258s Selecting previously unselected package r-cran-png. 1258s Preparing to unpack .../214-r-cran-png_0.1-8-1build2_arm64.deb ... 1258s Unpacking r-cran-png (0.1-8-1build2) ... 1258s Selecting previously unselected package r-bioc-zlibbioc. 1258s Preparing to unpack .../215-r-bioc-zlibbioc_1.52.0+dfsg-2_all.deb ... 1258s Unpacking r-bioc-zlibbioc (1.52.0+dfsg-2) ... 1258s Selecting previously unselected package r-bioc-xvector. 1258s Preparing to unpack .../216-r-bioc-xvector_0.46.0-2_arm64.deb ... 1258s Unpacking r-bioc-xvector (0.46.0-2) ... 1258s Selecting previously unselected package r-bioc-ucsc.utils. 1258s Preparing to unpack .../217-r-bioc-ucsc.utils_1.2.0+ds-2_all.deb ... 1258s Unpacking r-bioc-ucsc.utils (1.2.0+ds-2) ... 1258s Selecting previously unselected package r-bioc-genomeinfodbdata. 1258s Preparing to unpack .../218-r-bioc-genomeinfodbdata_1.2.13-2_all.deb ... 1258s Unpacking r-bioc-genomeinfodbdata (1.2.13-2) ... 1258s Selecting previously unselected package r-bioc-genomeinfodb. 1258s Preparing to unpack .../219-r-bioc-genomeinfodb_1.42.3+dfsg-1_all.deb ... 1258s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ... 1258s Selecting previously unselected package r-cran-crayon. 1259s Preparing to unpack .../220-r-cran-crayon_1.5.3-1_all.deb ... 1259s Unpacking r-cran-crayon (1.5.3-1) ... 1259s Selecting previously unselected package r-bioc-biostrings. 1259s Preparing to unpack .../221-r-bioc-biostrings_2.74.1+dfsg-2_arm64.deb ... 1259s Unpacking r-bioc-biostrings (2.74.1+dfsg-2) ... 1259s Selecting previously unselected package r-bioc-keggrest. 1259s Preparing to unpack .../222-r-bioc-keggrest_1.46.0+dfsg-3_all.deb ... 1259s Unpacking r-bioc-keggrest (1.46.0+dfsg-3) ... 1259s Selecting previously unselected package r-bioc-annotationdbi. 1259s Preparing to unpack .../223-r-bioc-annotationdbi_1.68.0-2_all.deb ... 1259s Unpacking r-bioc-annotationdbi (1.68.0-2) ... 1259s Selecting previously unselected package r-cran-r.methodss3. 1259s Preparing to unpack .../224-r-cran-r.methodss3_1.8.2-1_all.deb ... 1259s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 1259s Selecting previously unselected package r-cran-r.oo. 1259s Preparing to unpack .../225-r-cran-r.oo_1.27.1-1_all.deb ... 1259s Unpacking r-cran-r.oo (1.27.1-1) ... 1259s Selecting previously unselected package r-cran-r.utils. 1259s Preparing to unpack .../226-r-cran-r.utils_2.13.0-1_all.deb ... 1259s Unpacking r-cran-r.utils (2.13.0-1) ... 1259s Selecting previously unselected package r-cran-matrixstats. 1259s Preparing to unpack .../227-r-cran-matrixstats_1.5.0-1_arm64.deb ... 1259s Unpacking r-cran-matrixstats (1.5.0-1) ... 1259s Selecting previously unselected package r-bioc-aroma.light. 1259s Preparing to unpack .../228-r-bioc-aroma.light_3.36.0-2_all.deb ... 1259s Unpacking r-bioc-aroma.light (3.36.0-2) ... 1259s Selecting previously unselected package r-bioc-biocio. 1259s Preparing to unpack .../229-r-bioc-biocio_1.16.0+dfsg-2_all.deb ... 1259s Unpacking r-bioc-biocio (1.16.0+dfsg-2) ... 1259s Selecting previously unselected package r-cran-formatr. 1259s Preparing to unpack .../230-r-cran-formatr_1.14-2_all.deb ... 1259s Unpacking r-cran-formatr (1.14-2) ... 1259s Selecting previously unselected package r-cran-lambda.r. 1259s Preparing to unpack .../231-r-cran-lambda.r_1.2.4-2build2_all.deb ... 1259s Unpacking r-cran-lambda.r (1.2.4-2build2) ... 1259s Selecting previously unselected package r-cran-futile.options. 1259s Preparing to unpack .../232-r-cran-futile.options_1.0.1-3build2_all.deb ... 1259s Unpacking r-cran-futile.options (1.0.1-3build2) ... 1259s Selecting previously unselected package r-cran-futile.logger. 1259s Preparing to unpack .../233-r-cran-futile.logger_1.4.3-4build2_all.deb ... 1259s Unpacking r-cran-futile.logger (1.4.3-4build2) ... 1259s Selecting previously unselected package r-cran-snow. 1259s Preparing to unpack .../234-r-cran-snow_1%3a0.4.4-2build1_all.deb ... 1259s Unpacking r-cran-snow (1:0.4.4-2build1) ... 1259s Selecting previously unselected package r-cran-codetools. 1259s Preparing to unpack .../235-r-cran-codetools_0.2-20-1build1_all.deb ... 1259s Unpacking r-cran-codetools (0.2-20-1build1) ... 1259s Selecting previously unselected package r-cran-bh. 1260s Preparing to unpack .../236-r-cran-bh_1.84.0-1_all.deb ... 1260s Unpacking r-cran-bh (1.84.0-1) ... 1260s Selecting previously unselected package r-bioc-biocparallel. 1260s Preparing to unpack .../237-r-bioc-biocparallel_1.40.0-2_arm64.deb ... 1260s Unpacking r-bioc-biocparallel (1.40.0-2) ... 1260s Selecting previously unselected package r-cran-base64enc. 1260s Preparing to unpack .../238-r-cran-base64enc_0.1-3-3build1_arm64.deb ... 1260s Unpacking r-cran-base64enc (0.1-3-3build1) ... 1260s Selecting previously unselected package r-cran-digest. 1260s Preparing to unpack .../239-r-cran-digest_0.6.39-1_arm64.deb ... 1260s Unpacking r-cran-digest (0.6.39-1) ... 1260s Selecting previously unselected package r-cran-htmltools. 1260s Preparing to unpack .../240-r-cran-htmltools_0.5.8.1-1_arm64.deb ... 1260s Unpacking r-cran-htmltools (0.5.8.1-1) ... 1260s Selecting previously unselected package r-cran-evaluate. 1260s Preparing to unpack .../241-r-cran-evaluate_1.0.5-1_all.deb ... 1260s Unpacking r-cran-evaluate (1.0.5-1) ... 1260s Selecting previously unselected package r-cran-xfun. 1260s Preparing to unpack .../242-r-cran-xfun_0.55+dfsg-1_arm64.deb ... 1260s Unpacking r-cran-xfun (0.55+dfsg-1) ... 1260s Selecting previously unselected package r-cran-highr. 1260s Preparing to unpack .../243-r-cran-highr_0.11+dfsg-1_all.deb ... 1260s Unpacking r-cran-highr (0.11+dfsg-1) ... 1260s Selecting previously unselected package r-cran-yaml. 1260s Preparing to unpack .../244-r-cran-yaml_2.3.10-1_arm64.deb ... 1260s Unpacking r-cran-yaml (2.3.10-1) ... 1260s Selecting previously unselected package libjs-mathjax. 1260s Preparing to unpack .../245-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 1260s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 1260s Selecting previously unselected package r-cran-knitr. 1260s Preparing to unpack .../246-r-cran-knitr_1.51+dfsg-1_all.deb ... 1260s Unpacking r-cran-knitr (1.51+dfsg-1) ... 1260s Selecting previously unselected package r-cran-jquerylib. 1260s Preparing to unpack .../247-r-cran-jquerylib_0.1.4+dfsg-5_all.deb ... 1260s Unpacking r-cran-jquerylib (0.1.4+dfsg-5) ... 1260s Selecting previously unselected package r-cran-fs. 1260s Preparing to unpack .../248-r-cran-fs_1.6.5+dfsg-1_arm64.deb ... 1260s Unpacking r-cran-fs (1.6.5+dfsg-1) ... 1261s Selecting previously unselected package r-cran-rappdirs. 1261s Preparing to unpack .../249-r-cran-rappdirs_0.3.3-1build1_arm64.deb ... 1261s Unpacking r-cran-rappdirs (0.3.3-1build1) ... 1261s Selecting previously unselected package r-cran-sass. 1261s Preparing to unpack .../250-r-cran-sass_0.4.9+dfsg-1_arm64.deb ... 1261s Unpacking r-cran-sass (0.4.9+dfsg-1) ... 1261s Selecting previously unselected package r-cran-bslib. 1261s Preparing to unpack .../251-r-cran-bslib_0.9.0+dfsg-3build1_all.deb ... 1261s Unpacking r-cran-bslib (0.9.0+dfsg-3build1) ... 1261s Selecting previously unselected package r-cran-fontawesome. 1261s Preparing to unpack .../252-r-cran-fontawesome_0.5.3-1_all.deb ... 1261s Unpacking r-cran-fontawesome (0.5.3-1) ... 1261s Selecting previously unselected package r-cran-tinytex. 1261s Preparing to unpack .../253-r-cran-tinytex_0.58-1_all.deb ... 1261s Unpacking r-cran-tinytex (0.58-1) ... 1261s Selecting previously unselected package libjs-modernizr. 1261s Preparing to unpack .../254-libjs-modernizr_3.13.0-0.1build1_all.deb ... 1261s Unpacking libjs-modernizr (3.13.0-0.1build1) ... 1261s Selecting previously unselected package r-cran-littler. 1261s Preparing to unpack .../255-r-cran-littler_0.3.22-1_arm64.deb ... 1261s Unpacking r-cran-littler (0.3.22-1) ... 1261s Selecting previously unselected package r-cran-pkgkitten. 1261s Preparing to unpack .../256-r-cran-pkgkitten_0.2.4-1_all.deb ... 1261s Unpacking r-cran-pkgkitten (0.2.4-1) ... 1261s Selecting previously unselected package r-cran-rcpp. 1261s Preparing to unpack .../257-r-cran-rcpp_1.1.0-1_arm64.deb ... 1261s Unpacking r-cran-rcpp (1.1.0-1) ... 1261s Selecting previously unselected package r-cran-later. 1261s Preparing to unpack .../258-r-cran-later_1.4.1+dfsg-1_arm64.deb ... 1261s Unpacking r-cran-later (1.4.1+dfsg-1) ... 1261s Selecting previously unselected package r-cran-magrittr. 1261s Preparing to unpack .../259-r-cran-magrittr_2.0.3-1_arm64.deb ... 1261s Unpacking r-cran-magrittr (2.0.3-1) ... 1261s Selecting previously unselected package r-cran-promises. 1261s Preparing to unpack .../260-r-cran-promises_1.3.2+dfsg-1_arm64.deb ... 1261s Unpacking r-cran-promises (1.3.2+dfsg-1) ... 1261s Selecting previously unselected package r-cran-httpuv. 1261s Preparing to unpack .../261-r-cran-httpuv_1.6.15+dfsg-1_arm64.deb ... 1261s Unpacking r-cran-httpuv (1.6.15+dfsg-1) ... 1261s Selecting previously unselected package r-cran-xtable. 1261s Preparing to unpack .../262-r-cran-xtable_1%3a1.8-4-2build1_all.deb ... 1261s Unpacking r-cran-xtable (1:1.8-4-2build1) ... 1261s Selecting previously unselected package r-cran-sourcetools. 1261s Preparing to unpack .../263-r-cran-sourcetools_0.1.7-1-1_arm64.deb ... 1261s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 1261s Selecting previously unselected package r-cran-withr. 1261s Preparing to unpack .../264-r-cran-withr_3.0.2+dfsg-1_all.deb ... 1261s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 1261s Selecting previously unselected package r-cran-commonmark. 1262s Preparing to unpack .../265-r-cran-commonmark_1.9.5-1_arm64.deb ... 1262s Unpacking r-cran-commonmark (1.9.5-1) ... 1262s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 1262s Preparing to unpack .../266-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 1262s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 1262s Selecting previously unselected package r-cran-shiny. 1262s Preparing to unpack .../267-r-cran-shiny_1.10.0+dfsg-2_all.deb ... 1262s Unpacking r-cran-shiny (1.10.0+dfsg-2) ... 1262s Selecting previously unselected package r-cran-rmarkdown. 1262s Preparing to unpack .../268-r-cran-rmarkdown_2.30+dfsg-1_all.deb ... 1262s Unpacking r-cran-rmarkdown (2.30+dfsg-1) ... 1262s Selecting previously unselected package r-cran-bookdown. 1262s Preparing to unpack .../269-r-cran-bookdown_0.42+dfsg-1_all.deb ... 1262s Unpacking r-cran-bookdown (0.42+dfsg-1) ... 1262s Selecting previously unselected package r-cran-biocmanager. 1262s Preparing to unpack .../270-r-cran-biocmanager_1.30.25+dfsg-1_all.deb ... 1262s Unpacking r-cran-biocmanager (1.30.25+dfsg-1) ... 1262s Selecting previously unselected package tex-common. 1262s Preparing to unpack .../271-tex-common_6.20_all.deb ... 1262s Unpacking tex-common (6.20) ... 1262s Selecting previously unselected package t1utils. 1262s Preparing to unpack .../272-t1utils_1.41-4build4_arm64.deb ... 1262s Unpacking t1utils (1.41-4build4) ... 1262s Selecting previously unselected package texlive-binaries. 1262s Preparing to unpack .../273-texlive-binaries_2025.20250727.75242+ds-5build1_arm64.deb ... 1262s Unpacking texlive-binaries (2025.20250727.75242+ds-5build1) ... 1262s Selecting previously unselected package texlive-base. 1262s Preparing to unpack .../274-texlive-base_2025.20260124-1_all.deb ... 1262s Unpacking texlive-base (2025.20260124-1) ... 1263s Selecting previously unselected package texlive-latex-base. 1263s Preparing to unpack .../275-texlive-latex-base_2025.20260124-1_all.deb ... 1263s Unpacking texlive-latex-base (2025.20260124-1) ... 1264s Selecting previously unselected package texlive-bibtex-extra. 1264s Preparing to unpack .../276-texlive-bibtex-extra_2025.20260124-1_all.deb ... 1264s Unpacking texlive-bibtex-extra (2025.20260124-1) ... 1266s Selecting previously unselected package r-bioc-biocversion. 1266s Preparing to unpack .../277-r-bioc-biocversion_3.20.0-2_all.deb ... 1266s Unpacking r-bioc-biocversion (3.20.0-2) ... 1266s Selecting previously unselected package r-bioc-biocstyle. 1266s Preparing to unpack .../278-r-bioc-biocstyle_2.34.0+dfsg-1_all.deb ... 1266s Unpacking r-bioc-biocstyle (2.34.0+dfsg-1) ... 1266s Selecting previously unselected package r-bioc-genomicranges. 1266s Preparing to unpack .../279-r-bioc-genomicranges_1.58.0+dfsg-2_arm64.deb ... 1266s Unpacking r-bioc-genomicranges (1.58.0+dfsg-2) ... 1266s Selecting previously unselected package r-cran-xml. 1266s Preparing to unpack .../280-r-cran-xml_3.99-0.20-1_arm64.deb ... 1266s Unpacking r-cran-xml (3.99-0.20-1) ... 1266s Selecting previously unselected package r-cran-bitops. 1266s Preparing to unpack .../281-r-cran-bitops_1.0-9-1_arm64.deb ... 1266s Unpacking r-cran-bitops (1.0-9-1) ... 1266s Selecting previously unselected package r-bioc-rhtslib. 1266s Preparing to unpack .../282-r-bioc-rhtslib_3.2.0+dfsg-2_arm64.deb ... 1266s Unpacking r-bioc-rhtslib (3.2.0+dfsg-2) ... 1266s Selecting previously unselected package r-bioc-rsamtools. 1266s Preparing to unpack .../283-r-bioc-rsamtools_2.22.0+dfsg-2_arm64.deb ... 1266s Unpacking r-bioc-rsamtools (2.22.0+dfsg-2) ... 1267s Selecting previously unselected package r-bioc-matrixgenerics. 1267s Preparing to unpack .../284-r-bioc-matrixgenerics_1.18.1-1_all.deb ... 1267s Unpacking r-bioc-matrixgenerics (1.18.1-1) ... 1267s Selecting previously unselected package r-cran-lattice. 1267s Preparing to unpack .../285-r-cran-lattice_0.22-7-1_arm64.deb ... 1267s Unpacking r-cran-lattice (0.22-7-1) ... 1267s Selecting previously unselected package r-cran-matrix. 1267s Preparing to unpack .../286-r-cran-matrix_1.7-4-1_arm64.deb ... 1267s Unpacking r-cran-matrix (1.7-4-1) ... 1267s Selecting previously unselected package r-cran-abind. 1267s Preparing to unpack .../287-r-cran-abind_1.4-8-1build1_all.deb ... 1267s Unpacking r-cran-abind (1.4-8-1build1) ... 1267s Selecting previously unselected package r-bioc-s4arrays. 1267s Preparing to unpack .../288-r-bioc-s4arrays_1.6.0+dfsg-2_arm64.deb ... 1267s Unpacking r-bioc-s4arrays (1.6.0+dfsg-2) ... 1267s Selecting previously unselected package r-bioc-sparsearray. 1267s Preparing to unpack .../289-r-bioc-sparsearray_1.6.2+dfsg-2_arm64.deb ... 1267s Unpacking r-bioc-sparsearray (1.6.2+dfsg-2) ... 1267s Selecting previously unselected package r-bioc-delayedarray. 1267s Preparing to unpack .../290-r-bioc-delayedarray_0.32.0+dfsg-2_arm64.deb ... 1267s Unpacking r-bioc-delayedarray (0.32.0+dfsg-2) ... 1267s Selecting previously unselected package r-bioc-summarizedexperiment. 1267s Preparing to unpack .../291-r-bioc-summarizedexperiment_1.36.0+dfsg-2_all.deb ... 1267s Unpacking r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... 1267s Selecting previously unselected package r-bioc-genomicalignments. 1267s Preparing to unpack .../292-r-bioc-genomicalignments_1.42.0-2_arm64.deb ... 1267s Unpacking r-bioc-genomicalignments (1.42.0-2) ... 1267s Selecting previously unselected package r-cran-rcurl. 1267s Preparing to unpack .../293-r-cran-rcurl_1.98-1.16+dfsg-1_arm64.deb ... 1267s Unpacking r-cran-rcurl (1.98-1.16+dfsg-1) ... 1267s Selecting previously unselected package r-cran-rjson. 1267s Preparing to unpack .../294-r-cran-rjson_0.2.23-1_arm64.deb ... 1267s Unpacking r-cran-rjson (0.2.23-1) ... 1267s Selecting previously unselected package r-cran-restfulr. 1267s Preparing to unpack .../295-r-cran-restfulr_0.0.15-1_arm64.deb ... 1267s Unpacking r-cran-restfulr (0.0.15-1) ... 1267s Selecting previously unselected package r-bioc-rtracklayer. 1267s Preparing to unpack .../296-r-bioc-rtracklayer_1.66.0-3_arm64.deb ... 1267s Unpacking r-bioc-rtracklayer (1.66.0-3) ... 1267s Selecting previously unselected package r-bioc-bsgenome. 1267s Preparing to unpack .../297-r-bioc-bsgenome_1.74.0-2_all.deb ... 1267s Unpacking r-bioc-bsgenome (1.74.0-2) ... 1267s Selecting previously unselected package r-bioc-dnacopy. 1268s Preparing to unpack .../298-r-bioc-dnacopy_1.80.0-2_arm64.deb ... 1268s Unpacking r-bioc-dnacopy (1.80.0-2) ... 1268s Selecting previously unselected package r-bioc-genomicfeatures. 1268s Preparing to unpack .../299-r-bioc-genomicfeatures_1.58.0+dfsg-2_all.deb ... 1268s Unpacking r-bioc-genomicfeatures (1.58.0+dfsg-2) ... 1268s Selecting previously unselected package r-bioc-org.hs.eg.db. 1268s Preparing to unpack .../300-r-bioc-org.hs.eg.db_3.20.0-3_all.deb ... 1268s Unpacking r-bioc-org.hs.eg.db (3.20.0-3) ... 1269s Selecting previously unselected package r-bioc-variantannotation. 1269s Preparing to unpack .../301-r-bioc-variantannotation_1.52.0-2_arm64.deb ... 1269s Unpacking r-bioc-variantannotation (1.52.0-2) ... 1269s Selecting previously unselected package r-cran-rcolorbrewer. 1269s Preparing to unpack .../302-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 1269s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 1269s Selecting previously unselected package r-cran-data.table. 1269s Preparing to unpack .../303-r-cran-data.table_1.17.0+dfsg-1_arm64.deb ... 1269s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 1269s Selecting previously unselected package r-cran-gtable. 1269s Preparing to unpack .../304-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 1269s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 1269s Selecting previously unselected package r-cran-isoband. 1269s Preparing to unpack .../305-r-cran-isoband_0.2.7-1_arm64.deb ... 1269s Unpacking r-cran-isoband (0.2.7-1) ... 1269s Selecting previously unselected package r-cran-s7. 1269s Preparing to unpack .../306-r-cran-s7_0.2.0-1_arm64.deb ... 1269s Unpacking r-cran-s7 (0.2.0-1) ... 1269s Selecting previously unselected package r-cran-farver. 1269s Preparing to unpack .../307-r-cran-farver_2.1.2-1_arm64.deb ... 1269s Unpacking r-cran-farver (2.1.2-1) ... 1270s Selecting previously unselected package r-cran-labeling. 1270s Preparing to unpack .../308-r-cran-labeling_0.4.3-1_all.deb ... 1270s Unpacking r-cran-labeling (0.4.3-1) ... 1270s Selecting previously unselected package r-cran-viridislite. 1270s Preparing to unpack .../309-r-cran-viridislite_0.4.3-1_all.deb ... 1270s Unpacking r-cran-viridislite (0.4.3-1) ... 1270s Selecting previously unselected package r-cran-scales. 1270s Preparing to unpack .../310-r-cran-scales_1.4.0-1_all.deb ... 1270s Unpacking r-cran-scales (1.4.0-1) ... 1270s Selecting previously unselected package r-cran-ggplot2. 1270s Preparing to unpack .../311-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 1270s Unpacking r-cran-ggplot2 (4.0.2+dfsg-1) ... 1270s Selecting previously unselected package r-cran-gridextra. 1270s Preparing to unpack .../312-r-cran-gridextra_2.3-3build2_all.deb ... 1270s Unpacking r-cran-gridextra (2.3-3build2) ... 1270s Selecting previously unselected package r-cran-vgam. 1270s Preparing to unpack .../313-r-cran-vgam_1.1-13-1_arm64.deb ... 1270s Unpacking r-cran-vgam (1.1-13-1) ... 1270s Selecting previously unselected package r-cran-mclust. 1270s Preparing to unpack .../314-r-cran-mclust_6.1.1-1_arm64.deb ... 1270s Unpacking r-cran-mclust (6.1.1-1) ... 1270s Selecting previously unselected package r-bioc-rhdf5lib. 1270s Preparing to unpack .../315-r-bioc-rhdf5lib_1.28.0+dfsg-3_arm64.deb ... 1270s Unpacking r-bioc-rhdf5lib (1.28.0+dfsg-3) ... 1270s Selecting previously unselected package r-bioc-rhdf5filters. 1270s Preparing to unpack .../316-r-bioc-rhdf5filters_1.18.1+dfsg-1_arm64.deb ... 1270s Unpacking r-bioc-rhdf5filters (1.18.1+dfsg-1) ... 1270s Selecting previously unselected package r-bioc-rhdf5. 1270s Preparing to unpack .../317-r-bioc-rhdf5_2.50.2+dfsg-1build1_arm64.deb ... 1270s Unpacking r-bioc-rhdf5 (2.50.2+dfsg-1build1) ... 1270s Selecting previously unselected package r-bioc-purecn. 1270s Preparing to unpack .../318-r-bioc-purecn_2.12.0+dfsg-2_all.deb ... 1270s Unpacking r-bioc-purecn (2.12.0+dfsg-2) ... 1270s Selecting previously unselected package r-cran-brio. 1270s Preparing to unpack .../319-r-cran-brio_1.1.5-1_arm64.deb ... 1270s Unpacking r-cran-brio (1.1.5-1) ... 1270s Selecting previously unselected package r-cran-ps. 1270s Preparing to unpack .../320-r-cran-ps_1.9.0-1_arm64.deb ... 1270s Unpacking r-cran-ps (1.9.0-1) ... 1270s Selecting previously unselected package r-cran-processx. 1270s Preparing to unpack .../321-r-cran-processx_3.8.6-1_arm64.deb ... 1270s Unpacking r-cran-processx (3.8.6-1) ... 1270s Selecting previously unselected package r-cran-callr. 1270s Preparing to unpack .../322-r-cran-callr_3.7.6-1_all.deb ... 1270s Unpacking r-cran-callr (3.7.6-1) ... 1270s Selecting previously unselected package r-cran-lazyeval. 1270s Preparing to unpack .../323-r-cran-lazyeval_0.2.2-1build2_arm64.deb ... 1270s Unpacking r-cran-lazyeval (0.2.2-1build2) ... 1270s Selecting previously unselected package r-cran-rex. 1271s Preparing to unpack .../324-r-cran-rex_1.2.1-1build1_all.deb ... 1271s Unpacking r-cran-rex (1.2.1-1build1) ... 1271s Selecting previously unselected package r-cran-covr. 1271s Preparing to unpack .../325-r-cran-covr_3.6.4+dfsg-1_arm64.deb ... 1271s Unpacking r-cran-covr (3.6.4+dfsg-1) ... 1271s Selecting previously unselected package r-cran-desc. 1271s Preparing to unpack .../326-r-cran-desc_1.4.3-1_all.deb ... 1271s Unpacking r-cran-desc (1.4.3-1) ... 1271s Selecting previously unselected package r-cran-diffobj. 1271s Preparing to unpack .../327-r-cran-diffobj_0.3.5-1build1_arm64.deb ... 1271s Unpacking r-cran-diffobj (0.3.5-1build1) ... 1271s Selecting previously unselected package r-cran-globals. 1271s Preparing to unpack .../328-r-cran-globals_0.19.0-1_all.deb ... 1271s Unpacking r-cran-globals (0.19.0-1) ... 1271s Selecting previously unselected package r-cran-listenv. 1271s Preparing to unpack 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... 1271s Selecting previously unselected package r-cran-pkgbuild. 1271s Preparing to unpack .../335-r-cran-pkgbuild_1.4.8-1_all.deb ... 1271s Unpacking r-cran-pkgbuild (1.4.8-1) ... 1271s Selecting previously unselected package r-cran-rprojroot. 1271s Preparing to unpack .../336-r-cran-rprojroot_2.1.1-1_all.deb ... 1271s Unpacking r-cran-rprojroot (2.1.1-1) ... 1271s Selecting previously unselected package r-cran-pkgload. 1271s Preparing to unpack .../337-r-cran-pkgload_1.4.1-1_all.deb ... 1271s Unpacking r-cran-pkgload (1.4.1-1) ... 1271s Selecting previously unselected package r-cran-praise. 1271s Preparing to unpack .../338-r-cran-praise_1.0.0-4build2_all.deb ... 1271s Unpacking r-cran-praise (1.0.0-4build2) ... 1271s Selecting previously unselected package r-cran-r.cache. 1271s Preparing to unpack .../339-r-cran-r.cache_0.17.0-1_all.deb ... 1271s Unpacking r-cran-r.cache (0.17.0-1) ... 1271s Selecting previously unselected package r-cran-pscbs. 1271s Preparing to unpack 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... 1277s Setting up r-cran-cli (3.6.4-1) ... 1277s Setting up gfortran (4:15.2.0-4ubuntu1) ... 1277s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 1277s 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 1277s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 1277s 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 1277s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 1277s Setting up r-cran-bitops (1.0-9-1) ... 1277s Setting up r-bioc-biocversion (3.20.0-2) ... 1277s Setting up r-cran-rprojroot (2.1.1-1) ... 1277s Setting up r-cran-bit64 (4.6.0-1-4) ... 1277s Setting up r-cran-biocmanager (1.30.25+dfsg-1) ... 1277s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ... 1277s Setting up r-cran-askpass (1.2.1-1) ... 1277s Setting up r-cran-fastmap (1.2.0-1) ... 1277s Setting up r-cran-png (0.1-8-1build2) ... 1277s Setting up r-cran-r.methodss3 (1.8.2-1) ... 1277s Setting up r-bioc-biobase (2.66.0-2) ... 1277s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... 1277s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 1277s Setting up r-cran-getopt (1.20.4-1) ... 1277s Setting up r-cran-parallelly (1.42.0-1) ... 1277s Setting up texlive-latex-base (2025.20260124-1) ... 1277s Setting up r-cran-rex (1.2.1-1build1) ... 1277s Setting up r-cran-markdown (1.13-1) ... 1277s Setting up r-cran-s7 (0.2.0-1) ... 1277s Setting up libcurl4-openssl-dev:arm64 (8.18.0-1ubuntu1) ... 1277s Setting up r-cran-cpp11 (0.5.3-1) ... 1277s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 1277s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ... 1277s Setting up r-cran-isoband (0.2.7-1) ... 1277s Setting up r-cran-futile.logger (1.4.3-4build2) ... 1277s Setting up r-cran-waldo (0.6.2-1) ... 1277s Setting up libhdf5-dev (1.14.6+repack-2) ... 1277s update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode 1277s Setting up r-cran-scales (1.4.0-1) ... 1277s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 1277s Setting up r-cran-later (1.4.1+dfsg-1) ... 1277s Setting up r-cran-matrix (1.7-4-1) ... 1277s Setting up r-cran-htmltools (0.5.8.1-1) ... 1277s Setting up r-cran-tinytex (0.58-1) ... 1277s Setting up r-cran-knitr (1.51+dfsg-1) ... 1277s Setting up g++ (4:15.2.0-4ubuntu1) ... 1277s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1277s Setting up r-bioc-dnacopy (1.80.0-2) ... 1277s Setting up r-cran-cachem (1.1.0-1) ... 1277s Setting up r-cran-sass (0.4.9+dfsg-1) ... 1277s Setting up build-essential (12.12ubuntu2) ... 1277s Setting up r-bioc-iranges (2.40.1-3) ... 1277s Setting up r-cran-globals (0.19.0-1) ... 1277s Setting up r-cran-rcurl 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r-cran-httr (1.4.7+dfsg-1) ... 1277s Setting up r-cran-gridextra (2.3-3build2) ... 1277s Setting up r-cran-memoise (2.0.1-1build1) ... 1277s Setting up r-cran-covr (3.6.4+dfsg-1) ... 1277s Setting up r-cran-promises (1.3.2+dfsg-1) ... 1277s Setting up r-cran-blob (1.3.0-1) ... 1277s Setting up pkg-r-autopkgtest (20250812) ... 1277s Setting up r-bioc-xvector (0.46.0-2) ... 1277s Setting up r-cran-pkgbuild (1.4.8-1) ... 1277s Setting up r-cran-rsqlite (2.3.9-1) ... 1277s Setting up r-cran-pkgload (1.4.1-1) ... 1277s Setting up r-cran-r.utils (2.13.0-1) ... 1277s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ... 1277s Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ... 1277s Setting up r-bioc-rhdf5 (2.50.2+dfsg-1build1) ... 1277s Setting up r-cran-httpuv (1.6.15+dfsg-1) ... 1277s Setting up r-cran-testthat (3.2.3-1) ... 1277s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ... 1277s Setting up r-cran-bslib (0.9.0+dfsg-3build1) ... 1277s Setting up r-bioc-aroma.light (3.36.0-2) ... 1277s Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ... 1277s Setting up r-cran-r.cache (0.17.0-1) ... 1277s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ... 1277s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ... 1277s Setting up r-cran-shiny (1.10.0+dfsg-2) ... 1277s Setting up r-cran-pscbs (0.68.0-1) ... 1277s Setting up r-cran-rmarkdown (2.30+dfsg-1) ... 1277s Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ... 1277s Setting up r-cran-bookdown (0.42+dfsg-1) ... 1277s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... 1277s Setting up r-bioc-keggrest (1.46.0+dfsg-3) ... 1277s Setting up r-bioc-annotationdbi (1.68.0-2) ... 1277s Setting up r-bioc-biocstyle (2.34.0+dfsg-1) ... 1277s Setting up r-bioc-genomicalignments (1.42.0-2) ... 1277s Setting up r-bioc-org.hs.eg.db (3.20.0-3) ... 1277s Setting up r-bioc-rtracklayer (1.66.0-3) ... 1277s Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ... 1277s Setting up r-bioc-bsgenome (1.74.0-2) ... 1277s Setting up r-bioc-variantannotation (1.52.0-2) ... 1277s Setting up r-bioc-purecn (2.12.0+dfsg-2) ... 1277s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1277s Processing triggers for man-db (2.13.1-1build1) ... 1278s Processing triggers for install-info (7.2-5) ... 1278s Processing triggers for tex-common (6.20) ... 1279s Running updmap-sys. This may take some time... done. 1279s Running mktexlsr /var/lib/texmf ... done. 1279s Building format(s) --all. 1306s This may take some time... done. 1306s autopkgtest [23:43:16]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1306s autopkgtest [23:43:16]: test pkg-r-autopkgtest: [----------------------- 1307s Test: Try to load the R library PureCN 1307s 1307s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1307s Copyright (C) 2025 The R Foundation for Statistical Computing 1307s Platform: aarch64-unknown-linux-gnu 1307s 1307s R is free software and comes with ABSOLUTELY NO WARRANTY. 1307s You are welcome to redistribute it under certain conditions. 1307s Type 'license()' or 'licence()' for distribution details. 1307s 1307s R is a collaborative project with many contributors. 1307s Type 'contributors()' for more information and 1307s 'citation()' on how to cite R or R packages in publications. 1307s 1307s Type 'demo()' for some demos, 'help()' for on-line help, or 1307s 'help.start()' for an HTML browser interface to help. 1307s Type 'q()' to quit R. 1307s 1307s > library('PureCN') 1307s Loading required package: DNAcopy 1307s Loading required package: VariantAnnotation 1307s Loading required package: BiocGenerics 1307s 1307s Attaching package: ‘BiocGenerics’ 1307s 1307s The following objects are masked from ‘package:stats’: 1307s 1307s IQR, mad, sd, var, xtabs 1307s 1307s The following objects are masked from ‘package:base’: 1307s 1307s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 1307s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 1307s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 1307s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 1307s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 1307s table, tapply, union, unique, unsplit, which.max, which.min 1307s 1307s Loading required package: MatrixGenerics 1307s Loading required package: matrixStats 1307s 1307s Attaching package: ‘MatrixGenerics’ 1307s 1307s The following objects are masked from ‘package:matrixStats’: 1307s 1307s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 1307s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 1307s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 1307s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 1307s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 1307s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 1307s colWeightedMeans, colWeightedMedians, colWeightedSds, 1307s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 1307s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 1307s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 1307s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 1307s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 1307s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 1307s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 1307s rowWeightedSds, rowWeightedVars 1307s 1307s Loading required package: GenomeInfoDb 1307s Loading required package: S4Vectors 1307s Loading required package: stats4 1308s 1308s Attaching package: ‘S4Vectors’ 1308s 1308s The following object is masked from ‘package:utils’: 1308s 1308s findMatches 1308s 1308s The following objects are masked from ‘package:base’: 1308s 1308s expand.grid, I, unname 1308s 1308s Loading required package: IRanges 1309s Loading required package: GenomicRanges 1309s Loading required package: SummarizedExperiment 1309s Loading required package: Biobase 1309s Welcome to Bioconductor 1309s 1309s Vignettes contain introductory material; view with 1309s 'browseVignettes()'. To cite Bioconductor, see 1309s 'citation("Biobase")', and for packages 'citation("pkgname")'. 1309s 1309s 1309s Attaching package: ‘Biobase’ 1309s 1309s The following object is masked from ‘package:MatrixGenerics’: 1309s 1309s rowMedians 1309s 1309s The following objects are masked from ‘package:matrixStats’: 1309s 1309s anyMissing, rowMedians 1309s 1312s Loading required package: Rsamtools 1312s Loading required package: Biostrings 1312s Loading required package: XVector 1313s 1313s Attaching package: ‘Biostrings’ 1313s 1313s The following object is masked from ‘package:base’: 1313s 1313s strsplit 1313s 1317s 1317s Attaching package: ‘VariantAnnotation’ 1317s 1317s The following object is masked from ‘package:base’: 1317s 1317s tabulate 1317s 1318s > 1318s + cd tests 1318s + grep -l genomicsdb testthat/test_adjustLogRatio.R testthat/test_annotateTargets.R testthat/test_bootstrapResults.R testthat/test_calculateBamCoverageByInterval.R testthat/test_calculateLogRatio.R testthat/test_calculatePowerDetectSomatic.R testthat/test_callAlterations.R testthat/test_callAlterationsFromSegmentation.R testthat/test_callAmplificationsInLowPurity.R testthat/test_callCIN.R testthat/test_callLOH.R testthat/test_callMutationBurden.R testthat/test_correctCoverageBias.R testthat/test_createCurationFile.R testthat/test_createNormalDatabase.R testthat/test_filterVcf.R testthat/test_findFocal.R testthat/test_getSexFromCoverage.R testthat/test_getSexFromVcf.R testthat/test_plotAbs.R testthat/test_poolCoverage.R testthat/test_predictSomatic.R testthat/test_preprocessIntervals.R testthat/test_readAllelicCountsFile.R testthat/test_readCoverageFile.R testthat/test_readLogRatioFile.R testthat/test_readSegmentationFile.R testthat/test_runAbsoluteCN.R testthat/test_segmentation.R testthat/test_setMappingBiasVcf.R testthat/test_setPriorVcf.R 1318s + rm -f testthat/test_setMappingBiasVcf.R 1318s + rm -f testthat/test_processMultipleSamples.R 1318s + grep -Rl TxDb.Hsapiens.UCSC.hg19.knownGene testthat testthat.R 1318s + rm -f testthat/test_annotateTargets.R 1318s + FAILINGTESTS=test_runAbsoluteCN.R test_calculatePowerDetectSomatic.R test_callAmplificationsInLowPurity.R test_callMutationBurden.R test_correctCoverageBias.R test_createCurationFile.R test_createNormalDatabase.R test_getSexFromVcf.R test_plotAbs.R test_poolCoverage.R test_readLogRatioFile.R test_preprocessIntervals.R 1318s + rm -f testthat/test_runAbsoluteCN.R 1318s + rm -f testthat/test_calculatePowerDetectSomatic.R 1318s + rm -f testthat/test_callAmplificationsInLowPurity.R 1318s + rm -f testthat/test_callMutationBurden.R 1318s + rm -f testthat/test_correctCoverageBias.R 1318s + rm -f testthat/test_createCurationFile.R 1318s + rm -f testthat/test_createNormalDatabase.R 1318s + rm -f testthat/test_getSexFromVcf.R 1318s + rm -f testthat/test_plotAbs.R 1318s + rm -f testthat/test_poolCoverage.R 1318s + rm -f testthat/test_readLogRatioFile.R 1318s + rm -f testthat/test_preprocessIntervals.R 1318s + BEGIN TEST testthat.R 1318s ln -s /usr/lib/R/site-library/PureCN/extdata 1318s + echo BEGIN TEST testthat.R 1318s + LC_ALL=C.UTF-8 R --no-save 1318s 1318s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1318s Copyright (C) 2025 The R Foundation for Statistical Computing 1318s Platform: aarch64-unknown-linux-gnu 1318s 1318s R is free software and comes with ABSOLUTELY NO WARRANTY. 1318s You are welcome to redistribute it under certain conditions. 1318s Type 'license()' or 'licence()' for distribution details. 1318s 1318s R is a collaborative project with many contributors. 1318s Type 'contributors()' for more information and 1318s 'citation()' on how to cite R or R packages in publications. 1318s 1318s Type 'demo()' for some demos, 'help()' for on-line help, or 1318s 'help.start()' for an HTML browser interface to help. 1318s Type 'q()' to quit R. 1318s 1318s > library(testthat) 1318s > library(PureCN) 1318s Loading required package: DNAcopy 1318s Loading required package: VariantAnnotation 1318s Loading required package: BiocGenerics 1318s 1318s Attaching package: ‘BiocGenerics’ 1318s 1318s The following objects are masked from ‘package:stats’: 1318s 1318s IQR, mad, sd, var, xtabs 1318s 1318s The following objects are masked from ‘package:base’: 1318s 1318s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 1318s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 1318s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 1318s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 1318s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 1318s table, tapply, union, unique, unsplit, which.max, which.min 1318s 1318s Loading required package: MatrixGenerics 1318s Loading required package: matrixStats 1318s 1318s Attaching package: ‘MatrixGenerics’ 1318s 1318s The following objects are masked from ‘package:matrixStats’: 1318s 1318s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 1318s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 1318s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 1318s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 1318s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 1318s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 1318s colWeightedMeans, colWeightedMedians, colWeightedSds, 1318s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 1318s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 1318s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 1318s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 1318s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 1318s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 1318s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 1318s rowWeightedSds, rowWeightedVars 1318s 1318s Loading required package: GenomeInfoDb 1318s Loading required package: S4Vectors 1318s Loading required package: stats4 1319s 1319s Attaching package: ‘S4Vectors’ 1319s 1319s The following object is masked from ‘package:utils’: 1319s 1319s findMatches 1319s 1319s The following objects are masked from ‘package:base’: 1319s 1319s expand.grid, I, unname 1319s 1319s Loading required package: IRanges 1320s Loading required package: GenomicRanges 1320s Loading required package: SummarizedExperiment 1320s Loading required package: Biobase 1321s Welcome to Bioconductor 1321s 1321s Vignettes contain introductory material; view with 1321s 'browseVignettes()'. To cite Bioconductor, see 1321s 'citation("Biobase")', and for packages 'citation("pkgname")'. 1321s 1321s 1321s Attaching package: ‘Biobase’ 1321s 1321s The following object is masked from ‘package:MatrixGenerics’: 1321s 1321s rowMedians 1321s 1321s The following objects are masked from ‘package:matrixStats’: 1321s 1321s anyMissing, rowMedians 1321s 1323s Loading required package: Rsamtools 1323s Loading required package: Biostrings 1323s Loading required package: XVector 1324s 1324s Attaching package: ‘Biostrings’ 1324s 1324s The following object is masked from ‘package:base’: 1324s 1324s strsplit 1324s 1328s 1328s Attaching package: ‘VariantAnnotation’ 1328s 1328s The following object is masked from ‘package:base’: 1328s 1328s tabulate 1328s 1329s > 1329s > test_check("PureCN") 1332s FATAL [2026-02-09 23:43:42] tumor.coverage.file and interval.file do not align. 1332s 1332s FATAL [2026-02-09 23:43:42] 1332s 1332s FATAL [2026-02-09 23:43:42] This is most likely a user error due to invalid input data or 1332s 1332s FATAL [2026-02-09 23:43:42] parameters (PureCN 2.12.0). 1332s 1332s WARN [2026-02-09 23:43:42] Cannot find all contig lengths while exporting interval file. 1333s INFO [2026-02-09 23:43:43] Processing seq1:1-21 (1/3)... 1334s INFO [2026-02-09 23:43:44] Processing seq1:1227-1247 (2/3)... 1334s INFO [2026-02-09 23:43:44] Processing seq2:594-614 (3/3)... 1335s WARN [2026-02-09 23:43:45] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 1339s INFO [2026-02-09 23:43:49] ------------------------------------------------------------ 1339s INFO [2026-02-09 23:43:49] PureCN 2.12.0 1339s INFO [2026-02-09 23:43:49] ------------------------------------------------------------ 1339s INFO [2026-02-09 23:43:49] Loading coverage files... 1339s INFO [2026-02-09 23:43:49] Mean target coverages: 112X (tumor) 99X (normal). 1339s WARN [2026-02-09 23:43:49] Allosome coverage missing, cannot determine sex. 1339s WARN [2026-02-09 23:43:49] Allosome coverage missing, cannot determine sex. 1339s INFO [2026-02-09 23:43:49] Removing 228 intervals with missing log.ratio. 1339s INFO [2026-02-09 23:43:49] Removing 22 small (< 5bp) intervals. 1339s INFO [2026-02-09 23:43:49] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 1339s WARN [2026-02-09 23:43:49] No normalDB provided. Provide one for better results. 1339s INFO [2026-02-09 23:43:49] Removing 1724 low count (< 100 total reads) intervals. 1339s INFO [2026-02-09 23:43:49] Removing 6 low coverage (< 15.0000X) intervals. 1339s INFO [2026-02-09 23:43:49] Using 8050 intervals (8050 on-target, 0 off-target). 1339s INFO [2026-02-09 23:43:49] No off-target intervals. If this is hybrid-capture data, consider adding them. 1339s INFO [2026-02-09 23:43:50] No interval.file provided. Cannot check for any GC-biases. 1339s INFO [2026-02-09 23:43:50] Loading VCF... 1339s INFO [2026-02-09 23:43:50] Found 127 variants in VCF file. 1339s INFO [2026-02-09 23:43:50] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1340s INFO [2026-02-09 23:43:50] LIB-02240e4 is tumor in VCF file. 1340s INFO [2026-02-09 23:43:50] No homozygous variants in VCF, provide unfiltered VCF. 1340s INFO [2026-02-09 23:43:50] Removing 1 non heterozygous (in matched normal) germline SNPs. 1340s INFO [2026-02-09 23:43:50] Removing 0 low quality variants with non-offset BQ < 25. 1340s INFO [2026-02-09 23:43:50] Base quality scores range from 29 to 35 (offset by 1) 1340s INFO [2026-02-09 23:43:50] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 1340s INFO [2026-02-09 23:43:50] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1340s INFO [2026-02-09 23:43:50] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 1341s INFO [2026-02-09 23:43:51] 1.2% of targets contain variants. 1341s INFO [2026-02-09 23:43:51] Removing 4 variants outside intervals. 1341s INFO [2026-02-09 23:43:51] Found SOMATIC annotation in VCF. 1341s INFO [2026-02-09 23:43:51] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1341s INFO [2026-02-09 23:43:51] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 1341s INFO [2026-02-09 23:43:51] Excluding 0 novel or poor quality variants from segmentation. 1341s INFO [2026-02-09 23:43:51] Sample sex: ? 1341s INFO [2026-02-09 23:43:51] Segmenting data... 1341s INFO [2026-02-09 23:43:51] Loading pre-computed boundaries for DNAcopy... 1341s INFO [2026-02-09 23:43:51] Setting undo.SD parameter to 1.000000. 1342s INFO [2026-02-09 23:43:52] Setting prune.hclust.h parameter to 0.200000. 1342s INFO [2026-02-09 23:43:52] Found 59 segments with median size of 17.67Mb. 1342s INFO [2026-02-09 23:43:52] Using 121 variants. 1342s INFO [2026-02-09 23:43:52] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 1342s INFO [2026-02-09 23:43:52] 2D-grid search of purity and ploidy... 1343s INFO [2026-02-09 23:43:53] Local optima: 0.63/1.9, 0.5/2 1343s INFO [2026-02-09 23:43:53] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... 1344s INFO [2026-02-09 23:43:54] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... 1345s INFO [2026-02-09 23:43:55] Skipping 1 solutions that converged to the same optima. 1345s INFO [2026-02-09 23:43:55] Fitting variants with beta model for local optimum 1/2... 1345s INFO [2026-02-09 23:43:55] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 1348s INFO [2026-02-09 23:43:58] Optimized purity: 0.65 1348s INFO [2026-02-09 23:43:58] Done. 1348s INFO [2026-02-09 23:43:58] ------------------------------------------------------------ 1349s INFO [2026-02-09 23:43:59] Removing 22 non heterozygous (in matched normal) germline SNPs. 1349s INFO [2026-02-09 23:43:59] Removing 19 low quality variants with non-offset BQ < 25. 1349s INFO [2026-02-09 23:43:59] Base quality scores range from 24 to 35 (offset by 1) 1349s INFO [2026-02-09 23:43:59] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1349s INFO [2026-02-09 23:43:59] Initial testing for significant sample cross-contamination: unlikely 1349s INFO [2026-02-09 23:43:59] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1349s INFO [2026-02-09 23:43:59] Removing 22 non heterozygous (in matched normal) germline SNPs. 1349s INFO [2026-02-09 23:43:59] Removing 19 low quality variants with non-offset BQ < 25. 1349s INFO [2026-02-09 23:43:59] Base quality scores range from 24 to 35 (offset by 1) 1349s INFO [2026-02-09 23:44:00] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1350s INFO [2026-02-09 23:44:00] Initial testing for significant sample cross-contamination: unlikely 1350s INFO [2026-02-09 23:44:00] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1350s INFO [2026-02-09 23:44:00] Removing 6 blacklisted variants. 1350s INFO [2026-02-09 23:44:00] Removing 22 non heterozygous (in matched normal) germline SNPs. 1350s INFO [2026-02-09 23:44:00] Removing 19 low quality variants with non-offset BQ < 25. 1350s INFO [2026-02-09 23:44:00] Base quality scores range from 24 to 35 (offset by 1) 1350s INFO [2026-02-09 23:44:00] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1351s INFO [2026-02-09 23:44:01] Initial testing for significant sample cross-contamination: unlikely 1351s INFO [2026-02-09 23:44:01] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1351s WARN [2026-02-09 23:44:01] MuTect stats file lacks contig and position columns. 1351s INFO [2026-02-09 23:44:01] Removing 22 non heterozygous (in matched normal) germline SNPs. 1351s INFO [2026-02-09 23:44:01] Removing 19 low quality variants with non-offset BQ < 25. 1351s INFO [2026-02-09 23:44:01] Base quality scores range from 24 to 35 (offset by 1) 1351s INFO [2026-02-09 23:44:01] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1351s INFO [2026-02-09 23:44:02] Initial testing for significant sample cross-contamination: unlikely 1352s INFO [2026-02-09 23:44:02] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1352s WARN [2026-02-09 23:44:02] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. 1352s WARN [2026-02-09 23:44:02] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. 1352s INFO [2026-02-09 23:44:02] Removing 0 non heterozygous (in matched normal) germline SNPs. 1352s INFO [2026-02-09 23:44:02] Removing 0 low quality variants with non-offset BQ < 25. 1352s INFO [2026-02-09 23:44:02] Base quality scores range from 31 to 33 (offset by 1) 1352s INFO [2026-02-09 23:44:02] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. 1352s INFO [2026-02-09 23:44:02] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1352s INFO [2026-02-09 23:44:02] Removing 22 non heterozygous (in matched normal) germline SNPs. 1352s INFO [2026-02-09 23:44:02] Base quality scores range from 7 to 35 (offset by 1) 1352s INFO [2026-02-09 23:44:02] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 1353s INFO [2026-02-09 23:44:03] Initial testing for significant sample cross-contamination: unlikely 1353s INFO [2026-02-09 23:44:03] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1353s INFO [2026-02-09 23:44:03] Removing 22 non heterozygous (in matched normal) germline SNPs. 1353s INFO [2026-02-09 23:44:03] Base quality scores range from 7 to 35 (offset by 1) 1353s INFO [2026-02-09 23:44:03] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 1353s INFO [2026-02-09 23:44:04] Initial testing for significant sample cross-contamination: unlikely 1353s INFO [2026-02-09 23:44:04] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1354s INFO [2026-02-09 23:44:04] Removing 22 non heterozygous (in matched normal) germline SNPs. 1354s WARN [2026-02-09 23:44:04] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. 1354s FATAL [2026-02-09 23:44:04] No variants passed filter BQ. 1354s 1354s FATAL [2026-02-09 23:44:04] 1354s 1354s FATAL [2026-02-09 23:44:04] This is most likely a user error due to invalid input data or 1354s 1354s FATAL [2026-02-09 23:44:04] parameters (PureCN 2.12.0). 1354s 1354s INFO [2026-02-09 23:44:04] Found 11 variants in VCF file. 1354s WARN [2026-02-09 23:44:04] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 1354s INFO [2026-02-09 23:44:04] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1356s INFO [2026-02-09 23:44:06] Found 11 variants in VCF file. 1356s WARN [2026-02-09 23:44:06] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 1356s INFO [2026-02-09 23:44:06] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1357s INFO [2026-02-09 23:44:07] Found 11 variants in VCF file. 1357s WARN [2026-02-09 23:44:07] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. 1357s INFO [2026-02-09 23:44:07] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1357s INFO [2026-02-09 23:44:08] Found 1000 variants in VCF file. 1357s INFO [2026-02-09 23:44:08] Removing 2 triallelic sites. 1357s WARN [2026-02-09 23:44:08] Having trouble guessing SOMATIC status... 1358s WARN [2026-02-09 23:44:08] DP FORMAT field contains NAs. Removing 44 variants. 1358s INFO [2026-02-09 23:44:08] 954 (100.0%) variants annotated as likely germline (DB INFO flag). 1359s INFO [2026-02-09 23:44:09] Found 12 variants in VCF file. 1359s INFO [2026-02-09 23:44:09] Removing 1 triallelic sites. 1359s WARN [2026-02-09 23:44:09] DP FORMAT field contains NAs. Removing 1 variants. 1359s WARN [2026-02-09 23:44:09] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. 1359s INFO [2026-02-09 23:44:10] 8 (80.0%) variants annotated as likely germline (DB INFO flag). 1360s WARN [2026-02-09 23:44:10] BQ FORMAT field contains NAs. 1360s INFO [2026-02-09 23:44:10] Found 2331 variants in VCF file. 1360s INFO [2026-02-09 23:44:10] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1361s INFO [2026-02-09 23:44:11] Found 2331 variants in VCF file. 1361s INFO [2026-02-09 23:44:11] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1361s WARN [2026-02-09 23:44:11] Did not find base quality scores, will use global error rate of 0.0010 instead. 1361s INFO [2026-02-09 23:44:11] Removing 21 low quality variants with non-offset BQ < 25. 1361s INFO [2026-02-09 23:44:11] Base quality scores range from 24 to 35 (offset by 1) 1361s INFO [2026-02-09 23:44:11] Initial testing for significant sample cross-contamination: unlikely 1361s INFO [2026-02-09 23:44:11] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. 1361s INFO [2026-02-09 23:44:12] Found 2331 variants in VCF file. 1361s INFO [2026-02-09 23:44:12] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1362s WARN [2026-02-09 23:44:12] BQ FORMAT field contains NAs. 1363s WARN [2026-02-09 23:44:13] Allosome coverage missing, cannot determine sex. 1364s WARN [2026-02-09 23:44:14] Allosome coverage missing, cannot determine sex. 1364s INFO [2026-02-09 23:44:14] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. 1364s INFO [2026-02-09 23:44:14] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. 1364s INFO [2026-02-09 23:44:14] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. 1365s INFO [2026-02-09 23:44:15] Found 20 variants in VCF file. 1365s INFO [2026-02-09 23:44:15] 20 (100.0%) variants annotated as likely germline (DB INFO flag). 1365s WARN [2026-02-09 23:44:15] Did not find base quality scores, will use global error rate of 0.0010 instead. 1366s INFO [2026-02-09 23:44:16] Found 127 variants in VCF file. 1366s INFO [2026-02-09 23:44:16] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1366s WARN [2026-02-09 23:44:17] Did not find base quality scores, will use global error rate of 0.0010 instead. 1366s INFO [2026-02-09 23:44:17] ------------------------------------------------------------ 1366s INFO [2026-02-09 23:44:17] PureCN 2.12.0 1367s INFO [2026-02-09 23:44:17] ------------------------------------------------------------ 1367s INFO [2026-02-09 23:44:17] Loading coverage files... 1367s INFO [2026-02-09 23:44:17] Mean target coverages: 112X (tumor) 99X (normal). 1367s WARN [2026-02-09 23:44:17] Allosome coverage missing, cannot determine sex. 1367s WARN [2026-02-09 23:44:17] Allosome coverage missing, cannot determine sex. 1367s INFO [2026-02-09 23:44:17] Removing 228 intervals with missing log.ratio. 1367s INFO [2026-02-09 23:44:17] Removing 22 small (< 5bp) intervals. 1367s INFO [2026-02-09 23:44:17] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 1367s WARN [2026-02-09 23:44:17] No normalDB provided. Provide one for better results. 1367s INFO [2026-02-09 23:44:17] Removing 1724 low count (< 100 total reads) intervals. 1367s INFO [2026-02-09 23:44:17] Removing 6 low coverage (< 15.0000X) intervals. 1367s INFO [2026-02-09 23:44:17] Using 8050 intervals (8050 on-target, 0 off-target). 1367s INFO [2026-02-09 23:44:17] No off-target intervals. If this is hybrid-capture data, consider adding them. 1367s INFO [2026-02-09 23:44:17] No interval.file provided. Cannot check for any GC-biases. 1367s INFO [2026-02-09 23:44:17] Loading VCF... 1367s INFO [2026-02-09 23:44:18] Found 127 variants in VCF file. 1367s INFO [2026-02-09 23:44:18] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1368s INFO [2026-02-09 23:44:18] LIB-02240e4 is tumor in VCF file. 1368s INFO [2026-02-09 23:44:18] No homozygous variants in VCF, provide unfiltered VCF. 1368s INFO [2026-02-09 23:44:18] Removing 1 non heterozygous (in matched normal) germline SNPs. 1368s INFO [2026-02-09 23:44:18] Removing 0 low quality variants with non-offset BQ < 25. 1368s INFO [2026-02-09 23:44:18] Base quality scores range from 29 to 35 (offset by 1) 1368s INFO [2026-02-09 23:44:18] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 1368s INFO [2026-02-09 23:44:18] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1368s INFO [2026-02-09 23:44:18] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 1368s INFO [2026-02-09 23:44:19] 1.2% of targets contain variants. 1368s INFO [2026-02-09 23:44:19] Removing 4 variants outside intervals. 1368s INFO [2026-02-09 23:44:19] Found SOMATIC annotation in VCF. 1368s INFO [2026-02-09 23:44:19] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1369s INFO [2026-02-09 23:44:19] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 1369s INFO [2026-02-09 23:44:19] Excluding 0 novel or poor quality variants from segmentation. 1369s INFO [2026-02-09 23:44:19] Sample sex: ? 1369s INFO [2026-02-09 23:44:19] Segmenting data... 1369s INFO [2026-02-09 23:44:19] Loading pre-computed boundaries for DNAcopy... 1369s INFO [2026-02-09 23:44:19] Setting undo.SD parameter to 1.000000. 1369s INFO [2026-02-09 23:44:20] Setting prune.hclust.h parameter to 0.200000. 1370s INFO [2026-02-09 23:44:20] Found 59 segments with median size of 17.67Mb. 1370s INFO [2026-02-09 23:44:20] Using 121 variants. 1370s INFO [2026-02-09 23:44:20] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 1370s INFO [2026-02-09 23:44:20] 2D-grid search of purity and ploidy... 1370s INFO [2026-02-09 23:44:20] Local optima: 0.65/1.8, 0.52/2 1370s INFO [2026-02-09 23:44:20] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... 1371s INFO [2026-02-09 23:44:21] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... 1372s INFO [2026-02-09 23:44:22] Skipping 1 solutions that converged to the same optima. 1372s INFO [2026-02-09 23:44:22] Fitting variants with beta model for local optimum 1/2... 1372s INFO [2026-02-09 23:44:22] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 1375s INFO [2026-02-09 23:44:25] Optimized purity: 0.65 1375s INFO [2026-02-09 23:44:25] Done. 1375s INFO [2026-02-09 23:44:25] ------------------------------------------------------------ 1376s INFO [2026-02-09 23:44:26] Loaded provided segmentation file example_seg.txt (format DNAcopy). 1376s INFO [2026-02-09 23:44:26] Re-centering provided segment means (offset -0.0033). 1376s INFO [2026-02-09 23:44:26] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). 1376s WARN [2026-02-09 23:44:26] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. 1376s INFO [2026-02-09 23:44:26] Re-centering provided segment means (offset -0.0037). 1381s sh: 1: gatk: not found 1381s WARN [2026-02-09 23:44:31] Cannot find gatk binary in path. 1381s INFO [2026-02-09 23:44:31] ------------------------------------------------------------ 1381s INFO [2026-02-09 23:44:31] PureCN 2.12.0 1381s INFO [2026-02-09 23:44:31] ------------------------------------------------------------ 1381s INFO [2026-02-09 23:44:31] Loading coverage files... 1381s INFO [2026-02-09 23:44:31] Mean target coverages: 109X (tumor) 102X (normal). 1381s WARN [2026-02-09 23:44:32] Allosome coverage missing, cannot determine sex. 1381s WARN [2026-02-09 23:44:32] Allosome coverage missing, cannot determine sex. 1381s INFO [2026-02-09 23:44:32] Removing 9 intervals with missing log.ratio. 1381s INFO [2026-02-09 23:44:32] Removing 1 small (< 5bp) intervals. 1381s INFO [2026-02-09 23:44:32] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 1381s WARN [2026-02-09 23:44:32] No normalDB provided. Provide one for better results. 1381s INFO [2026-02-09 23:44:32] Removing 73 low count (< 100 total reads) intervals. 1381s INFO [2026-02-09 23:44:32] Removing 1 low coverage (< 15.0000X) intervals. 1381s INFO [2026-02-09 23:44:32] Using 411 intervals (411 on-target, 0 off-target). 1381s INFO [2026-02-09 23:44:32] No off-target intervals. If this is hybrid-capture data, consider adding them. 1381s INFO [2026-02-09 23:44:32] No interval.file provided. Cannot check for any GC-biases. 1381s INFO [2026-02-09 23:44:32] Sample sex: ? 1381s INFO [2026-02-09 23:44:32] Segmenting data... 1381s FATAL [2026-02-09 23:44:32] segmentationHclust requires an input segmentation. 1381s 1381s FATAL [2026-02-09 23:44:32] 1381s 1381s FATAL [2026-02-09 23:44:32] This is most likely a user error due to invalid input data or 1381s 1381s FATAL [2026-02-09 23:44:32] parameters (PureCN 2.12.0). 1381s 1382s INFO [2026-02-09 23:44:32] Loaded provided segmentation file example_seg.txt (format DNAcopy). 1382s INFO [2026-02-09 23:44:32] Re-centering provided segment means (offset -0.0033). 1382s INFO [2026-02-09 23:44:32] ------------------------------------------------------------ 1382s INFO [2026-02-09 23:44:32] PureCN 2.12.0 1382s INFO [2026-02-09 23:44:32] ------------------------------------------------------------ 1382s INFO [2026-02-09 23:44:32] Loading coverage files... 1382s INFO [2026-02-09 23:44:32] Mean target coverages: 109X (tumor) 102X (normal). 1382s WARN [2026-02-09 23:44:32] Allosome coverage missing, cannot determine sex. 1382s WARN [2026-02-09 23:44:32] Allosome coverage missing, cannot determine sex. 1382s INFO [2026-02-09 23:44:32] Removing 9 intervals with missing log.ratio. 1382s INFO [2026-02-09 23:44:32] Removing 1 small (< 5bp) intervals. 1382s INFO [2026-02-09 23:44:32] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 1382s WARN [2026-02-09 23:44:32] No normalDB provided. Provide one for better results. 1382s INFO [2026-02-09 23:44:32] Removing 73 low count (< 100 total reads) intervals. 1382s INFO [2026-02-09 23:44:32] Removing 1 low coverage (< 15.0000X) intervals. 1382s INFO [2026-02-09 23:44:32] Using 411 intervals (411 on-target, 0 off-target). 1382s INFO [2026-02-09 23:44:32] No off-target intervals. If this is hybrid-capture data, consider adding them. 1382s INFO [2026-02-09 23:44:32] No interval.file provided. Cannot check for any GC-biases. 1382s INFO [2026-02-09 23:44:32] Sample sex: ? 1382s INFO [2026-02-09 23:44:32] Segmenting data... 1383s INFO [2026-02-09 23:44:33] Found SOMATIC annotation in VCF. 1383s INFO [2026-02-09 23:44:33] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1383s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 1383s 1383s ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ 1383s • gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4' 1383s 1383s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 1383s > 1383s + cd .. 1383s + find tests+ wc -l 1383s -type f -iname *.R 1383s + NBTEST=18 1383s + [ 18 -gt 0 ] 1383s + echo Test: Run tests for PureCN 1383s + cd tests 1383s + echo Start: testthat.R 1383s + R --no-save 1383s Test: Run tests for PureCN 1383s Start: testthat.R 1383s 1383s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1383s Copyright (C) 2025 The R Foundation for Statistical Computing 1383s Platform: aarch64-unknown-linux-gnu 1383s 1383s R is free software and comes with ABSOLUTELY NO WARRANTY. 1383s You are welcome to redistribute it under certain conditions. 1383s Type 'license()' or 'licence()' for distribution details. 1383s 1383s R is a collaborative project with many contributors. 1383s Type 'contributors()' for more information and 1383s 'citation()' on how to cite R or R packages in publications. 1383s 1383s Type 'demo()' for some demos, 'help()' for on-line help, or 1383s 'help.start()' for an HTML browser interface to help. 1383s Type 'q()' to quit R. 1383s 1383s > library(testthat) 1383s > library(PureCN) 1383s Loading required package: DNAcopy 1383s Loading required package: VariantAnnotation 1383s Loading required package: BiocGenerics 1383s 1383s Attaching package: ‘BiocGenerics’ 1383s 1383s The following objects are masked from ‘package:stats’: 1383s 1383s IQR, mad, sd, var, xtabs 1383s 1383s The following objects are masked from ‘package:base’: 1383s 1383s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 1383s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 1383s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 1383s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 1383s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 1383s table, tapply, union, unique, unsplit, which.max, which.min 1383s 1383s Loading required package: MatrixGenerics 1383s Loading required package: matrixStats 1383s 1383s Attaching package: ‘MatrixGenerics’ 1383s 1383s The following objects are masked from ‘package:matrixStats’: 1383s 1383s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 1383s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 1383s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 1383s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 1383s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 1383s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 1383s colWeightedMeans, colWeightedMedians, colWeightedSds, 1383s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 1383s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 1383s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 1383s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 1383s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 1383s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 1383s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 1383s rowWeightedSds, rowWeightedVars 1383s 1383s Loading required package: GenomeInfoDb 1383s Loading required package: S4Vectors 1383s Loading required package: stats4 1384s 1384s Attaching package: ‘S4Vectors’ 1384s 1384s The following object is masked from ‘package:utils’: 1384s 1384s findMatches 1384s 1384s The following objects are masked from ‘package:base’: 1384s 1384s expand.grid, I, unname 1384s 1384s Loading required package: IRanges 1385s Loading required package: GenomicRanges 1385s Loading required package: SummarizedExperiment 1385s Loading required package: Biobase 1386s Welcome to Bioconductor 1386s 1386s Vignettes contain introductory material; view with 1386s 'browseVignettes()'. To cite Bioconductor, see 1386s 'citation("Biobase")', and for packages 'citation("pkgname")'. 1386s 1386s 1386s Attaching package: ‘Biobase’ 1386s 1386s The following object is masked from ‘package:MatrixGenerics’: 1386s 1386s rowMedians 1386s 1386s The following objects are masked from ‘package:matrixStats’: 1386s 1386s anyMissing, rowMedians 1386s 1388s Loading required package: Rsamtools 1388s Loading required package: Biostrings 1388s Loading required package: XVector 1389s 1389s Attaching package: ‘Biostrings’ 1389s 1389s The following object is masked from ‘package:base’: 1389s 1389s strsplit 1389s 1393s 1393s Attaching package: ‘VariantAnnotation’ 1393s 1393s The following object is masked from ‘package:base’: 1393s 1393s tabulate 1393s 1395s > 1395s > test_check("PureCN") 1398s FATAL [2026-02-09 23:44:48] tumor.coverage.file and interval.file do not align. 1398s 1398s FATAL [2026-02-09 23:44:48] 1398s 1398s FATAL [2026-02-09 23:44:48] This is most likely a user error due to invalid input data or 1398s 1398s FATAL [2026-02-09 23:44:48] parameters (PureCN 2.12.0). 1398s 1398s WARN [2026-02-09 23:44:48] Cannot find all contig lengths while exporting interval file. 1399s INFO [2026-02-09 23:44:49] Processing seq1:1-21 (1/3)... 1400s INFO [2026-02-09 23:44:50] Processing seq1:1227-1247 (2/3)... 1400s INFO [2026-02-09 23:44:50] Processing seq2:594-614 (3/3)... 1401s WARN [2026-02-09 23:44:51] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 1405s INFO [2026-02-09 23:44:55] ------------------------------------------------------------ 1405s INFO [2026-02-09 23:44:55] PureCN 2.12.0 1405s INFO [2026-02-09 23:44:55] ------------------------------------------------------------ 1405s INFO [2026-02-09 23:44:55] Loading coverage files... 1405s INFO [2026-02-09 23:44:55] Mean target coverages: 112X (tumor) 99X (normal). 1405s WARN [2026-02-09 23:44:55] Allosome coverage missing, cannot determine sex. 1405s WARN [2026-02-09 23:44:55] Allosome coverage missing, cannot determine sex. 1405s INFO [2026-02-09 23:44:56] Removing 228 intervals with missing log.ratio. 1405s INFO [2026-02-09 23:44:56] Removing 22 small (< 5bp) intervals. 1405s INFO [2026-02-09 23:44:56] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 1405s WARN [2026-02-09 23:44:56] No normalDB provided. Provide one for better results. 1405s INFO [2026-02-09 23:44:56] Removing 1724 low count (< 100 total reads) intervals. 1405s INFO [2026-02-09 23:44:56] Removing 6 low coverage (< 15.0000X) intervals. 1405s INFO [2026-02-09 23:44:56] Using 8050 intervals (8050 on-target, 0 off-target). 1405s INFO [2026-02-09 23:44:56] No off-target intervals. If this is hybrid-capture data, consider adding them. 1405s INFO [2026-02-09 23:44:56] No interval.file provided. Cannot check for any GC-biases. 1405s INFO [2026-02-09 23:44:56] Loading VCF... 1405s INFO [2026-02-09 23:44:56] Found 127 variants in VCF file. 1406s INFO [2026-02-09 23:44:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1406s INFO [2026-02-09 23:44:56] LIB-02240e4 is tumor in VCF file. 1406s INFO [2026-02-09 23:44:56] No homozygous variants in VCF, provide unfiltered VCF. 1406s INFO [2026-02-09 23:44:56] Removing 1 non heterozygous (in matched normal) germline SNPs. 1406s INFO [2026-02-09 23:44:56] Removing 0 low quality variants with non-offset BQ < 25. 1406s INFO [2026-02-09 23:44:56] Base quality scores range from 29 to 35 (offset by 1) 1406s INFO [2026-02-09 23:44:56] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 1406s INFO [2026-02-09 23:44:57] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1406s INFO [2026-02-09 23:44:57] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 1407s INFO [2026-02-09 23:44:57] 1.2% of targets contain variants. 1407s INFO [2026-02-09 23:44:57] Removing 4 variants outside intervals. 1407s INFO [2026-02-09 23:44:57] Found SOMATIC annotation in VCF. 1407s INFO [2026-02-09 23:44:57] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1407s INFO [2026-02-09 23:44:57] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 1407s INFO [2026-02-09 23:44:57] Excluding 0 novel or poor quality variants from segmentation. 1407s INFO [2026-02-09 23:44:57] Sample sex: ? 1407s INFO [2026-02-09 23:44:57] Segmenting data... 1407s INFO [2026-02-09 23:44:57] Loading pre-computed boundaries for DNAcopy... 1407s INFO [2026-02-09 23:44:57] Setting undo.SD parameter to 1.000000. 1408s INFO [2026-02-09 23:44:58] Setting prune.hclust.h parameter to 0.200000. 1408s INFO [2026-02-09 23:44:58] Found 59 segments with median size of 17.67Mb. 1408s INFO [2026-02-09 23:44:58] Using 121 variants. 1408s INFO [2026-02-09 23:44:58] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 1408s INFO [2026-02-09 23:44:58] 2D-grid search of purity and ploidy... 1409s INFO [2026-02-09 23:44:59] Local optima: 0.63/1.9, 0.5/2 1409s INFO [2026-02-09 23:44:59] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... 1410s INFO [2026-02-09 23:45:00] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... 1411s INFO [2026-02-09 23:45:01] Skipping 1 solutions that converged to the same optima. 1411s INFO [2026-02-09 23:45:01] Fitting variants with beta model for local optimum 1/2... 1411s INFO [2026-02-09 23:45:01] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 1414s INFO [2026-02-09 23:45:04] Optimized purity: 0.65 1414s INFO [2026-02-09 23:45:04] Done. 1414s INFO [2026-02-09 23:45:04] ------------------------------------------------------------ 1415s INFO [2026-02-09 23:45:05] Removing 22 non heterozygous (in matched normal) germline SNPs. 1415s INFO [2026-02-09 23:45:05] Removing 19 low quality variants with non-offset BQ < 25. 1415s INFO [2026-02-09 23:45:05] Base quality scores range from 24 to 35 (offset by 1) 1415s INFO [2026-02-09 23:45:05] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1415s INFO [2026-02-09 23:45:05] Initial testing for significant sample cross-contamination: unlikely 1415s INFO [2026-02-09 23:45:05] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1415s INFO [2026-02-09 23:45:06] Removing 22 non heterozygous (in matched normal) germline SNPs. 1415s INFO [2026-02-09 23:45:06] Removing 19 low quality variants with non-offset BQ < 25. 1415s INFO [2026-02-09 23:45:06] Base quality scores range from 24 to 35 (offset by 1) 1415s INFO [2026-02-09 23:45:06] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1416s INFO [2026-02-09 23:45:06] Initial testing for significant sample cross-contamination: unlikely 1416s INFO [2026-02-09 23:45:06] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1416s INFO [2026-02-09 23:45:06] Removing 6 blacklisted variants. 1416s INFO [2026-02-09 23:45:06] Removing 22 non heterozygous (in matched normal) germline SNPs. 1416s INFO [2026-02-09 23:45:06] Removing 19 low quality variants with non-offset BQ < 25. 1416s INFO [2026-02-09 23:45:06] Base quality scores range from 24 to 35 (offset by 1) 1416s INFO [2026-02-09 23:45:06] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1417s INFO [2026-02-09 23:45:07] Initial testing for significant sample cross-contamination: unlikely 1417s INFO [2026-02-09 23:45:07] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1417s WARN [2026-02-09 23:45:07] MuTect stats file lacks contig and position columns. 1417s INFO [2026-02-09 23:45:07] Removing 22 non heterozygous (in matched normal) germline SNPs. 1417s INFO [2026-02-09 23:45:07] Removing 19 low quality variants with non-offset BQ < 25. 1417s INFO [2026-02-09 23:45:07] Base quality scores range from 24 to 35 (offset by 1) 1417s INFO [2026-02-09 23:45:07] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1417s INFO [2026-02-09 23:45:08] Initial testing for significant sample cross-contamination: unlikely 1418s INFO [2026-02-09 23:45:08] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1418s WARN [2026-02-09 23:45:08] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. 1418s WARN [2026-02-09 23:45:08] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. 1418s INFO [2026-02-09 23:45:08] Removing 0 non heterozygous (in matched normal) germline SNPs. 1418s INFO [2026-02-09 23:45:08] Removing 0 low quality variants with non-offset BQ < 25. 1418s INFO [2026-02-09 23:45:08] Base quality scores range from 31 to 33 (offset by 1) 1418s INFO [2026-02-09 23:45:08] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. 1418s INFO [2026-02-09 23:45:08] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1418s INFO [2026-02-09 23:45:08] Removing 22 non heterozygous (in matched normal) germline SNPs. 1418s INFO [2026-02-09 23:45:08] Base quality scores range from 7 to 35 (offset by 1) 1418s INFO [2026-02-09 23:45:08] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 1419s INFO [2026-02-09 23:45:09] Initial testing for significant sample cross-contamination: unlikely 1419s INFO [2026-02-09 23:45:09] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1419s INFO [2026-02-09 23:45:09] Removing 22 non heterozygous (in matched normal) germline SNPs. 1419s INFO [2026-02-09 23:45:09] Base quality scores range from 7 to 35 (offset by 1) 1419s INFO [2026-02-09 23:45:09] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 1419s INFO [2026-02-09 23:45:10] Initial testing for significant sample cross-contamination: unlikely 1420s INFO [2026-02-09 23:45:10] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1420s INFO [2026-02-09 23:45:10] Removing 22 non heterozygous (in matched normal) germline SNPs. 1420s WARN [2026-02-09 23:45:10] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. 1420s FATAL [2026-02-09 23:45:10] No variants passed filter BQ. 1420s 1420s FATAL [2026-02-09 23:45:10] 1420s 1420s FATAL [2026-02-09 23:45:10] This is most likely a user error due to invalid input data or 1420s 1420s FATAL [2026-02-09 23:45:10] parameters (PureCN 2.12.0). 1420s 1420s INFO [2026-02-09 23:45:10] Found 11 variants in VCF file. 1420s WARN [2026-02-09 23:45:10] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 1420s INFO [2026-02-09 23:45:10] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1422s INFO [2026-02-09 23:45:12] Found 11 variants in VCF file. 1422s WARN [2026-02-09 23:45:12] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 1422s INFO [2026-02-09 23:45:12] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1423s INFO [2026-02-09 23:45:13] Found 11 variants in VCF file. 1423s WARN [2026-02-09 23:45:13] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. 1423s INFO [2026-02-09 23:45:13] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1424s INFO [2026-02-09 23:45:14] Found 1000 variants in VCF file. 1424s INFO [2026-02-09 23:45:14] Removing 2 triallelic sites. 1424s WARN [2026-02-09 23:45:14] Having trouble guessing SOMATIC status... 1424s WARN [2026-02-09 23:45:14] DP FORMAT field contains NAs. Removing 44 variants. 1424s INFO [2026-02-09 23:45:14] 954 (100.0%) variants annotated as likely germline (DB INFO flag). 1425s INFO [2026-02-09 23:45:16] Found 12 variants in VCF file. 1426s INFO [2026-02-09 23:45:16] Removing 1 triallelic sites. 1426s WARN [2026-02-09 23:45:16] DP FORMAT field contains NAs. Removing 1 variants. 1426s WARN [2026-02-09 23:45:16] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. 1426s INFO [2026-02-09 23:45:16] 8 (80.0%) variants annotated as likely germline (DB INFO flag). 1426s WARN [2026-02-09 23:45:16] BQ FORMAT field contains NAs. 1426s INFO [2026-02-09 23:45:16] Found 2331 variants in VCF file. 1426s INFO [2026-02-09 23:45:17] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1427s INFO [2026-02-09 23:45:17] Found 2331 variants in VCF file. 1427s INFO [2026-02-09 23:45:17] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1427s WARN [2026-02-09 23:45:17] Did not find base quality scores, will use global error rate of 0.0010 instead. 1427s INFO [2026-02-09 23:45:17] Removing 21 low quality variants with non-offset BQ < 25. 1427s INFO [2026-02-09 23:45:17] Base quality scores range from 24 to 35 (offset by 1) 1427s INFO [2026-02-09 23:45:18] Initial testing for significant sample cross-contamination: unlikely 1428s INFO [2026-02-09 23:45:18] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. 1428s INFO [2026-02-09 23:45:18] Found 2331 variants in VCF file. 1428s INFO [2026-02-09 23:45:18] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1428s WARN [2026-02-09 23:45:18] BQ FORMAT field contains NAs. 1429s WARN [2026-02-09 23:45:19] Allosome coverage missing, cannot determine sex. 1430s WARN [2026-02-09 23:45:20] Allosome coverage missing, cannot determine sex. 1430s INFO [2026-02-09 23:45:20] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. 1430s INFO [2026-02-09 23:45:20] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. 1430s INFO [2026-02-09 23:45:20] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. 1431s INFO [2026-02-09 23:45:21] Found 20 variants in VCF file. 1431s INFO [2026-02-09 23:45:22] 20 (100.0%) variants annotated as likely germline (DB INFO flag). 1432s WARN [2026-02-09 23:45:22] Did not find base quality scores, will use global error rate of 0.0010 instead. 1432s INFO [2026-02-09 23:45:23] Found 127 variants in VCF file. 1432s INFO [2026-02-09 23:45:23] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1433s WARN [2026-02-09 23:45:23] Did not find base quality scores, will use global error rate of 0.0010 instead. 1433s INFO [2026-02-09 23:45:23] ------------------------------------------------------------ 1433s INFO [2026-02-09 23:45:23] PureCN 2.12.0 1433s INFO [2026-02-09 23:45:23] ------------------------------------------------------------ 1433s INFO [2026-02-09 23:45:23] Loading coverage files... 1433s INFO [2026-02-09 23:45:23] Mean target coverages: 112X (tumor) 99X (normal). 1433s WARN [2026-02-09 23:45:24] Allosome coverage missing, cannot determine sex. 1433s WARN [2026-02-09 23:45:24] Allosome coverage missing, cannot determine sex. 1433s INFO [2026-02-09 23:45:24] Removing 228 intervals with missing log.ratio. 1433s INFO [2026-02-09 23:45:24] Removing 22 small (< 5bp) intervals. 1433s INFO [2026-02-09 23:45:24] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 1433s WARN [2026-02-09 23:45:24] No normalDB provided. Provide one for better results. 1433s INFO [2026-02-09 23:45:24] Removing 1724 low count (< 100 total reads) intervals. 1433s INFO [2026-02-09 23:45:24] Removing 6 low coverage (< 15.0000X) intervals. 1433s INFO [2026-02-09 23:45:24] Using 8050 intervals (8050 on-target, 0 off-target). 1433s INFO [2026-02-09 23:45:24] No off-target intervals. If this is hybrid-capture data, consider adding them. 1434s INFO [2026-02-09 23:45:24] No interval.file provided. Cannot check for any GC-biases. 1434s INFO [2026-02-09 23:45:24] Loading VCF... 1434s INFO [2026-02-09 23:45:24] Found 127 variants in VCF file. 1434s INFO [2026-02-09 23:45:24] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1434s INFO [2026-02-09 23:45:24] LIB-02240e4 is tumor in VCF file. 1434s INFO [2026-02-09 23:45:24] No homozygous variants in VCF, provide unfiltered VCF. 1434s INFO [2026-02-09 23:45:24] Removing 1 non heterozygous (in matched normal) germline SNPs. 1434s INFO [2026-02-09 23:45:24] Removing 0 low quality variants with non-offset BQ < 25. 1434s INFO [2026-02-09 23:45:24] Base quality scores range from 29 to 35 (offset by 1) 1434s INFO [2026-02-09 23:45:24] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 1434s INFO [2026-02-09 23:45:25] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1434s INFO [2026-02-09 23:45:25] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 1435s INFO [2026-02-09 23:45:25] 1.2% of targets contain variants. 1435s INFO [2026-02-09 23:45:25] Removing 4 variants outside intervals. 1435s INFO [2026-02-09 23:45:25] Found SOMATIC annotation in VCF. 1435s INFO [2026-02-09 23:45:25] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1435s INFO [2026-02-09 23:45:25] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 1435s INFO [2026-02-09 23:45:25] Excluding 0 novel or poor quality variants from segmentation. 1435s INFO [2026-02-09 23:45:25] Sample sex: ? 1435s INFO [2026-02-09 23:45:25] Segmenting data... 1435s INFO [2026-02-09 23:45:25] Loading pre-computed boundaries for DNAcopy... 1435s INFO [2026-02-09 23:45:25] Setting undo.SD parameter to 1.000000. 1436s INFO [2026-02-09 23:45:26] Setting prune.hclust.h parameter to 0.200000. 1436s INFO [2026-02-09 23:45:26] Found 59 segments with median size of 17.67Mb. 1436s INFO [2026-02-09 23:45:26] Using 121 variants. 1436s INFO [2026-02-09 23:45:26] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 1436s INFO [2026-02-09 23:45:26] 2D-grid search of purity and ploidy... 1436s INFO [2026-02-09 23:45:26] Local optima: 0.65/1.8, 0.52/2 1436s INFO [2026-02-09 23:45:26] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... 1437s INFO [2026-02-09 23:45:27] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... 1438s INFO [2026-02-09 23:45:28] Skipping 1 solutions that converged to the same optima. 1438s INFO [2026-02-09 23:45:28] Fitting variants with beta model for local optimum 1/2... 1438s INFO [2026-02-09 23:45:28] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 1441s INFO [2026-02-09 23:45:31] Optimized purity: 0.65 1441s INFO [2026-02-09 23:45:31] Done. 1441s INFO [2026-02-09 23:45:31] ------------------------------------------------------------ 1442s INFO [2026-02-09 23:45:32] Loaded provided segmentation file example_seg.txt (format DNAcopy). 1442s INFO [2026-02-09 23:45:32] Re-centering provided segment means (offset -0.0033). 1442s INFO [2026-02-09 23:45:32] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). 1442s WARN [2026-02-09 23:45:32] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. 1442s INFO [2026-02-09 23:45:32] Re-centering provided segment means (offset -0.0037). 1447s sh: 1: gatk: not found 1447s WARN [2026-02-09 23:45:37] Cannot find gatk binary in path. 1447s INFO [2026-02-09 23:45:37] ------------------------------------------------------------ 1447s INFO [2026-02-09 23:45:37] PureCN 2.12.0 1447s INFO [2026-02-09 23:45:37] ------------------------------------------------------------ 1447s INFO [2026-02-09 23:45:37] Loading coverage files... 1447s INFO [2026-02-09 23:45:38] Mean target coverages: 109X (tumor) 102X (normal). 1448s WARN [2026-02-09 23:45:38] Allosome coverage missing, cannot determine sex. 1448s WARN [2026-02-09 23:45:38] Allosome coverage missing, cannot determine sex. 1448s INFO [2026-02-09 23:45:38] Removing 9 intervals with missing log.ratio. 1448s INFO [2026-02-09 23:45:38] Removing 1 small (< 5bp) intervals. 1448s INFO [2026-02-09 23:45:38] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 1448s WARN [2026-02-09 23:45:38] No normalDB provided. Provide one for better results. 1448s INFO [2026-02-09 23:45:38] Removing 73 low count (< 100 total reads) intervals. 1448s INFO [2026-02-09 23:45:38] Removing 1 low coverage (< 15.0000X) intervals. 1448s INFO [2026-02-09 23:45:38] Using 411 intervals (411 on-target, 0 off-target). 1448s INFO [2026-02-09 23:45:38] No off-target intervals. If this is hybrid-capture data, consider adding them. 1448s INFO [2026-02-09 23:45:38] No interval.file provided. Cannot check for any GC-biases. 1448s INFO [2026-02-09 23:45:38] Sample sex: ? 1448s INFO [2026-02-09 23:45:38] Segmenting data... 1448s FATAL [2026-02-09 23:45:38] segmentationHclust requires an input segmentation. 1448s 1448s FATAL [2026-02-09 23:45:38] 1448s 1448s FATAL [2026-02-09 23:45:38] This is most likely a user error due to invalid input data or 1448s 1448s FATAL [2026-02-09 23:45:38] parameters (PureCN 2.12.0). 1448s 1448s INFO [2026-02-09 23:45:38] Loaded provided segmentation file example_seg.txt (format DNAcopy). 1448s INFO [2026-02-09 23:45:38] Re-centering provided segment means (offset -0.0033). 1448s INFO [2026-02-09 23:45:38] ------------------------------------------------------------ 1448s INFO [2026-02-09 23:45:38] PureCN 2.12.0 1448s INFO [2026-02-09 23:45:38] ------------------------------------------------------------ 1448s INFO [2026-02-09 23:45:38] Loading coverage files... 1448s INFO [2026-02-09 23:45:38] Mean target coverages: 109X (tumor) 102X (normal). 1448s WARN [2026-02-09 23:45:38] Allosome coverage missing, cannot determine sex. 1448s WARN [2026-02-09 23:45:38] Allosome coverage missing, cannot determine sex. 1448s INFO [2026-02-09 23:45:38] Removing 9 intervals with missing log.ratio. 1448s INFO [2026-02-09 23:45:38] Removing 1 small (< 5bp) intervals. 1448s INFO [2026-02-09 23:45:38] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 1448s WARN [2026-02-09 23:45:38] No normalDB provided. Provide one for better results. 1448s INFO [2026-02-09 23:45:38] Removing 73 low count (< 100 total reads) intervals. 1448s INFO [2026-02-09 23:45:38] Removing 1 low coverage (< 15.0000X) intervals. 1448s INFO [2026-02-09 23:45:38] Using 411 intervals (411 on-target, 0 off-target). 1448s INFO [2026-02-09 23:45:39] No off-target intervals. If this is hybrid-capture data, consider adding them. 1448s INFO [2026-02-09 23:45:39] No interval.file provided. Cannot check for any GC-biases. 1448s INFO [2026-02-09 23:45:39] Sample sex: ? 1448s INFO [2026-02-09 23:45:39] Segmenting data... 1449s INFO [2026-02-09 23:45:39] Found SOMATIC annotation in VCF. 1449s INFO [2026-02-09 23:45:39] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1449s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 1449s 1449s ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ 1449s • gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4' 1449s 1449s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 1449s > 1449s + exit 0 1449s autopkgtest [23:45:39]: test pkg-r-autopkgtest: -----------------------] 1450s pkg-r-autopkgtest PASS 1450s autopkgtest [23:45:40]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1450s autopkgtest [23:45:40]: @@@@@@@@@@@@@@@@@@@@ summary 1450s pkg-r-autopkgtest PASS