0s autopkgtest [22:59:56]: starting date and time: 2026-02-09 22:59:56+0000 0s autopkgtest [22:59:56]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [22:59:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r0xfx3dw/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-8.secgroup --name adt-resolute-ppc64el-r-bioc-purecn-20260209-225956-juju-7f2275-prod-proposed-migration-environment-2-5dc2a093-8e17-4789-af50-1fe2eba0e08a --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-ppc64el-r-bioc-purecn-20260209-225956-juju-7f2275-prod-proposed-migration-environment-2-5dc2a093-8e17-4789-af50-1fe2eba0e08a from image adt/ubuntu-resolute-ppc64el-server-20260209.img (UUID f7f31435-4cd1-4090-aa55-59cfefa097ca)... 113s autopkgtest [23:01:49]: testbed dpkg architecture: ppc64el 113s autopkgtest [23:01:49]: testbed apt version: 3.1.15 114s autopkgtest [23:01:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 114s autopkgtest [23:01:50]: testbed release detected to be: None 114s autopkgtest [23:01:50]: updating testbed package index (apt update) 115s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 115s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 115s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 115s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 115s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 121s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 121s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 121s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [246 kB] 121s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1534 kB] 125s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [19.4 kB] 126s Fetched 3774 kB in 11s (343 kB/s) 126s Reading package lists... 127s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 127s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 127s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 127s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 128s Reading package lists... 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Calculating upgrade... 129s The following packages will be upgraded: 129s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 129s libip6tc2 libxtables12 wget 129s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Need to get 3125 kB of archives. 129s After this operation, 78.8 kB of additional disk space will be used. 129s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el iptables ppc64el 1.8.11-2ubuntu3 [464 kB] 129s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip4tc2 ppc64el 1.8.11-2ubuntu3 [27.8 kB] 129s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip6tc2 ppc64el 1.8.11-2ubuntu3 [28.2 kB] 129s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxtables12 ppc64el 1.8.11-2ubuntu3 [41.2 kB] 129s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el iproute2 ppc64el 6.18.0-1ubuntu1 [1458 kB] 131s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcryptsetup12 ppc64el 2:2.8.0-1ubuntu3 [404 kB] 131s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el wget ppc64el 1.25.0-2ubuntu4 [401 kB] 131s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cryptsetup-bin ppc64el 2:2.8.0-1ubuntu3 [250 kB] 131s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el dracut-install ppc64el 109-11ubuntu1 [51.3 kB] 132s dpkg-preconfigure: unable to re-open stdin: No such file or directory 132s Fetched 3125 kB in 3s (1243 kB/s) 133s (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 ... 122003 files and directories currently installed.) 133s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_ppc64el.deb ... 133s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 133s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_ppc64el.deb ... 133s Unpacking libip4tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 133s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_ppc64el.deb ... 133s Unpacking libip6tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 133s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_ppc64el.deb ... 133s Unpacking libxtables12:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 133s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_ppc64el.deb ... 134s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 134s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 134s Unpacking libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 134s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_ppc64el.deb ... 134s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 134s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 134s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 134s Preparing to unpack .../8-dracut-install_109-11ubuntu1_ppc64el.deb ... 135s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 135s Setting up libip4tc2:ppc64el (1.8.11-2ubuntu3) ... 135s Setting up wget (1.25.0-2ubuntu4) ... 135s Setting up libip6tc2:ppc64el (1.8.11-2ubuntu3) ... 135s Setting up libxtables12:ppc64el (1.8.11-2ubuntu3) ... 135s Setting up dracut-install (109-11ubuntu1) ... 135s Setting up libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) ... 135s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 135s Setting up iptables (1.8.11-2ubuntu3) ... 135s Setting up iproute2 (6.18.0-1ubuntu1) ... 135s Processing triggers for man-db (2.13.1-1build1) ... 138s Processing triggers for install-info (7.2-5) ... 138s Processing triggers for libc-bin (2.42-2ubuntu4) ... 138s autopkgtest [23:02:14]: upgrading testbed (apt dist-upgrade and autopurge) 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Calculating upgrade... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Solving dependencies... 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s autopkgtest [23:02:17]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:13:51 UTC 2026 141s autopkgtest [23:02:17]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-purecn 152s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-purecn 2.12.0+dfsg-2 (dsc) [2504 B] 152s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-purecn 2.12.0+dfsg-2 (tar) [5496 kB] 152s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-purecn 2.12.0+dfsg-2 (diff) [6696 B] 153s gpgv: Signature made Tue Jan 14 08:02:30 2025 UTC 153s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 153s gpgv: issuer "crusoe@debian.org" 153s gpgv: Can't check signature: No public key 153s dpkg-source: warning: cannot verify inline signature for ./r-bioc-purecn_2.12.0+dfsg-2.dsc: no acceptable signature found 154s autopkgtest [23:02:30]: testing package r-bioc-purecn version 2.12.0+dfsg-2 154s autopkgtest [23:02:30]: build not needed 156s autopkgtest [23:02:32]: test pkg-r-autopkgtest: preparing testbed 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Solving dependencies... 157s The following NEW packages will be installed: 157s build-essential comerr-dev cpp cpp-15 cpp-15-powerpc64le-linux-gnu 157s cpp-powerpc64le-linux-gnu dctrl-tools fontconfig fontconfig-config 157s fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 157s fonts-glyphicons-halflings fonts-lmodern fonts-mathjax g++ g++-15 157s g++-15-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-15 157s gcc-15-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-15 157s gfortran-15-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 157s hdf5-helpers icu-devtools javascript-common krb5-multidev libaec-dev libaec0 157s libasan8 libbibtex-parser-perl libblas-dev libblas3 libblosc1 libboost-dev 157s libboost1.90-dev libbrotli-dev libbz2-dev libc-dev-bin libc6-dev libcairo2 157s libcc1-0 libcrypt-dev libcurl4-openssl-dev libdatrie1 libdeflate-dev 157s libdeflate0 libevent-2.1-7t64 libfontconfig1 libgcc-15-dev 157s libgfortran-15-dev libgfortran5 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 157s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libgraphite2-3 libgssrpc4t64 157s libharfbuzz0b libhdf5-310 libhdf5-cpp-310 libhdf5-dev libhdf5-fortran-310 157s libhdf5-hl-310 libhdf5-hl-cpp-310 libhdf5-hl-fortran-310 libice6 libicu-dev 157s libidn2-dev libio-string-perl libisl23 libitm1 libjbig0 libjpeg-dev 157s libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-bootstrap 157s libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery 157s libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json 157s libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr 157s libjs-popper.js libjs-prettify libjs-sifter.js 157s libjs-twitter-bootstrap-datepicker libkadm5clnt-mit12 libkadm5srv-mit12 157s libkdb5-10t64 libkpathsea6 libkrb5-dev liblapack-dev liblapack3 157s liblatex-tounicode-perl libldap-dev liblerc4 liblsan0 liblua5.4-0 157s liblzma-dev libmpc3 libmpfi0 libncurses-dev libnghttp2-dev libp11-kit-dev 157s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 157s libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 157s libpixman-1-0 libpkgconf3 libpng-dev libpotrace0 libpsl-dev libptexenc1 157s libquadmath0 libreadline-dev librtmp-dev libsharpyuv0 libsm6 libsnappy1v5 157s libssh2-1-dev libssl-dev libstdc++-15-dev libsynctex2 libsz2 libtasn1-6-dev 157s libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 157s libtirpc-dev libtk8.6 libtsan2 libubsan1 libunbound8 libwebp7 libxaw7 157s libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 157s libxss1 libxt6t64 libzstd-dev libzzip-0-13t64 linux-libc-dev nettle-dev 157s node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data 157s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev 157s r-bioc-annotationdbi r-bioc-aroma.light r-bioc-biobase r-bioc-biocgenerics 157s r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion 157s r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-dnacopy 157s r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments 157s r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest 157s r-bioc-matrixgenerics r-bioc-org.hs.eg.db r-bioc-purecn r-bioc-rhdf5 157s r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-rhtslib r-bioc-rsamtools 157s r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray 157s r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation 157s r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-base64enc 157s r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops 157s r-cran-blob r-cran-bookdown r-cran-brio r-cran-bslib r-cran-cachem 157s r-cran-callr r-cran-cli r-cran-codetools r-cran-commonmark r-cran-covr 157s r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi 157s r-cran-desc r-cran-diffobj r-cran-digest r-cran-evaluate r-cran-farver 157s r-cran-fastmap r-cran-fontawesome r-cran-formatr r-cran-fs 157s r-cran-futile.logger r-cran-futile.options r-cran-future r-cran-getopt 157s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gridextra r-cran-gtable 157s r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-isoband 157s r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling 157s r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle 157s r-cran-listenv r-cran-littler r-cran-magrittr r-cran-markdown r-cran-matrix 157s r-cran-matrixstats r-cran-mclust r-cran-memoise r-cran-mime r-cran-openssl 157s r-cran-optparse r-cran-parallelly r-cran-pkgbuild r-cran-pkgconfig 157s r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-png r-cran-praise 157s r-cran-processx r-cran-promises r-cran-ps r-cran-pscbs r-cran-r.cache 157s r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs 157s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rex 157s r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rprojroot r-cran-rsqlite 157s r-cran-s7 r-cran-sass r-cran-scales r-cran-shiny r-cran-snow 157s r-cran-sourcetools r-cran-sys r-cran-testthat r-cran-tinytex r-cran-vctrs 157s r-cran-vgam r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xfun 157s r-cran-xml r-cran-xtable r-cran-yaml rpcsvc-proto t1utils tex-common 157s texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base unzip 157s x11-common xdg-utils zip zlib1g-dev 157s 0 upgraded, 343 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 569 MB of archives. 157s After this operation, 2006 MB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc-dev-bin ppc64el 2.42-2ubuntu4 [23.9 kB] 157s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el linux-libc-dev ppc64el 6.19.0-3.3 [1832 kB] 160s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcrypt-dev ppc64el 1:4.5.1-1 [162 kB] 160s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el rpcsvc-proto ppc64el 1.4.3-1build1 [84.2 kB] 160s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc6-dev ppc64el 2.42-2ubuntu4 [2080 kB] 164s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libisl23 ppc64el 0.27-1build1 [893 kB] 166s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libmpc3 ppc64el 1.3.1-2 [62.5 kB] 166s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [11.4 MB] 186s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15 ppc64el 15.2.0-12ubuntu1 [1038 B] 186s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [5746 B] 186s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp ppc64el 4:15.2.0-4ubuntu1 [22.4 kB] 186s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcc1-0 ppc64el 15.2.0-12ubuntu1 [49.0 kB] 186s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB] 186s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libitm1 ppc64el 15.2.0-12ubuntu1 [32.2 kB] 186s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libasan8 ppc64el 15.2.0-12ubuntu1 [3006 kB] 194s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblsan0 ppc64el 15.2.0-12ubuntu1 [1374 kB] 198s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtsan2 ppc64el 15.2.0-12ubuntu1 [2729 kB] 207s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libubsan1 ppc64el 15.2.0-12ubuntu1 [1231 kB] 210s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libquadmath0 ppc64el 15.2.0-12ubuntu1 [160 kB] 210s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgcc-15-dev ppc64el 15.2.0-12ubuntu1 [1670 kB] 213s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [22.4 MB] 256s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15 ppc64el 15.2.0-12ubuntu1 [530 kB] 257s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1220 B] 257s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc ppc64el 4:15.2.0-4ubuntu1 [5032 B] 257s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libstdc++-15-dev ppc64el 15.2.0-12ubuntu1 [2747 kB] 262s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [13.0 MB] 289s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15 ppc64el 15.2.0-12ubuntu1 [25.3 kB] 289s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [970 B] 289s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++ ppc64el 4:15.2.0-4ubuntu1 [1092 B] 289s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el build-essential ppc64el 12.12ubuntu2 [5256 B] 289s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el dctrl-tools ppc64el 2.24-3build4 [108 kB] 289s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB] 289s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB] 291s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB] 291s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB] 291s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.17.1-3ubuntu1 [182 kB] 291s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 292s Get:38 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 292s Get:39 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fonts-lmodern all 2.005-1build1 [4788 kB] 301s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 305s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB] 306s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran-15-dev ppc64el 15.2.0-12ubuntu1 [651 kB] 308s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [12.3 MB] 330s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15 ppc64el 15.2.0-12ubuntu1 [18.1 kB] 330s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1020 B] 330s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran ppc64el 4:15.2.0-4ubuntu1 [1166 B] 330s Get:47 http://ftpmaster.internal/ubuntu resolute/universe ppc64el hdf5-helpers ppc64el 1.14.6+repack-2 [17.3 kB] 330s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el icu-devtools ppc64el 78.2-1ubuntu1 [246 kB] 330s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el javascript-common all 12+nmu1build1 [4864 B] 330s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el comerr-dev ppc64el 2.1-1.47.2-3ubuntu2 [45.4 kB] 330s Get:51 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgssrpc4t64 ppc64el 1.22.1-2 [64.9 kB] 330s Get:52 http://ftpmaster.internal/ubuntu resolute/main ppc64el libkadm5clnt-mit12 ppc64el 1.22.1-2 [43.9 kB] 330s Get:53 http://ftpmaster.internal/ubuntu resolute/main ppc64el libkdb5-10t64 ppc64el 1.22.1-2 [48.6 kB] 330s Get:54 http://ftpmaster.internal/ubuntu resolute/main ppc64el libkadm5srv-mit12 ppc64el 1.22.1-2 [64.5 kB] 330s Get:55 http://ftpmaster.internal/ubuntu resolute/main ppc64el krb5-multidev ppc64el 1.22.1-2 [126 kB] 330s Get:56 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libaec0 ppc64el 1.1.5-1 [29.7 kB] 330s Get:57 http://ftpmaster.internal/ubuntu resolute/main ppc64el libio-string-perl all 1.08-4 [11.1 kB] 330s Get:58 http://ftpmaster.internal/ubuntu resolute/universe ppc64el liblatex-tounicode-perl all 1.93-1 [29.2 kB] 330s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libbibtex-parser-perl all 1.93+dfsg-1 [17.4 kB] 330s Get:60 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 330s Get:61 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas-dev ppc64el 3.12.1-7ubuntu1 [306 kB] 330s Get:62 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsnappy1v5 ppc64el 1.2.2-2 [33.5 kB] 330s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libblosc1 ppc64el 1.21.5+ds-2 [35.0 kB] 330s Get:64 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost1.90-dev ppc64el 1.90.0-2ubuntu1 [11.5 MB] 368s Get:65 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-dev ppc64el 1.90.0.0ubuntu3 [4766 B] 368s Get:66 http://ftpmaster.internal/ubuntu resolute/main ppc64el libbrotli-dev ppc64el 1.1.0-2build6 [428 kB] 368s Get:67 http://ftpmaster.internal/ubuntu resolute/main ppc64el libbz2-dev ppc64el 1.0.8-6build2 [50.0 kB] 368s Get:68 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 368s Get:69 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB] 368s Get:70 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B] 368s Get:71 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 368s Get:72 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB] 370s Get:73 http://ftpmaster.internal/ubuntu resolute/main ppc64el libidn2-dev ppc64el 2.3.8-4build1 [125 kB] 370s Get:74 http://ftpmaster.internal/ubuntu resolute/main ppc64el libkrb5-dev ppc64el 1.22.1-2 [11.9 kB] 370s Get:75 http://ftpmaster.internal/ubuntu resolute/main ppc64el libldap-dev ppc64el 2.6.10+dfsg-1ubuntu5 [381 kB] 370s Get:76 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpkgconf3 ppc64el 1.8.1-4build1 [37.9 kB] 370s Get:77 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf-bin ppc64el 1.8.1-4build1 [22.7 kB] 370s Get:78 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf ppc64el 1.8.1-4build1 [16.8 kB] 370s Get:79 http://ftpmaster.internal/ubuntu resolute/main ppc64el libnghttp2-dev ppc64el 1.64.0-1.1ubuntu1 [138 kB] 370s Get:80 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpsl-dev ppc64el 0.21.2-1.1build2 [80.9 kB] 370s Get:81 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgmpxx4ldbl ppc64el 2:6.3.0+dfsg-5ubuntu1 [10.2 kB] 370s Get:82 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgmp-dev ppc64el 2:6.3.0+dfsg-5ubuntu1 [382 kB] 370s Get:83 http://ftpmaster.internal/ubuntu resolute/main ppc64el libevent-2.1-7t64 ppc64el 2.1.12-stable-10build2 [172 kB] 370s Get:84 http://ftpmaster.internal/ubuntu resolute/main ppc64el libunbound8 ppc64el 1.24.2-1ubuntu1 [576 kB] 371s Get:85 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgnutls-dane0t64 ppc64el 3.8.10-3ubuntu1 [25.5 kB] 371s Get:86 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgnutls-openssl27t64 ppc64el 3.8.10-3ubuntu1 [25.0 kB] 371s Get:87 http://ftpmaster.internal/ubuntu resolute/main ppc64el libp11-kit-dev ppc64el 0.25.10-1 [29.3 kB] 371s Get:88 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtasn1-6-dev ppc64el 4.21.0-2 [106 kB] 371s Get:89 http://ftpmaster.internal/ubuntu resolute/main ppc64el nettle-dev ppc64el 3.10.2-1 [1235 kB] 373s Get:90 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgnutls28-dev ppc64el 3.8.10-3ubuntu1 [1252 kB] 375s Get:91 http://ftpmaster.internal/ubuntu resolute/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu2 [903 kB] 376s Get:92 http://ftpmaster.internal/ubuntu resolute/main ppc64el librtmp-dev ppc64el 2.4+20151223.gitfa8646d.1-3 [77.1 kB] 376s Get:93 http://ftpmaster.internal/ubuntu resolute/main ppc64el libssl-dev ppc64el 3.5.3-1ubuntu2 [3418 kB] 381s Get:94 http://ftpmaster.internal/ubuntu resolute/main ppc64el libssh2-1-dev ppc64el 1.11.1-1build1 [318 kB] 381s Get:95 http://ftpmaster.internal/ubuntu resolute/main ppc64el libzstd-dev ppc64el 1.5.7+dfsg-3 [528 kB] 381s Get:96 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcurl4-openssl-dev ppc64el 8.18.0-1ubuntu1 [660 kB] 382s Get:97 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB] 382s Get:98 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2build1 [64.1 kB] 382s Get:99 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate-dev ppc64el 1.23-2build1 [71.8 kB] 382s Get:100 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-11ubuntu1 [85.3 kB] 382s Get:101 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.3.2-1 [663 kB] 383s Get:102 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libsz2 ppc64el 1.1.5-1 [25.3 kB] 383s Get:103 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-310 ppc64el 1.14.6+repack-2 [1545 kB] 385s Get:104 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-cpp-310 ppc64el 1.14.6+repack-2 [128 kB] 385s Get:105 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-fortran-310 ppc64el 1.14.6+repack-2 [117 kB] 385s Get:106 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-hl-310 ppc64el 1.14.6+repack-2 [76.3 kB] 385s Get:107 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-hl-fortran-310 ppc64el 1.14.6+repack-2 [35.1 kB] 385s Get:108 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-hl-cpp-310 ppc64el 1.14.6+repack-2 [11.7 kB] 385s Get:109 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu3 [214 kB] 385s Get:110 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-4ubuntu3 [358 kB] 385s Get:111 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 385s Get:112 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B] 385s Get:113 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B] 385s Get:114 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libaec-dev ppc64el 1.1.5-1 [31.9 kB] 385s Get:115 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhdf5-dev ppc64el 1.14.6+repack-2 [3941 kB] 391s Get:116 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 391s Get:117 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1build1 [51.9 kB] 391s Get:118 http://ftpmaster.internal/ubuntu resolute/main ppc64el libicu-dev ppc64el 78.2-1ubuntu1 [13.3 MB] 419s Get:119 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 419s Get:120 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-popper.js all 1.16.1+ds-6build1 [53.8 kB] 419s Get:121 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB] 420s Get:122 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-d3 all 3.5.17-4build1 [136 kB] 420s Get:123 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-es5-shim all 4.6.7-2 [39.8 kB] 420s Get:124 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 420s Get:125 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 420s Get:126 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 420s Get:127 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 420s Get:128 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-microplugin.js all 0.0.3+dfsg-2 [3946 B] 420s Get:129 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 420s Get:130 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1build1 [251 kB] 420s Get:131 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-json all 0~20221030+~1.0.8-1build1 [20.6 kB] 420s Get:132 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-lunr all 2.3.9~dfsg-2 [66.8 kB] 420s Get:133 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-prettify all 2015.12.04+dfsg-3 [41.4 kB] 420s Get:134 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libkpathsea6 ppc64el 2025.20250727.75242+ds-5build1 [74.7 kB] 420s Get:135 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB] 424s Get:136 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack-dev ppc64el 3.12.1-7ubuntu1 [6357 kB] 433s Get:137 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu2 [315 kB] 433s Get:138 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblua5.4-0 ppc64el 5.4.8-1 [213 kB] 433s Get:139 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libmpfi0 ppc64el 1.5.4+ds-4build1 [39.6 kB] 433s Get:140 http://ftpmaster.internal/ubuntu resolute/main ppc64el libncurses-dev ppc64el 6.6+20251231-1 [505 kB] 433s Get:141 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.30-1 [155 kB] 433s Get:142 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.30-1 [22.5 kB] 433s Get:143 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.57.0-1 [283 kB] 433s Get:144 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.57.0-1 [61.2 kB] 433s Get:145 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.57.0-1 [31.0 kB] 433s Get:146 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3build1 [18.1 kB] 433s Get:147 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3build1 [15.7 kB] 433s Get:148 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-16-0 ppc64el 10.46-1 [292 kB] 433s Get:149 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-32-0 ppc64el 10.46-1 [275 kB] 433s Get:150 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-posix3 ppc64el 10.46-1 [7334 B] 433s Get:151 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-dev ppc64el 10.46-1 [937 kB] 436s Get:152 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpng-dev ppc64el 1.6.54-1 [326 kB] 436s Get:153 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libpotrace0 ppc64el 1.16-2build2 [23.8 kB] 436s Get:154 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libptexenc1 ppc64el 2025.20250727.75242+ds-5build1 [49.5 kB] 436s Get:155 http://ftpmaster.internal/ubuntu resolute/main ppc64el libreadline-dev ppc64el 8.3-3 [252 kB] 436s Get:156 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1build1 [24.7 kB] 436s Get:157 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1build1 [18.6 kB] 436s Get:158 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libsynctex2 ppc64el 2025.20250727.75242+ds-5build1 [70.5 kB] 436s Get:159 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1build1 [1239 kB] 439s Get:160 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libteckit0 ppc64el 2.5.13+ds-1 [407 kB] 439s Get:161 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libtexlua53-5 ppc64el 2025.20250727.75242+ds-5build1 [166 kB] 439s Get:162 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu3 [37.1 kB] 439s Get:163 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1build1 [330 kB] 440s Get:164 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 440s Get:165 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB] 440s Get:166 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B] 440s Get:167 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB] 441s Get:168 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB] 441s Get:169 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxmu6 ppc64el 2:1.1.3-4 [56.9 kB] 441s Get:170 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxpm4 ppc64el 1:3.5.17-1build3 [50.5 kB] 441s Get:171 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxaw7 ppc64el 2:1.0.16-1build1 [234 kB] 441s Get:172 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxi6 ppc64el 2:1.8.2-2 [37.0 kB] 441s Get:173 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libzzip-0-13t64 ppc64el 0.13.78+dfsg.1-0.2 [33.7 kB] 441s Get:174 http://ftpmaster.internal/ubuntu resolute/universe ppc64el node-bootstrap-sass all 3.4.3-2 [187 kB] 441s Get:175 http://ftpmaster.internal/ubuntu resolute/universe ppc64el node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 441s Get:176 http://ftpmaster.internal/ubuntu resolute/universe ppc64el node-normalize.css all 8.0.1-5.1 [10.4 kB] 441s Get:177 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pandoc-data all 3.1.11.1-3build1 [78.8 kB] 441s Get:178 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pandoc ppc64el 3.1.11.1+ds-4 [30.9 MB] 488s Get:179 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu3 [198 kB] 488s Get:180 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-29ubuntu1 [200 kB] 488s Get:181 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 489s Get:182 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1ubuntu2 [29.3 MB] 536s Get:183 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblzma-dev ppc64el 5.8.2-2 [210 kB] 536s Get:184 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtirpc-dev ppc64el 1.3.6+ds-1 [223 kB] 536s Get:185 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-dev all 4.5.2-1ubuntu2 [1880 B] 536s Get:186 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pkg-r-autopkgtest all 20250812 [6158 B] 537s Get:187 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-biocgenerics all 0.52.0-2 [624 kB] 538s Get:188 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-biobase ppc64el 2.66.0-2 [2341 kB] 541s Get:189 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-s4vectors ppc64el 0.44.0+dfsg-2 [2078 kB] 544s Get:190 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-iranges ppc64el 2.40.1-3 [2309 kB] 547s Get:191 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dbi all 1.2.3-1build1 [855 kB] 549s Get:192 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bit ppc64el 4.6.0+dfsg-1 [475 kB] 549s Get:193 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bit64 ppc64el 4.6.0-1-4 [507 kB] 549s Get:194 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rlang ppc64el 1.1.5-3 [1738 kB] 551s Get:195 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cli ppc64el 3.6.4-1 [1411 kB] 553s Get:196 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-glue ppc64el 1.8.0-1 [165 kB] 553s Get:197 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 553s Get:198 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vctrs ppc64el 0.6.5-1 [1399 kB] 555s Get:199 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-blob all 1.3.0-1 [54.1 kB] 555s Get:200 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fastmap ppc64el 1.2.0-1 [75.0 kB] 555s Get:201 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cachem ppc64el 1.1.0-1 [74.1 kB] 555s Get:202 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-memoise all 2.0.1-1build1 [54.5 kB] 555s Get:203 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 555s Get:204 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-plogr all 0.2.0-3build2 [15.8 kB] 555s Get:205 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cpp11 all 0.5.3-1 [242 kB] 555s Get:206 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rsqlite ppc64el 2.3.9-1 [1572 kB] 558s Get:207 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-curl ppc64el 7.0.0+dfsg-1 [205 kB] 558s Get:208 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-jsonlite ppc64el 1.9.1+dfsg-1 [452 kB] 558s Get:209 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mime ppc64el 0.12-2 [35.9 kB] 558s Get:210 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-sys ppc64el 3.4.3-1 [45.5 kB] 558s Get:211 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-askpass ppc64el 1.2.1-1 [24.9 kB] 558s Get:212 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-openssl ppc64el 2.3.2+dfsg-1 [409 kB] 558s Get:213 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r6 all 2.6.1-1 [101 kB] 558s Get:214 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-httr all 1.4.7+dfsg-1 [459 kB] 558s Get:215 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-png ppc64el 0.1-8-1build2 [44.3 kB] 558s Get:216 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB] 558s Get:217 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-xvector ppc64el 0.46.0-2 [629 kB] 559s Get:218 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB] 559s Get:219 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB] 580s Get:220 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB] 586s Get:221 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-crayon all 1.5.3-1 [165 kB] 586s Get:222 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-biostrings ppc64el 2.74.1+dfsg-2 [13.3 MB] 604s Get:223 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-keggrest all 1.46.0+dfsg-3 [183 kB] 604s Get:224 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-annotationdbi all 1.68.0-2 [4857 kB] 611s Get:225 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 611s Get:226 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r.oo all 1.27.1-1 [978 kB] 613s Get:227 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r.utils all 2.13.0-1 [1423 kB] 615s Get:228 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrixstats ppc64el 1.5.0-1 [578 kB] 616s Get:229 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-aroma.light all 3.36.0-2 [583 kB] 617s Get:230 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-biocio all 1.16.0+dfsg-2 [209 kB] 617s Get:231 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-formatr all 1.14-2 [152 kB] 617s Get:232 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lambda.r all 1.2.4-2build2 [118 kB] 617s Get:233 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-futile.options all 1.0.1-3build2 [20.5 kB] 617s Get:234 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-futile.logger all 1.4.3-4build2 [98.4 kB] 617s Get:235 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-snow all 1:0.4.4-2build1 [98.7 kB] 617s Get:236 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-codetools all 0.2-20-1build1 [91.1 kB] 617s Get:237 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bh all 1.84.0-1 [5962 B] 617s Get:238 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-biocparallel ppc64el 1.40.0-2 [1346 kB] 619s Get:239 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-base64enc ppc64el 0.1-3-3build1 [29.3 kB] 619s Get:240 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-digest ppc64el 0.6.39-1 [238 kB] 619s Get:241 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-htmltools ppc64el 0.5.8.1-1 [373 kB] 619s Get:242 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-evaluate all 1.0.5-1 [117 kB] 619s Get:243 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xfun ppc64el 0.55+dfsg-1 [589 kB] 620s Get:244 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-highr all 0.11+dfsg-1 [38.5 kB] 620s Get:245 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-yaml ppc64el 2.3.10-1 [123 kB] 620s Get:246 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 630s Get:247 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-knitr all 1.51+dfsg-1 [847 kB] 631s Get:248 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-jquerylib all 0.1.4+dfsg-5 [13.7 kB] 631s Get:249 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fs ppc64el 1.6.5+dfsg-1 [248 kB] 631s Get:250 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rappdirs ppc64el 0.3.3-1build1 [49.4 kB] 631s Get:251 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-sass ppc64el 0.4.9+dfsg-1 [1034 kB] 633s Get:252 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB] 639s Get:253 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fontawesome all 0.5.3-1 [1331 kB] 641s Get:254 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tinytex all 0.58-1 [148 kB] 641s Get:255 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-modernizr all 3.13.0-0.1build1 [100 kB] 641s Get:256 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-littler ppc64el 0.3.22-1 [85.5 kB] 641s Get:257 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 641s Get:258 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpp ppc64el 1.1.0-1 [2037 kB] 645s Get:259 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-later ppc64el 1.4.1+dfsg-1 [153 kB] 645s Get:260 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-magrittr ppc64el 2.0.3-1 [154 kB] 645s Get:261 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-promises ppc64el 1.3.2+dfsg-1 [297 kB] 645s Get:262 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-httpuv ppc64el 1.6.15+dfsg-1 [521 kB] 645s Get:263 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xtable all 1:1.8-4-2build1 [691 kB] 646s Get:264 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-sourcetools ppc64el 0.1.7-1-1 [52.4 kB] 646s Get:265 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-withr all 3.0.2+dfsg-1 [214 kB] 646s Get:266 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-commonmark ppc64el 1.9.5-1 [142 kB] 646s Get:267 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 646s Get:268 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-shiny all 1.10.0+dfsg-2 [3124 kB] 650s Get:269 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rmarkdown all 2.30+dfsg-1 [1501 kB] 653s Get:270 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bookdown all 0.42+dfsg-1 [1409 kB] 655s Get:271 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB] 655s Get:272 http://ftpmaster.internal/ubuntu resolute/universe ppc64el tex-common all 6.20 [30.0 kB] 655s Get:273 http://ftpmaster.internal/ubuntu resolute/main ppc64el t1utils ppc64el 1.41-4build4 [76.9 kB] 655s Get:274 http://ftpmaster.internal/ubuntu resolute/universe ppc64el texlive-binaries ppc64el 2025.20250727.75242+ds-5build1 [12.6 MB] 673s Get:275 http://ftpmaster.internal/ubuntu resolute/universe ppc64el texlive-base all 2025.20260124-1 [22.8 MB] 698s Get:276 http://ftpmaster.internal/ubuntu resolute/universe ppc64el texlive-latex-base all 2025.20260124-1 [1321 kB] 699s Get:277 http://ftpmaster.internal/ubuntu resolute/universe ppc64el texlive-bibtex-extra all 2025.20260124-1 [80.6 MB] 801s Get:278 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-biocversion all 3.20.0-2 [11.1 kB] 801s Get:279 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-biocstyle all 2.34.0+dfsg-1 [451 kB] 801s Get:280 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-genomicranges ppc64el 1.58.0+dfsg-2 [2088 kB] 804s Get:281 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xml ppc64el 3.99-0.20-1 [1761 kB] 806s Get:282 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bitops ppc64el 1.0-9-1 [30.4 kB] 806s Get:283 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-rhtslib ppc64el 3.2.0+dfsg-2 [1620 kB] 808s Get:284 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-rsamtools ppc64el 2.22.0+dfsg-2 [3855 kB] 812s Get:285 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-matrixgenerics all 1.18.1-1 [450 kB] 812s Get:286 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lattice ppc64el 0.22-7-1 [1366 kB] 814s Get:287 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrix ppc64el 1.7-4-1 [4584 kB] 820s Get:288 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-abind all 1.4-8-1build1 [67.0 kB] 820s Get:289 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-s4arrays ppc64el 1.6.0+dfsg-2 [701 kB] 821s Get:290 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-sparsearray ppc64el 1.6.2+dfsg-2 [1418 kB] 823s Get:291 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-delayedarray ppc64el 0.32.0+dfsg-2 [2068 kB] 827s Get:292 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB] 829s Get:293 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-genomicalignments ppc64el 1.42.0-2 [2158 kB] 832s Get:294 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcurl ppc64el 1.98-1.16+dfsg-1 [810 kB] 833s Get:295 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rjson ppc64el 0.2.23-1 [106 kB] 833s Get:296 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-restfulr ppc64el 0.0.15-1 [380 kB] 833s Get:297 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-rtracklayer ppc64el 1.66.0-3 [5257 kB] 840s Get:298 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-bsgenome all 1.74.0-2 [7001 kB] 849s Get:299 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-dnacopy ppc64el 1.80.0-2 [504 kB] 850s Get:300 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-genomicfeatures all 1.58.0+dfsg-2 [937 kB] 851s Get:301 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-org.hs.eg.db all 3.20.0-3 [63.1 MB] 929s Get:302 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-variantannotation ppc64el 1.52.0-2 [3771 kB] 934s Get:303 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 935s Get:304 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-data.table ppc64el 1.17.0+dfsg-1 [2197 kB] 938s Get:305 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 938s Get:306 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-isoband ppc64el 0.2.7-1 [1486 kB] 940s Get:307 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-s7 ppc64el 0.2.0-1 [330 kB] 940s Get:308 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-farver ppc64el 2.1.2-1 [1389 kB] 942s Get:309 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-labeling all 0.4.3-1 [62.1 kB] 942s Get:310 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-viridislite all 0.4.3-1 [1088 kB] 944s Get:311 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-scales all 1.4.0-1 [725 kB] 945s Get:312 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 952s Get:313 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gridextra all 2.3-3build2 [1032 kB] 953s Get:314 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vgam ppc64el 1.1-13-1 [7810 kB] 963s Get:315 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mclust ppc64el 6.1.1-1 [3980 kB] 968s Get:316 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-rhdf5lib ppc64el 1.28.0+dfsg-3 [97.2 kB] 968s Get:317 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-rhdf5filters ppc64el 1.18.1+dfsg-1 [125 kB] 968s Get:318 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-rhdf5 ppc64el 2.50.2+dfsg-1build1 [832 kB] 969s Get:319 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-bioc-purecn all 2.12.0+dfsg-2 [6054 kB] 979s Get:320 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-brio ppc64el 1.1.5-1 [39.1 kB] 979s Get:321 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ps ppc64el 1.9.0-1 [412 kB] 979s Get:322 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-processx ppc64el 3.8.6-1 [369 kB] 979s Get:323 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-callr all 3.7.6-1 [458 kB] 979s Get:324 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lazyeval ppc64el 0.2.2-1build2 [147 kB] 979s Get:325 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rex all 1.2.1-1build1 [126 kB] 979s Get:326 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-covr ppc64el 3.6.4+dfsg-1 [302 kB] 979s Get:327 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-desc all 1.4.3-1 [359 kB] 979s Get:328 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-diffobj ppc64el 0.3.5-1build1 [1150 kB] 980s Get:329 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-globals all 0.19.0-1 [160 kB] 980s Get:330 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-listenv all 0.10.0+dfsg-1 [113 kB] 980s Get:331 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-parallelly ppc64el 1.42.0-1 [540 kB] 981s Get:332 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-future all 1.34.0+dfsg-1 [646 kB] 982s Get:333 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-getopt all 1.20.4-1 [38.4 kB] 982s Get:334 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-markdown all 1.13-1 [162 kB] 982s Get:335 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-optparse all 1.7.5-1 [83.6 kB] 982s Get:336 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgbuild all 1.4.8-1 [219 kB] 982s Get:337 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rprojroot all 2.1.1-1 [131 kB] 982s Get:338 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgload all 1.4.1-1 [252 kB] 982s Get:339 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-praise all 1.0.0-4build2 [20.9 kB] 982s Get:340 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r.cache all 0.17.0-1 [117 kB] 982s Get:341 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pscbs all 0.68.0-1 [4234 kB] 988s Get:342 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-waldo all 0.6.2-1 [153 kB] 988s Get:343 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-testthat ppc64el 3.2.3-1 [1649 kB] 991s Preconfiguring packages ... 991s Fetched 569 MB in 13min 54s (682 kB/s) 991s Selecting previously unselected package libc-dev-bin. 991s (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 ... 122006 files and directories currently installed.) 991s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_ppc64el.deb ... 991s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 991s Selecting previously unselected package linux-libc-dev:ppc64el. 991s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_ppc64el.deb ... 991s Unpacking linux-libc-dev:ppc64el (6.19.0-3.3) ... 991s Selecting previously unselected package libcrypt-dev:ppc64el. 991s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_ppc64el.deb ... 991s Unpacking libcrypt-dev:ppc64el (1:4.5.1-1) ... 992s Selecting previously unselected package rpcsvc-proto. 992s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_ppc64el.deb ... 992s Unpacking rpcsvc-proto (1.4.3-1build1) ... 992s Selecting previously unselected package libc6-dev:ppc64el. 992s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_ppc64el.deb ... 992s Unpacking libc6-dev:ppc64el (2.42-2ubuntu4) ... 992s Selecting previously unselected package libisl23:ppc64el. 992s Preparing to unpack .../005-libisl23_0.27-1build1_ppc64el.deb ... 992s Unpacking libisl23:ppc64el (0.27-1build1) ... 992s Selecting previously unselected package libmpc3:ppc64el. 992s Preparing to unpack .../006-libmpc3_1.3.1-2_ppc64el.deb ... 992s Unpacking libmpc3:ppc64el (1.3.1-2) ... 992s Selecting previously unselected package cpp-15-powerpc64le-linux-gnu. 992s Preparing to unpack .../007-cpp-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package cpp-15. 992s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 992s Preparing to unpack .../009-cpp-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 992s Unpacking cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 992s Selecting previously unselected package cpp. 992s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 992s Unpacking cpp (4:15.2.0-4ubuntu1) ... 992s Selecting previously unselected package libcc1-0:ppc64el. 992s Preparing to unpack .../011-libcc1-0_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package libgomp1:ppc64el. 992s Preparing to unpack .../012-libgomp1_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking libgomp1:ppc64el (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package libitm1:ppc64el. 992s Preparing to unpack .../013-libitm1_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking libitm1:ppc64el (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package libasan8:ppc64el. 992s Preparing to unpack .../014-libasan8_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking libasan8:ppc64el (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package liblsan0:ppc64el. 992s Preparing to unpack .../015-liblsan0_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking liblsan0:ppc64el (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package libtsan2:ppc64el. 992s Preparing to unpack .../016-libtsan2_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking libtsan2:ppc64el (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package libubsan1:ppc64el. 992s Preparing to unpack .../017-libubsan1_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking libubsan1:ppc64el (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package libquadmath0:ppc64el. 992s Preparing to unpack .../018-libquadmath0_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking libquadmath0:ppc64el (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package libgcc-15-dev:ppc64el. 992s Preparing to unpack .../019-libgcc-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 992s Selecting previously unselected package gcc-15-powerpc64le-linux-gnu. 992s Preparing to unpack .../020-gcc-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 992s Unpacking gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 993s Selecting previously unselected package gcc-15. 993s Preparing to unpack .../021-gcc-15_15.2.0-12ubuntu1_ppc64el.deb ... 993s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 993s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 993s Preparing to unpack .../022-gcc-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 993s Unpacking gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 993s Selecting previously unselected package gcc. 993s Preparing to unpack .../023-gcc_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 993s Unpacking gcc (4:15.2.0-4ubuntu1) ... 993s Selecting previously unselected package libstdc++-15-dev:ppc64el. 993s Preparing to unpack .../024-libstdc++-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 993s Unpacking libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 993s Selecting previously unselected package g++-15-powerpc64le-linux-gnu. 993s Preparing to unpack .../025-g++-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 993s Unpacking g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 993s Selecting previously unselected package g++-15. 993s Preparing to unpack .../026-g++-15_15.2.0-12ubuntu1_ppc64el.deb ... 993s Unpacking g++-15 (15.2.0-12ubuntu1) ... 993s Selecting previously unselected package g++-powerpc64le-linux-gnu. 993s Preparing to unpack .../027-g++-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 993s Unpacking g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 993s Selecting previously unselected package g++. 993s Preparing to unpack .../028-g++_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 993s Unpacking g++ (4:15.2.0-4ubuntu1) ... 993s Selecting previously unselected package build-essential. 993s Preparing to unpack .../029-build-essential_12.12ubuntu2_ppc64el.deb ... 993s Unpacking build-essential (12.12ubuntu2) ... 993s Selecting previously unselected package dctrl-tools. 993s Preparing to unpack .../030-dctrl-tools_2.24-3build4_ppc64el.deb ... 993s Unpacking dctrl-tools (2.24-3build4) ... 993s Selecting previously unselected package fonts-dejavu-mono. 993s Preparing to unpack .../031-fonts-dejavu-mono_2.37-8build1_all.deb ... 993s Unpacking fonts-dejavu-mono (2.37-8build1) ... 993s Selecting previously unselected package fonts-dejavu-core. 993s Preparing to unpack .../032-fonts-dejavu-core_2.37-8build1_all.deb ... 993s Unpacking fonts-dejavu-core (2.37-8build1) ... 993s Selecting previously unselected package fontconfig-config. 993s Preparing to unpack .../033-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ... 993s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 993s Selecting previously unselected package libfontconfig1:ppc64el. 993s Preparing to unpack .../034-libfontconfig1_2.17.1-3ubuntu1_ppc64el.deb ... 993s Unpacking libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 993s Selecting previously unselected package fontconfig. 993s Preparing to unpack .../035-fontconfig_2.17.1-3ubuntu1_ppc64el.deb ... 993s Unpacking fontconfig (2.17.1-3ubuntu1) ... 993s Selecting previously unselected package fonts-font-awesome. 993s Preparing to unpack .../036-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ... 993s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 993s Selecting previously unselected package fonts-glyphicons-halflings. 993s Preparing to unpack .../037-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 993s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 993s Selecting previously unselected package fonts-lmodern. 993s Preparing to unpack .../038-fonts-lmodern_2.005-1build1_all.deb ... 993s Unpacking fonts-lmodern (2.005-1build1) ... 993s Selecting previously unselected package fonts-mathjax. 993s Preparing to unpack .../039-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 993s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 993s Selecting previously unselected package libgfortran5:ppc64el. 993s Preparing to unpack .../040-libgfortran5_15.2.0-12ubuntu1_ppc64el.deb ... 993s Unpacking libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 993s Selecting previously unselected package libgfortran-15-dev:ppc64el. 994s Preparing to unpack .../041-libgfortran-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 994s Unpacking libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 994s Selecting previously unselected package gfortran-15-powerpc64le-linux-gnu. 994s Preparing to unpack .../042-gfortran-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 994s Unpacking gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 994s Selecting previously unselected package gfortran-15. 994s Preparing to unpack .../043-gfortran-15_15.2.0-12ubuntu1_ppc64el.deb ... 994s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 994s Selecting previously unselected package gfortran-powerpc64le-linux-gnu. 994s Preparing to unpack .../044-gfortran-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 994s Unpacking gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 994s Selecting previously unselected package gfortran. 994s Preparing to unpack .../045-gfortran_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 994s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 994s Selecting previously unselected package hdf5-helpers. 994s Preparing to unpack .../046-hdf5-helpers_1.14.6+repack-2_ppc64el.deb ... 994s Unpacking hdf5-helpers (1.14.6+repack-2) ... 994s Selecting previously unselected package icu-devtools. 994s Preparing to unpack .../047-icu-devtools_78.2-1ubuntu1_ppc64el.deb ... 994s Unpacking icu-devtools (78.2-1ubuntu1) ... 994s Selecting previously unselected package javascript-common. 994s Preparing to unpack .../048-javascript-common_12+nmu1build1_all.deb ... 994s Unpacking javascript-common (12+nmu1build1) ... 994s Selecting previously unselected package comerr-dev:ppc64el. 994s Preparing to unpack .../049-comerr-dev_2.1-1.47.2-3ubuntu2_ppc64el.deb ... 994s Unpacking comerr-dev:ppc64el (2.1-1.47.2-3ubuntu2) ... 994s Selecting previously unselected package libgssrpc4t64:ppc64el. 994s Preparing to unpack .../050-libgssrpc4t64_1.22.1-2_ppc64el.deb ... 994s Unpacking libgssrpc4t64:ppc64el (1.22.1-2) ... 994s Selecting previously unselected package libkadm5clnt-mit12:ppc64el. 994s Preparing to unpack .../051-libkadm5clnt-mit12_1.22.1-2_ppc64el.deb ... 994s Unpacking libkadm5clnt-mit12:ppc64el (1.22.1-2) ... 994s Selecting previously unselected package libkdb5-10t64:ppc64el. 994s Preparing to unpack .../052-libkdb5-10t64_1.22.1-2_ppc64el.deb ... 994s Unpacking libkdb5-10t64:ppc64el (1.22.1-2) ... 994s Selecting previously unselected package libkadm5srv-mit12:ppc64el. 994s Preparing to unpack .../053-libkadm5srv-mit12_1.22.1-2_ppc64el.deb ... 994s Unpacking libkadm5srv-mit12:ppc64el (1.22.1-2) ... 994s Selecting previously unselected package krb5-multidev:ppc64el. 994s Preparing to unpack .../054-krb5-multidev_1.22.1-2_ppc64el.deb ... 994s Unpacking krb5-multidev:ppc64el (1.22.1-2) ... 994s Selecting previously unselected package libaec0:ppc64el. 994s Preparing to unpack .../055-libaec0_1.1.5-1_ppc64el.deb ... 994s Unpacking libaec0:ppc64el (1.1.5-1) ... 994s Selecting previously unselected package libio-string-perl. 994s Preparing to unpack .../056-libio-string-perl_1.08-4_all.deb ... 994s Unpacking libio-string-perl (1.08-4) ... 994s Selecting previously unselected package liblatex-tounicode-perl. 994s Preparing to unpack .../057-liblatex-tounicode-perl_1.93-1_all.deb ... 994s Unpacking liblatex-tounicode-perl (1.93-1) ... 994s Selecting previously unselected package libbibtex-parser-perl. 994s Preparing to unpack .../058-libbibtex-parser-perl_1.93+dfsg-1_all.deb ... 994s Unpacking libbibtex-parser-perl (1.93+dfsg-1) ... 994s Selecting previously unselected package libblas3:ppc64el. 994s Preparing to unpack .../059-libblas3_3.12.1-7ubuntu1_ppc64el.deb ... 994s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ... 994s Selecting previously unselected package libblas-dev:ppc64el. 994s Preparing to unpack .../060-libblas-dev_3.12.1-7ubuntu1_ppc64el.deb ... 994s Unpacking libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 994s Selecting previously unselected package libsnappy1v5:ppc64el. 994s Preparing to unpack .../061-libsnappy1v5_1.2.2-2_ppc64el.deb ... 994s Unpacking libsnappy1v5:ppc64el (1.2.2-2) ... 994s Selecting previously unselected package libblosc1:ppc64el. 994s Preparing to unpack .../062-libblosc1_1.21.5+ds-2_ppc64el.deb ... 994s Unpacking libblosc1:ppc64el (1.21.5+ds-2) ... 994s Selecting previously unselected package libboost1.90-dev:ppc64el. 994s Preparing to unpack .../063-libboost1.90-dev_1.90.0-2ubuntu1_ppc64el.deb ... 994s Unpacking libboost1.90-dev:ppc64el (1.90.0-2ubuntu1) ... 996s Selecting previously unselected package libboost-dev:ppc64el. 996s Preparing to unpack .../064-libboost-dev_1.90.0.0ubuntu3_ppc64el.deb ... 996s Unpacking libboost-dev:ppc64el (1.90.0.0ubuntu3) ... 996s Selecting previously unselected package libbrotli-dev:ppc64el. 996s Preparing to unpack .../065-libbrotli-dev_1.1.0-2build6_ppc64el.deb ... 996s Unpacking libbrotli-dev:ppc64el (1.1.0-2build6) ... 996s Selecting previously unselected package libbz2-dev:ppc64el. 996s Preparing to unpack .../066-libbz2-dev_1.0.8-6build2_ppc64el.deb ... 996s Unpacking libbz2-dev:ppc64el (1.0.8-6build2) ... 996s Selecting previously unselected package libpixman-1-0:ppc64el. 996s Preparing to unpack .../067-libpixman-1-0_0.46.4-1_ppc64el.deb ... 996s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 996s Selecting previously unselected package libxcb-render0:ppc64el. 996s Preparing to unpack .../068-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ... 996s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 996s Selecting previously unselected package libxcb-shm0:ppc64el. 996s Preparing to unpack .../069-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ... 996s Unpacking libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 996s Selecting previously unselected package libxrender1:ppc64el. 996s Preparing to unpack .../070-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 996s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 996s Selecting previously unselected package libcairo2:ppc64el. 996s Preparing to unpack .../071-libcairo2_1.18.4-3_ppc64el.deb ... 996s Unpacking libcairo2:ppc64el (1.18.4-3) ... 996s Selecting previously unselected package libidn2-dev:ppc64el. 996s Preparing to unpack .../072-libidn2-dev_2.3.8-4build1_ppc64el.deb ... 996s Unpacking libidn2-dev:ppc64el (2.3.8-4build1) ... 996s Selecting previously unselected package libkrb5-dev:ppc64el. 996s Preparing to unpack .../073-libkrb5-dev_1.22.1-2_ppc64el.deb ... 996s Unpacking libkrb5-dev:ppc64el (1.22.1-2) ... 996s Selecting previously unselected package libldap-dev:ppc64el. 996s Preparing to unpack .../074-libldap-dev_2.6.10+dfsg-1ubuntu5_ppc64el.deb ... 996s Unpacking libldap-dev:ppc64el (2.6.10+dfsg-1ubuntu5) ... 996s Selecting previously unselected package libpkgconf3:ppc64el. 996s Preparing to unpack .../075-libpkgconf3_1.8.1-4build1_ppc64el.deb ... 996s Unpacking libpkgconf3:ppc64el (1.8.1-4build1) ... 996s Selecting previously unselected package pkgconf-bin. 996s Preparing to unpack .../076-pkgconf-bin_1.8.1-4build1_ppc64el.deb ... 996s Unpacking pkgconf-bin (1.8.1-4build1) ... 996s Selecting previously unselected package pkgconf:ppc64el. 996s Preparing to unpack .../077-pkgconf_1.8.1-4build1_ppc64el.deb ... 996s Unpacking pkgconf:ppc64el (1.8.1-4build1) ... 996s Selecting previously unselected package libnghttp2-dev:ppc64el. 996s Preparing to unpack .../078-libnghttp2-dev_1.64.0-1.1ubuntu1_ppc64el.deb ... 996s Unpacking libnghttp2-dev:ppc64el (1.64.0-1.1ubuntu1) ... 996s Selecting previously unselected package libpsl-dev:ppc64el. 996s Preparing to unpack .../079-libpsl-dev_0.21.2-1.1build2_ppc64el.deb ... 996s Unpacking libpsl-dev:ppc64el (0.21.2-1.1build2) ... 996s Selecting previously unselected package libgmpxx4ldbl:ppc64el. 996s Preparing to unpack .../080-libgmpxx4ldbl_2%3a6.3.0+dfsg-5ubuntu1_ppc64el.deb ... 996s Unpacking libgmpxx4ldbl:ppc64el (2:6.3.0+dfsg-5ubuntu1) ... 996s Selecting previously unselected package libgmp-dev:ppc64el. 996s Preparing to unpack .../081-libgmp-dev_2%3a6.3.0+dfsg-5ubuntu1_ppc64el.deb ... 996s Unpacking libgmp-dev:ppc64el (2:6.3.0+dfsg-5ubuntu1) ... 996s Selecting previously unselected package libevent-2.1-7t64:ppc64el. 996s Preparing to unpack .../082-libevent-2.1-7t64_2.1.12-stable-10build2_ppc64el.deb ... 996s Unpacking libevent-2.1-7t64:ppc64el (2.1.12-stable-10build2) ... 996s Selecting previously unselected package libunbound8:ppc64el. 996s Preparing to unpack .../083-libunbound8_1.24.2-1ubuntu1_ppc64el.deb ... 996s Unpacking libunbound8:ppc64el (1.24.2-1ubuntu1) ... 997s Selecting previously unselected package libgnutls-dane0t64:ppc64el. 997s Preparing to unpack .../084-libgnutls-dane0t64_3.8.10-3ubuntu1_ppc64el.deb ... 997s Unpacking libgnutls-dane0t64:ppc64el (3.8.10-3ubuntu1) ... 997s Selecting previously unselected package libgnutls-openssl27t64:ppc64el. 997s Preparing to unpack .../085-libgnutls-openssl27t64_3.8.10-3ubuntu1_ppc64el.deb ... 997s Unpacking libgnutls-openssl27t64:ppc64el (3.8.10-3ubuntu1) ... 997s Selecting previously unselected package libp11-kit-dev:ppc64el. 997s Preparing to unpack .../086-libp11-kit-dev_0.25.10-1_ppc64el.deb ... 997s Unpacking libp11-kit-dev:ppc64el (0.25.10-1) ... 997s Selecting previously unselected package libtasn1-6-dev:ppc64el. 997s Preparing to unpack .../087-libtasn1-6-dev_4.21.0-2_ppc64el.deb ... 997s Unpacking libtasn1-6-dev:ppc64el (4.21.0-2) ... 997s Selecting previously unselected package nettle-dev:ppc64el. 997s Preparing to unpack .../088-nettle-dev_3.10.2-1_ppc64el.deb ... 997s Unpacking nettle-dev:ppc64el (3.10.2-1) ... 997s Selecting previously unselected package libgnutls28-dev:ppc64el. 997s Preparing to unpack .../089-libgnutls28-dev_3.8.10-3ubuntu1_ppc64el.deb ... 997s Unpacking libgnutls28-dev:ppc64el (3.8.10-3ubuntu1) ... 997s Selecting previously unselected package zlib1g-dev:ppc64el. 997s Preparing to unpack .../090-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_ppc64el.deb ... 997s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 997s Selecting previously unselected package librtmp-dev:ppc64el. 997s Preparing to unpack .../091-librtmp-dev_2.4+20151223.gitfa8646d.1-3_ppc64el.deb ... 997s Unpacking librtmp-dev:ppc64el (2.4+20151223.gitfa8646d.1-3) ... 997s Selecting previously unselected package libssl-dev:ppc64el. 997s Preparing to unpack .../092-libssl-dev_3.5.3-1ubuntu2_ppc64el.deb ... 997s Unpacking libssl-dev:ppc64el (3.5.3-1ubuntu2) ... 997s Selecting previously unselected package libssh2-1-dev:ppc64el. 997s Preparing to unpack .../093-libssh2-1-dev_1.11.1-1build1_ppc64el.deb ... 997s Unpacking libssh2-1-dev:ppc64el (1.11.1-1build1) ... 997s Selecting previously unselected package libzstd-dev:ppc64el. 997s Preparing to unpack .../094-libzstd-dev_1.5.7+dfsg-3_ppc64el.deb ... 997s Unpacking libzstd-dev:ppc64el (1.5.7+dfsg-3) ... 997s Selecting previously unselected package libcurl4-openssl-dev:ppc64el. 997s Preparing to unpack .../095-libcurl4-openssl-dev_8.18.0-1ubuntu1_ppc64el.deb ... 997s Unpacking libcurl4-openssl-dev:ppc64el (8.18.0-1ubuntu1) ... 997s Selecting previously unselected package libdatrie1:ppc64el. 997s Preparing to unpack .../096-libdatrie1_0.2.14-1_ppc64el.deb ... 997s Unpacking libdatrie1:ppc64el (0.2.14-1) ... 997s Selecting previously unselected package libdeflate0:ppc64el. 997s Preparing to unpack .../097-libdeflate0_1.23-2build1_ppc64el.deb ... 997s Unpacking libdeflate0:ppc64el (1.23-2build1) ... 997s Selecting previously unselected package libdeflate-dev:ppc64el. 997s Preparing to unpack .../098-libdeflate-dev_1.23-2build1_ppc64el.deb ... 997s Unpacking libdeflate-dev:ppc64el (1.23-2build1) ... 997s Selecting previously unselected package libgraphite2-3:ppc64el. 997s Preparing to unpack .../099-libgraphite2-3_1.3.14-11ubuntu1_ppc64el.deb ... 997s Unpacking libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ... 997s Selecting previously unselected package libharfbuzz0b:ppc64el. 997s Preparing to unpack .../100-libharfbuzz0b_12.3.2-1_ppc64el.deb ... 997s Unpacking libharfbuzz0b:ppc64el (12.3.2-1) ... 997s Selecting previously unselected package libsz2:ppc64el. 997s Preparing to unpack .../101-libsz2_1.1.5-1_ppc64el.deb ... 997s Unpacking libsz2:ppc64el (1.1.5-1) ... 997s Selecting previously unselected package libhdf5-310:ppc64el. 997s Preparing to unpack .../102-libhdf5-310_1.14.6+repack-2_ppc64el.deb ... 997s Unpacking libhdf5-310:ppc64el (1.14.6+repack-2) ... 997s Selecting previously unselected package libhdf5-cpp-310:ppc64el. 997s Preparing to unpack .../103-libhdf5-cpp-310_1.14.6+repack-2_ppc64el.deb ... 997s Unpacking libhdf5-cpp-310:ppc64el (1.14.6+repack-2) ... 997s Selecting previously unselected package libhdf5-fortran-310:ppc64el. 997s Preparing to unpack .../104-libhdf5-fortran-310_1.14.6+repack-2_ppc64el.deb ... 997s Unpacking libhdf5-fortran-310:ppc64el (1.14.6+repack-2) ... 997s Selecting previously unselected package libhdf5-hl-310:ppc64el. 997s Preparing to unpack .../105-libhdf5-hl-310_1.14.6+repack-2_ppc64el.deb ... 997s Unpacking libhdf5-hl-310:ppc64el (1.14.6+repack-2) ... 997s Selecting previously unselected package libhdf5-hl-fortran-310:ppc64el. 997s Preparing to unpack .../106-libhdf5-hl-fortran-310_1.14.6+repack-2_ppc64el.deb ... 997s Unpacking libhdf5-hl-fortran-310:ppc64el (1.14.6+repack-2) ... 997s Selecting previously unselected package libhdf5-hl-cpp-310:ppc64el. 997s Preparing to unpack .../107-libhdf5-hl-cpp-310_1.14.6+repack-2_ppc64el.deb ... 997s Unpacking libhdf5-hl-cpp-310:ppc64el (1.14.6+repack-2) ... 997s Selecting previously unselected package libjpeg-turbo8:ppc64el. 997s Preparing to unpack .../108-libjpeg-turbo8_2.1.5-4ubuntu3_ppc64el.deb ... 997s Unpacking libjpeg-turbo8:ppc64el (2.1.5-4ubuntu3) ... 997s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el. 997s Preparing to unpack .../109-libjpeg-turbo8-dev_2.1.5-4ubuntu3_ppc64el.deb ... 997s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 997s Selecting previously unselected package libjpeg8:ppc64el. 997s Preparing to unpack .../110-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 997s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 997s Selecting previously unselected package libjpeg8-dev:ppc64el. 997s Preparing to unpack .../111-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ... 997s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 997s Selecting previously unselected package libjpeg-dev:ppc64el. 997s Preparing to unpack .../112-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ... 997s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ... 997s Selecting previously unselected package libaec-dev:ppc64el. 997s Preparing to unpack .../113-libaec-dev_1.1.5-1_ppc64el.deb ... 997s Unpacking libaec-dev:ppc64el (1.1.5-1) ... 997s Selecting previously unselected package libhdf5-dev. 997s Preparing to unpack .../114-libhdf5-dev_1.14.6+repack-2_ppc64el.deb ... 997s Unpacking libhdf5-dev (1.14.6+repack-2) ... 997s Selecting previously unselected package x11-common. 997s Preparing to unpack .../115-x11-common_1%3a7.7+24ubuntu1_all.deb ... 997s Unpacking x11-common (1:7.7+24ubuntu1) ... 997s Selecting previously unselected package libice6:ppc64el. 997s Preparing to unpack .../116-libice6_2%3a1.1.1-1build1_ppc64el.deb ... 997s Unpacking libice6:ppc64el (2:1.1.1-1build1) ... 997s Selecting previously unselected package libicu-dev:ppc64el. 997s Preparing to unpack .../117-libicu-dev_78.2-1ubuntu1_ppc64el.deb ... 997s Unpacking libicu-dev:ppc64el (78.2-1ubuntu1) ... 998s Selecting previously unselected package libjs-bootstrap. 998s Preparing to unpack .../118-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 998s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 998s Selecting previously unselected package libjs-popper.js. 998s Preparing to unpack .../119-libjs-popper.js_1.16.1+ds-6build1_all.deb ... 998s Unpacking libjs-popper.js (1.16.1+ds-6build1) ... 998s Selecting previously unselected package libjs-bootstrap4. 998s Preparing to unpack .../120-libjs-bootstrap4_4.6.2+dfsg-1_all.deb ... 998s Unpacking libjs-bootstrap4 (4.6.2+dfsg-1) ... 998s Selecting previously unselected package libjs-d3. 998s Preparing to unpack .../121-libjs-d3_3.5.17-4build1_all.deb ... 998s Unpacking libjs-d3 (3.5.17-4build1) ... 998s Selecting previously unselected package libjs-es5-shim. 998s Preparing to unpack .../122-libjs-es5-shim_4.6.7-2_all.deb ... 998s Unpacking libjs-es5-shim (4.6.7-2) ... 998s Selecting previously unselected package libjs-highlight.js. 998s Preparing to unpack .../123-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 998s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 998s Selecting previously unselected package libjs-jquery. 998s Preparing to unpack .../124-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 998s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 998s Selecting previously unselected package libjs-jquery-datatables. 998s Preparing to unpack .../125-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 998s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 998s Selecting previously unselected package libjs-sifter.js. 998s Preparing to unpack .../126-libjs-sifter.js_0.6.0+dfsg-3_all.deb ... 998s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ... 998s Selecting previously unselected package libjs-microplugin.js. 998s Preparing to unpack .../127-libjs-microplugin.js_0.0.3+dfsg-2_all.deb ... 998s Unpacking libjs-microplugin.js (0.0.3+dfsg-2) ... 998s Selecting previously unselected package libjs-jquery-selectize.js. 998s Preparing to unpack .../128-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ... 998s Unpacking libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 998s Selecting previously unselected package libjs-jquery-ui. 998s Preparing to unpack .../129-libjs-jquery-ui_1.13.2+dfsg-1build1_all.deb ... 998s Unpacking libjs-jquery-ui (1.13.2+dfsg-1build1) ... 998s Selecting previously unselected package libjs-json. 998s Preparing to unpack .../130-libjs-json_0~20221030+~1.0.8-1build1_all.deb ... 998s Unpacking libjs-json (0~20221030+~1.0.8-1build1) ... 998s Selecting previously unselected package libjs-lunr. 998s Preparing to unpack .../131-libjs-lunr_2.3.9~dfsg-2_all.deb ... 998s Unpacking libjs-lunr (2.3.9~dfsg-2) ... 998s Selecting previously unselected package libjs-prettify. 998s Preparing to unpack .../132-libjs-prettify_2015.12.04+dfsg-3_all.deb ... 998s Unpacking libjs-prettify (2015.12.04+dfsg-3) ... 998s Selecting previously unselected package libkpathsea6:ppc64el. 998s Preparing to unpack .../133-libkpathsea6_2025.20250727.75242+ds-5build1_ppc64el.deb ... 998s Unpacking libkpathsea6:ppc64el (2025.20250727.75242+ds-5build1) ... 998s Selecting previously unselected package liblapack3:ppc64el. 998s Preparing to unpack .../134-liblapack3_3.12.1-7ubuntu1_ppc64el.deb ... 998s Unpacking liblapack3:ppc64el (3.12.1-7ubuntu1) ... 998s Selecting previously unselected package liblapack-dev:ppc64el. 998s Preparing to unpack .../135-liblapack-dev_3.12.1-7ubuntu1_ppc64el.deb ... 998s Unpacking liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 998s Selecting previously unselected package liblerc4:ppc64el. 998s Preparing to unpack .../136-liblerc4_4.0.0+ds-5ubuntu2_ppc64el.deb ... 998s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu2) ... 998s Selecting previously unselected package liblua5.4-0:ppc64el. 998s Preparing to unpack .../137-liblua5.4-0_5.4.8-1_ppc64el.deb ... 998s Unpacking liblua5.4-0:ppc64el (5.4.8-1) ... 998s Selecting previously unselected package libmpfi0:ppc64el. 998s Preparing to unpack .../138-libmpfi0_1.5.4+ds-4build1_ppc64el.deb ... 998s Unpacking libmpfi0:ppc64el (1.5.4+ds-4build1) ... 998s Selecting previously unselected package libncurses-dev:ppc64el. 998s Preparing to unpack .../139-libncurses-dev_6.6+20251231-1_ppc64el.deb ... 998s Unpacking libncurses-dev:ppc64el (6.6+20251231-1) ... 998s Selecting previously unselected package libthai-data. 998s Preparing to unpack .../140-libthai-data_0.1.30-1_all.deb ... 998s Unpacking libthai-data (0.1.30-1) ... 998s Selecting previously unselected package libthai0:ppc64el. 998s Preparing to unpack .../141-libthai0_0.1.30-1_ppc64el.deb ... 998s Unpacking libthai0:ppc64el (0.1.30-1) ... 998s Selecting previously unselected package libpango-1.0-0:ppc64el. 998s Preparing to unpack .../142-libpango-1.0-0_1.57.0-1_ppc64el.deb ... 998s Unpacking libpango-1.0-0:ppc64el (1.57.0-1) ... 998s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 998s Preparing to unpack .../143-libpangoft2-1.0-0_1.57.0-1_ppc64el.deb ... 998s Unpacking libpangoft2-1.0-0:ppc64el (1.57.0-1) ... 998s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 998s Preparing to unpack .../144-libpangocairo-1.0-0_1.57.0-1_ppc64el.deb ... 998s Unpacking libpangocairo-1.0-0:ppc64el (1.57.0-1) ... 998s Selecting previously unselected package libpaper2:ppc64el. 998s Preparing to unpack .../145-libpaper2_2.2.5-0.3build1_ppc64el.deb ... 998s Unpacking libpaper2:ppc64el (2.2.5-0.3build1) ... 998s Selecting previously unselected package libpaper-utils. 998s Preparing to unpack .../146-libpaper-utils_2.2.5-0.3build1_ppc64el.deb ... 998s Unpacking libpaper-utils (2.2.5-0.3build1) ... 998s Selecting previously unselected package libpcre2-16-0:ppc64el. 999s Preparing to unpack .../147-libpcre2-16-0_10.46-1_ppc64el.deb ... 999s Unpacking libpcre2-16-0:ppc64el (10.46-1) ... 999s Selecting previously unselected package libpcre2-32-0:ppc64el. 999s Preparing to unpack .../148-libpcre2-32-0_10.46-1_ppc64el.deb ... 999s Unpacking libpcre2-32-0:ppc64el (10.46-1) ... 999s Selecting previously unselected package libpcre2-posix3:ppc64el. 999s Preparing to unpack .../149-libpcre2-posix3_10.46-1_ppc64el.deb ... 999s Unpacking libpcre2-posix3:ppc64el (10.46-1) ... 999s Selecting previously unselected package libpcre2-dev:ppc64el. 999s Preparing to unpack .../150-libpcre2-dev_10.46-1_ppc64el.deb ... 999s Unpacking libpcre2-dev:ppc64el (10.46-1) ... 999s Selecting previously unselected package libpng-dev:ppc64el. 999s Preparing to unpack .../151-libpng-dev_1.6.54-1_ppc64el.deb ... 999s Unpacking libpng-dev:ppc64el (1.6.54-1) ... 999s Selecting previously unselected package libpotrace0:ppc64el. 999s Preparing to unpack .../152-libpotrace0_1.16-2build2_ppc64el.deb ... 999s Unpacking libpotrace0:ppc64el (1.16-2build2) ... 999s Selecting previously unselected package libptexenc1:ppc64el. 999s Preparing to unpack .../153-libptexenc1_2025.20250727.75242+ds-5build1_ppc64el.deb ... 999s Unpacking libptexenc1:ppc64el (2025.20250727.75242+ds-5build1) ... 999s Selecting previously unselected package libreadline-dev:ppc64el. 999s Preparing to unpack .../154-libreadline-dev_8.3-3_ppc64el.deb ... 999s Unpacking libreadline-dev:ppc64el (8.3-3) ... 999s Selecting previously unselected package libsharpyuv0:ppc64el. 999s Preparing to unpack .../155-libsharpyuv0_1.5.0-0.1build1_ppc64el.deb ... 999s Unpacking libsharpyuv0:ppc64el (1.5.0-0.1build1) ... 999s Selecting previously unselected package libsm6:ppc64el. 999s Preparing to unpack .../156-libsm6_2%3a1.2.6-1build1_ppc64el.deb ... 999s Unpacking libsm6:ppc64el (2:1.2.6-1build1) ... 999s Selecting previously unselected package libsynctex2:ppc64el. 999s Preparing to unpack .../157-libsynctex2_2025.20250727.75242+ds-5build1_ppc64el.deb ... 999s Unpacking libsynctex2:ppc64el (2025.20250727.75242+ds-5build1) ... 999s Selecting previously unselected package libtcl8.6:ppc64el. 999s Preparing to unpack .../158-libtcl8.6_8.6.17+dfsg-1build1_ppc64el.deb ... 999s Unpacking libtcl8.6:ppc64el (8.6.17+dfsg-1build1) ... 999s Selecting previously unselected package libteckit0:ppc64el. 999s Preparing to unpack .../159-libteckit0_2.5.13+ds-1_ppc64el.deb ... 999s Unpacking libteckit0:ppc64el (2.5.13+ds-1) ... 999s Selecting previously unselected package libtexlua53-5:ppc64el. 999s Preparing to unpack .../160-libtexlua53-5_2025.20250727.75242+ds-5build1_ppc64el.deb ... 999s Unpacking libtexlua53-5:ppc64el (2025.20250727.75242+ds-5build1) ... 999s Selecting previously unselected package libjbig0:ppc64el. 999s Preparing to unpack .../161-libjbig0_2.1-6.1ubuntu3_ppc64el.deb ... 999s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu3) ... 999s Selecting previously unselected package libwebp7:ppc64el. 999s Preparing to unpack .../162-libwebp7_1.5.0-0.1build1_ppc64el.deb ... 999s Unpacking libwebp7:ppc64el (1.5.0-0.1build1) ... 999s Selecting previously unselected package libtiff6:ppc64el. 999s Preparing to unpack .../163-libtiff6_4.7.0-3ubuntu3_ppc64el.deb ... 999s Unpacking libtiff6:ppc64el (4.7.0-3ubuntu3) ... 999s Selecting previously unselected package libxft2:ppc64el. 999s Preparing to unpack .../164-libxft2_2.3.6-1build2_ppc64el.deb ... 999s Unpacking libxft2:ppc64el (2.3.6-1build2) ... 999s Selecting previously unselected package libxss1:ppc64el. 999s Preparing to unpack .../165-libxss1_1%3a1.2.3-1build4_ppc64el.deb ... 999s Unpacking libxss1:ppc64el (1:1.2.3-1build4) ... 999s Selecting previously unselected package libtk8.6:ppc64el. 999s Preparing to unpack .../166-libtk8.6_8.6.17-1_ppc64el.deb ... 999s Unpacking libtk8.6:ppc64el (8.6.17-1) ... 999s Selecting previously unselected package libxt6t64:ppc64el. 999s Preparing to unpack .../167-libxt6t64_1%3a1.2.1-1.3_ppc64el.deb ... 999s Unpacking libxt6t64:ppc64el (1:1.2.1-1.3) ... 999s Selecting previously unselected package libxmu6:ppc64el. 999s Preparing to unpack .../168-libxmu6_2%3a1.1.3-4_ppc64el.deb ... 999s Unpacking libxmu6:ppc64el (2:1.1.3-4) ... 999s Selecting previously unselected package libxpm4:ppc64el. 999s Preparing to unpack .../169-libxpm4_1%3a3.5.17-1build3_ppc64el.deb ... 999s Unpacking libxpm4:ppc64el (1:3.5.17-1build3) ... 999s Selecting previously unselected package libxaw7:ppc64el. 999s Preparing to unpack .../170-libxaw7_2%3a1.0.16-1build1_ppc64el.deb ... 999s Unpacking libxaw7:ppc64el (2:1.0.16-1build1) ... 999s Selecting previously unselected package libxi6:ppc64el. 999s Preparing to unpack .../171-libxi6_2%3a1.8.2-2_ppc64el.deb ... 999s Unpacking libxi6:ppc64el (2:1.8.2-2) ... 999s Selecting previously unselected package libzzip-0-13t64:ppc64el. 999s Preparing to unpack .../172-libzzip-0-13t64_0.13.78+dfsg.1-0.2_ppc64el.deb ... 999s Unpacking libzzip-0-13t64:ppc64el (0.13.78+dfsg.1-0.2) ... 999s Selecting previously unselected package node-bootstrap-sass. 999s Preparing to unpack .../173-node-bootstrap-sass_3.4.3-2_all.deb ... 999s Unpacking node-bootstrap-sass (3.4.3-2) ... 999s Selecting previously unselected package node-html5shiv. 999s Preparing to unpack .../174-node-html5shiv_3.7.3+dfsg-5_all.deb ... 999s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 999s Selecting previously unselected package node-normalize.css. 999s Preparing to unpack .../175-node-normalize.css_8.0.1-5.1_all.deb ... 999s Unpacking node-normalize.css (8.0.1-5.1) ... 999s Selecting previously unselected package pandoc-data. 999s Preparing to unpack .../176-pandoc-data_3.1.11.1-3build1_all.deb ... 999s Unpacking pandoc-data (3.1.11.1-3build1) ... 999s Selecting previously unselected package pandoc. 999s Preparing to unpack .../177-pandoc_3.1.11.1+ds-4_ppc64el.deb ... 999s Unpacking pandoc (3.1.11.1+ds-4) ... 1000s Selecting previously unselected package zip. 1000s Preparing to unpack .../178-zip_3.0-15ubuntu3_ppc64el.deb ... 1000s Unpacking zip (3.0-15ubuntu3) ... 1000s Selecting previously unselected package unzip. 1000s Preparing to unpack .../179-unzip_6.0-29ubuntu1_ppc64el.deb ... 1000s Unpacking unzip (6.0-29ubuntu1) ... 1001s Selecting previously unselected package xdg-utils. 1001s Preparing to unpack .../180-xdg-utils_1.2.1-2ubuntu2_all.deb ... 1001s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 1001s Selecting previously unselected package r-base-core. 1001s Preparing to unpack .../181-r-base-core_4.5.2-1ubuntu2_ppc64el.deb ... 1001s Unpacking r-base-core (4.5.2-1ubuntu2) ... 1001s Selecting previously unselected package liblzma-dev:ppc64el. 1001s Preparing to unpack .../182-liblzma-dev_5.8.2-2_ppc64el.deb ... 1001s Unpacking liblzma-dev:ppc64el (5.8.2-2) ... 1001s Selecting previously unselected package libtirpc-dev:ppc64el. 1001s Preparing to unpack .../183-libtirpc-dev_1.3.6+ds-1_ppc64el.deb ... 1001s Unpacking libtirpc-dev:ppc64el (1.3.6+ds-1) ... 1001s Selecting previously unselected package r-base-dev. 1001s Preparing to unpack .../184-r-base-dev_4.5.2-1ubuntu2_all.deb ... 1001s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 1001s Selecting previously unselected package pkg-r-autopkgtest. 1001s Preparing to unpack .../185-pkg-r-autopkgtest_20250812_all.deb ... 1001s Unpacking pkg-r-autopkgtest (20250812) ... 1001s Selecting previously unselected package r-bioc-biocgenerics. 1001s Preparing to unpack .../186-r-bioc-biocgenerics_0.52.0-2_all.deb ... 1001s Unpacking r-bioc-biocgenerics (0.52.0-2) ... 1001s Selecting previously unselected package r-bioc-biobase. 1001s Preparing to unpack .../187-r-bioc-biobase_2.66.0-2_ppc64el.deb ... 1001s Unpacking r-bioc-biobase (2.66.0-2) ... 1001s Selecting previously unselected package r-bioc-s4vectors. 1001s Preparing to unpack .../188-r-bioc-s4vectors_0.44.0+dfsg-2_ppc64el.deb ... 1001s Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) ... 1001s Selecting previously unselected package r-bioc-iranges. 1001s Preparing to unpack .../189-r-bioc-iranges_2.40.1-3_ppc64el.deb ... 1001s Unpacking r-bioc-iranges (2.40.1-3) ... 1001s Selecting previously unselected package r-cran-dbi. 1001s Preparing to unpack .../190-r-cran-dbi_1.2.3-1build1_all.deb ... 1001s Unpacking r-cran-dbi (1.2.3-1build1) ... 1001s Selecting previously unselected package r-cran-bit. 1001s Preparing to unpack .../191-r-cran-bit_4.6.0+dfsg-1_ppc64el.deb ... 1001s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 1001s Selecting previously unselected package r-cran-bit64. 1001s Preparing to unpack .../192-r-cran-bit64_4.6.0-1-4_ppc64el.deb ... 1001s Unpacking r-cran-bit64 (4.6.0-1-4) ... 1001s Selecting previously unselected package r-cran-rlang. 1001s Preparing to unpack .../193-r-cran-rlang_1.1.5-3_ppc64el.deb ... 1001s Unpacking r-cran-rlang (1.1.5-3) ... 1001s Selecting previously unselected package r-cran-cli. 1001s Preparing to unpack .../194-r-cran-cli_3.6.4-1_ppc64el.deb ... 1001s Unpacking r-cran-cli (3.6.4-1) ... 1002s Selecting previously unselected package r-cran-glue. 1002s Preparing to unpack .../195-r-cran-glue_1.8.0-1_ppc64el.deb ... 1002s Unpacking r-cran-glue (1.8.0-1) ... 1002s Selecting previously unselected package r-cran-lifecycle. 1002s Preparing to unpack .../196-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 1002s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 1002s Selecting previously unselected package r-cran-vctrs. 1002s Preparing to unpack .../197-r-cran-vctrs_0.6.5-1_ppc64el.deb ... 1002s Unpacking r-cran-vctrs (0.6.5-1) ... 1002s Selecting previously unselected package r-cran-blob. 1002s Preparing to unpack .../198-r-cran-blob_1.3.0-1_all.deb ... 1002s Unpacking r-cran-blob (1.3.0-1) ... 1002s Selecting previously unselected package r-cran-fastmap. 1002s Preparing to unpack .../199-r-cran-fastmap_1.2.0-1_ppc64el.deb ... 1002s Unpacking r-cran-fastmap (1.2.0-1) ... 1002s Selecting previously unselected package r-cran-cachem. 1002s Preparing to unpack .../200-r-cran-cachem_1.1.0-1_ppc64el.deb ... 1002s Unpacking r-cran-cachem (1.1.0-1) ... 1002s Selecting previously unselected package r-cran-memoise. 1002s Preparing to unpack .../201-r-cran-memoise_2.0.1-1build1_all.deb ... 1002s Unpacking r-cran-memoise (2.0.1-1build1) ... 1002s Selecting previously unselected package r-cran-pkgconfig. 1002s Preparing to unpack .../202-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 1002s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 1002s Selecting previously unselected package r-cran-plogr. 1002s Preparing to unpack .../203-r-cran-plogr_0.2.0-3build2_all.deb ... 1002s Unpacking r-cran-plogr (0.2.0-3build2) ... 1002s Selecting previously unselected package r-cran-cpp11. 1002s Preparing to unpack .../204-r-cran-cpp11_0.5.3-1_all.deb ... 1002s Unpacking r-cran-cpp11 (0.5.3-1) ... 1002s Selecting previously unselected package r-cran-rsqlite. 1002s Preparing to unpack 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previously unselected package r-cran-openssl. 1002s Preparing to unpack .../211-r-cran-openssl_2.3.2+dfsg-1_ppc64el.deb ... 1002s Unpacking r-cran-openssl (2.3.2+dfsg-1) ... 1002s Selecting previously unselected package r-cran-r6. 1002s Preparing to unpack .../212-r-cran-r6_2.6.1-1_all.deb ... 1002s Unpacking r-cran-r6 (2.6.1-1) ... 1002s Selecting previously unselected package r-cran-httr. 1002s Preparing to unpack .../213-r-cran-httr_1.4.7+dfsg-1_all.deb ... 1002s Unpacking r-cran-httr (1.4.7+dfsg-1) ... 1002s Selecting previously unselected package r-cran-png. 1002s Preparing to unpack .../214-r-cran-png_0.1-8-1build2_ppc64el.deb ... 1002s Unpacking r-cran-png (0.1-8-1build2) ... 1002s Selecting previously unselected package r-bioc-zlibbioc. 1002s Preparing to unpack .../215-r-bioc-zlibbioc_1.52.0+dfsg-2_all.deb ... 1002s Unpacking r-bioc-zlibbioc (1.52.0+dfsg-2) ... 1002s Selecting previously unselected package r-bioc-xvector. 1002s Preparing to unpack .../216-r-bioc-xvector_0.46.0-2_ppc64el.deb ... 1002s Unpacking r-bioc-xvector (0.46.0-2) ... 1002s Selecting previously unselected package r-bioc-ucsc.utils. 1002s Preparing to unpack .../217-r-bioc-ucsc.utils_1.2.0+ds-2_all.deb ... 1002s Unpacking r-bioc-ucsc.utils (1.2.0+ds-2) ... 1002s Selecting previously unselected package r-bioc-genomeinfodbdata. 1002s Preparing to unpack .../218-r-bioc-genomeinfodbdata_1.2.13-2_all.deb ... 1002s Unpacking r-bioc-genomeinfodbdata (1.2.13-2) ... 1002s Selecting previously unselected package r-bioc-genomeinfodb. 1002s Preparing to unpack .../219-r-bioc-genomeinfodb_1.42.3+dfsg-1_all.deb ... 1002s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ... 1002s Selecting previously unselected package r-cran-crayon. 1002s Preparing to unpack .../220-r-cran-crayon_1.5.3-1_all.deb ... 1002s Unpacking r-cran-crayon (1.5.3-1) ... 1002s Selecting previously unselected package r-bioc-biostrings. 1002s Preparing to unpack .../221-r-bioc-biostrings_2.74.1+dfsg-2_ppc64el.deb ... 1002s Unpacking r-bioc-biostrings (2.74.1+dfsg-2) ... 1002s Selecting previously unselected package r-bioc-keggrest. 1002s Preparing to unpack .../222-r-bioc-keggrest_1.46.0+dfsg-3_all.deb ... 1002s Unpacking r-bioc-keggrest (1.46.0+dfsg-3) ... 1002s Selecting previously unselected package r-bioc-annotationdbi. 1002s Preparing to unpack .../223-r-bioc-annotationdbi_1.68.0-2_all.deb ... 1002s Unpacking r-bioc-annotationdbi (1.68.0-2) ... 1002s Selecting previously unselected package r-cran-r.methodss3. 1002s Preparing to unpack .../224-r-cran-r.methodss3_1.8.2-1_all.deb ... 1002s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 1002s Selecting previously unselected package r-cran-r.oo. 1002s Preparing to unpack .../225-r-cran-r.oo_1.27.1-1_all.deb ... 1002s Unpacking r-cran-r.oo (1.27.1-1) ... 1002s Selecting previously unselected package r-cran-r.utils. 1002s Preparing to unpack .../226-r-cran-r.utils_2.13.0-1_all.deb ... 1002s Unpacking r-cran-r.utils (2.13.0-1) ... 1002s Selecting previously unselected package r-cran-matrixstats. 1002s Preparing to unpack .../227-r-cran-matrixstats_1.5.0-1_ppc64el.deb ... 1002s Unpacking r-cran-matrixstats (1.5.0-1) ... 1002s Selecting previously unselected package r-bioc-aroma.light. 1003s Preparing to unpack .../228-r-bioc-aroma.light_3.36.0-2_all.deb ... 1003s Unpacking r-bioc-aroma.light (3.36.0-2) ... 1003s Selecting previously unselected package r-bioc-biocio. 1003s Preparing to unpack .../229-r-bioc-biocio_1.16.0+dfsg-2_all.deb ... 1003s Unpacking r-bioc-biocio (1.16.0+dfsg-2) ... 1003s Selecting previously unselected package r-cran-formatr. 1003s Preparing to unpack .../230-r-cran-formatr_1.14-2_all.deb ... 1003s Unpacking r-cran-formatr (1.14-2) ... 1003s Selecting previously unselected package r-cran-lambda.r. 1003s Preparing to unpack .../231-r-cran-lambda.r_1.2.4-2build2_all.deb ... 1003s Unpacking r-cran-lambda.r (1.2.4-2build2) ... 1003s Selecting previously unselected package r-cran-futile.options. 1003s Preparing to unpack .../232-r-cran-futile.options_1.0.1-3build2_all.deb ... 1003s Unpacking r-cran-futile.options (1.0.1-3build2) ... 1003s Selecting previously unselected package r-cran-futile.logger. 1003s Preparing to unpack .../233-r-cran-futile.logger_1.4.3-4build2_all.deb ... 1003s Unpacking r-cran-futile.logger (1.4.3-4build2) ... 1003s Selecting previously unselected package r-cran-snow. 1003s Preparing to unpack .../234-r-cran-snow_1%3a0.4.4-2build1_all.deb ... 1003s Unpacking r-cran-snow (1:0.4.4-2build1) ... 1003s Selecting previously unselected package r-cran-codetools. 1003s Preparing to unpack .../235-r-cran-codetools_0.2-20-1build1_all.deb ... 1003s Unpacking r-cran-codetools (0.2-20-1build1) ... 1003s Selecting previously unselected package r-cran-bh. 1003s Preparing to unpack .../236-r-cran-bh_1.84.0-1_all.deb ... 1003s Unpacking r-cran-bh (1.84.0-1) ... 1003s Selecting previously unselected package r-bioc-biocparallel. 1003s Preparing to unpack .../237-r-bioc-biocparallel_1.40.0-2_ppc64el.deb ... 1003s Unpacking r-bioc-biocparallel (1.40.0-2) ... 1003s Selecting previously unselected package r-cran-base64enc. 1003s Preparing to unpack .../238-r-cran-base64enc_0.1-3-3build1_ppc64el.deb ... 1003s Unpacking r-cran-base64enc (0.1-3-3build1) ... 1003s Selecting previously unselected package r-cran-digest. 1003s Preparing to unpack .../239-r-cran-digest_0.6.39-1_ppc64el.deb ... 1003s Unpacking r-cran-digest (0.6.39-1) ... 1003s Selecting previously unselected package r-cran-htmltools. 1003s Preparing to unpack .../240-r-cran-htmltools_0.5.8.1-1_ppc64el.deb ... 1003s Unpacking r-cran-htmltools (0.5.8.1-1) ... 1003s Selecting previously unselected package r-cran-evaluate. 1003s Preparing to unpack .../241-r-cran-evaluate_1.0.5-1_all.deb ... 1003s Unpacking r-cran-evaluate (1.0.5-1) ... 1003s Selecting previously unselected package r-cran-xfun. 1003s Preparing to unpack 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r-cran-tinytex. 1004s Preparing to unpack .../253-r-cran-tinytex_0.58-1_all.deb ... 1004s Unpacking r-cran-tinytex (0.58-1) ... 1004s Selecting previously unselected package libjs-modernizr. 1004s Preparing to unpack .../254-libjs-modernizr_3.13.0-0.1build1_all.deb ... 1004s Unpacking libjs-modernizr (3.13.0-0.1build1) ... 1004s Selecting previously unselected package r-cran-littler. 1004s Preparing to unpack .../255-r-cran-littler_0.3.22-1_ppc64el.deb ... 1004s Unpacking r-cran-littler (0.3.22-1) ... 1004s Selecting previously unselected package r-cran-pkgkitten. 1004s Preparing to unpack .../256-r-cran-pkgkitten_0.2.4-1_all.deb ... 1004s Unpacking r-cran-pkgkitten (0.2.4-1) ... 1004s Selecting previously unselected package r-cran-rcpp. 1004s Preparing to unpack .../257-r-cran-rcpp_1.1.0-1_ppc64el.deb ... 1004s Unpacking r-cran-rcpp (1.1.0-1) ... 1004s Selecting previously unselected package r-cran-later. 1004s Preparing to unpack .../258-r-cran-later_1.4.1+dfsg-1_ppc64el.deb ... 1004s Unpacking r-cran-later (1.4.1+dfsg-1) ... 1004s Selecting previously unselected package r-cran-magrittr. 1004s Preparing to unpack .../259-r-cran-magrittr_2.0.3-1_ppc64el.deb ... 1004s Unpacking r-cran-magrittr (2.0.3-1) ... 1004s Selecting previously unselected package r-cran-promises. 1004s Preparing to unpack .../260-r-cran-promises_1.3.2+dfsg-1_ppc64el.deb ... 1004s Unpacking r-cran-promises (1.3.2+dfsg-1) ... 1004s Selecting previously unselected package r-cran-httpuv. 1004s Preparing to unpack .../261-r-cran-httpuv_1.6.15+dfsg-1_ppc64el.deb ... 1004s Unpacking r-cran-httpuv (1.6.15+dfsg-1) ... 1004s Selecting previously unselected package r-cran-xtable. 1004s Preparing to unpack .../262-r-cran-xtable_1%3a1.8-4-2build1_all.deb ... 1004s Unpacking r-cran-xtable (1:1.8-4-2build1) ... 1004s Selecting previously unselected package r-cran-sourcetools. 1004s Preparing to unpack .../263-r-cran-sourcetools_0.1.7-1-1_ppc64el.deb ... 1004s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 1004s Selecting previously unselected package r-cran-withr. 1004s Preparing to unpack .../264-r-cran-withr_3.0.2+dfsg-1_all.deb ... 1004s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 1004s Selecting previously unselected package r-cran-commonmark. 1004s Preparing to unpack .../265-r-cran-commonmark_1.9.5-1_ppc64el.deb ... 1004s Unpacking r-cran-commonmark (1.9.5-1) ... 1004s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 1004s Preparing to unpack .../266-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 1004s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 1004s Selecting previously unselected package r-cran-shiny. 1004s Preparing to unpack .../267-r-cran-shiny_1.10.0+dfsg-2_all.deb ... 1004s Unpacking r-cran-shiny (1.10.0+dfsg-2) ... 1004s Selecting previously unselected package r-cran-rmarkdown. 1004s Preparing to unpack .../268-r-cran-rmarkdown_2.30+dfsg-1_all.deb ... 1004s Unpacking r-cran-rmarkdown (2.30+dfsg-1) ... 1005s Selecting previously unselected package r-cran-bookdown. 1005s Preparing to unpack .../269-r-cran-bookdown_0.42+dfsg-1_all.deb ... 1005s Unpacking r-cran-bookdown (0.42+dfsg-1) ... 1005s Selecting previously unselected package r-cran-biocmanager. 1005s Preparing to unpack .../270-r-cran-biocmanager_1.30.25+dfsg-1_all.deb ... 1005s Unpacking r-cran-biocmanager (1.30.25+dfsg-1) ... 1005s Selecting previously unselected package tex-common. 1005s Preparing to unpack .../271-tex-common_6.20_all.deb ... 1005s Unpacking tex-common (6.20) ... 1005s Selecting previously unselected package t1utils. 1005s Preparing to unpack .../272-t1utils_1.41-4build4_ppc64el.deb ... 1005s Unpacking t1utils (1.41-4build4) ... 1005s Selecting previously unselected package texlive-binaries. 1005s Preparing to unpack .../273-texlive-binaries_2025.20250727.75242+ds-5build1_ppc64el.deb ... 1005s Unpacking texlive-binaries (2025.20250727.75242+ds-5build1) ... 1005s Selecting previously unselected package texlive-base. 1005s Preparing to unpack .../274-texlive-base_2025.20260124-1_all.deb ... 1005s Unpacking texlive-base (2025.20260124-1) ... 1006s Selecting previously unselected package texlive-latex-base. 1006s Preparing to unpack .../275-texlive-latex-base_2025.20260124-1_all.deb ... 1006s Unpacking texlive-latex-base (2025.20260124-1) ... 1007s Selecting previously unselected package texlive-bibtex-extra. 1007s Preparing to unpack .../276-texlive-bibtex-extra_2025.20260124-1_all.deb ... 1007s Unpacking texlive-bibtex-extra (2025.20260124-1) ... 1010s Selecting previously unselected package r-bioc-biocversion. 1010s Preparing to unpack .../277-r-bioc-biocversion_3.20.0-2_all.deb ... 1010s Unpacking r-bioc-biocversion (3.20.0-2) ... 1010s Selecting previously unselected package r-bioc-biocstyle. 1010s Preparing to unpack .../278-r-bioc-biocstyle_2.34.0+dfsg-1_all.deb ... 1010s Unpacking r-bioc-biocstyle (2.34.0+dfsg-1) ... 1010s Selecting previously unselected package r-bioc-genomicranges. 1010s Preparing to unpack .../279-r-bioc-genomicranges_1.58.0+dfsg-2_ppc64el.deb ... 1010s Unpacking r-bioc-genomicranges (1.58.0+dfsg-2) ... 1010s Selecting previously unselected package r-cran-xml. 1010s Preparing to unpack .../280-r-cran-xml_3.99-0.20-1_ppc64el.deb ... 1010s Unpacking r-cran-xml (3.99-0.20-1) ... 1010s Selecting previously unselected package r-cran-bitops. 1010s Preparing to unpack .../281-r-cran-bitops_1.0-9-1_ppc64el.deb ... 1010s Unpacking r-cran-bitops (1.0-9-1) ... 1010s Selecting previously unselected package r-bioc-rhtslib. 1010s Preparing to unpack .../282-r-bioc-rhtslib_3.2.0+dfsg-2_ppc64el.deb ... 1010s Unpacking r-bioc-rhtslib (3.2.0+dfsg-2) ... 1010s Selecting previously unselected package r-bioc-rsamtools. 1010s Preparing to unpack .../283-r-bioc-rsamtools_2.22.0+dfsg-2_ppc64el.deb ... 1010s Unpacking r-bioc-rsamtools (2.22.0+dfsg-2) ... 1010s Selecting previously unselected package r-bioc-matrixgenerics. 1010s Preparing to unpack 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r-bioc-genomicfeatures (1.58.0+dfsg-2) ... 1011s Selecting previously unselected package r-bioc-org.hs.eg.db. 1011s Preparing to unpack .../300-r-bioc-org.hs.eg.db_3.20.0-3_all.deb ... 1011s Unpacking r-bioc-org.hs.eg.db (3.20.0-3) ... 1012s Selecting previously unselected package r-bioc-variantannotation. 1012s Preparing to unpack .../301-r-bioc-variantannotation_1.52.0-2_ppc64el.deb ... 1012s Unpacking r-bioc-variantannotation (1.52.0-2) ... 1012s Selecting previously unselected package r-cran-rcolorbrewer. 1012s Preparing to unpack .../302-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 1012s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 1012s Selecting previously unselected package r-cran-data.table. 1012s Preparing to unpack .../303-r-cran-data.table_1.17.0+dfsg-1_ppc64el.deb ... 1012s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 1012s Selecting previously unselected package r-cran-gtable. 1012s Preparing to unpack .../304-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 1012s 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Setting up libtsan2:ppc64el (15.2.0-12ubuntu1) ... 1016s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 1016s Setting up libisl23:ppc64el (0.27-1build1) ... 1016s Setting up libc-dev-bin (2.42-2ubuntu4) ... 1016s Setting up libtasn1-6-dev:ppc64el (4.21.0-2) ... 1016s Setting up libdeflate-dev:ppc64el (1.23-2build1) ... 1016s Setting up node-normalize.css (8.0.1-5.1) ... 1016s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 1016s Setting up xdg-utils (1.2.1-2ubuntu2) ... 1016s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 1016s Setting up libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 1016s Setting up libbrotli-dev:ppc64el (1.1.0-2build6) ... 1016s Setting up liblsan0:ppc64el (15.2.0-12ubuntu1) ... 1016s Setting up libp11-kit-dev:ppc64el (0.25.10-1) ... 1016s Setting up libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 1016s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode 1016s Setting up libsz2:ppc64el (1.1.5-1) ... 1016s Setting up dctrl-tools (2.24-3build4) ... 1016s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 1016s Setting up libitm1:ppc64el (15.2.0-12ubuntu1) ... 1016s Setting up libsynctex2:ppc64el (2025.20250727.75242+ds-5build1) ... 1016s Setting up libkadm5clnt-mit12:ppc64el (1.22.1-2) ... 1016s Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 1016s Setting up libpotrace0:ppc64el (1.16-2build2) ... 1016s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 1016s Setting up libice6:ppc64el (2:1.1.1-1build1) ... 1016s Setting up liblapack3:ppc64el (3.12.1-7ubuntu1) ... 1016s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 1016s Setting up libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 1016s Setting up libgmp-dev:ppc64el (2:6.3.0+dfsg-5ubuntu1) ... 1016s Setting up nettle-dev:ppc64el (3.10.2-1) ... 1016s Setting up libkdb5-10t64:ppc64el (1.22.1-2) ... 1016s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 1016s Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 1016s Setting up libaec-dev:ppc64el (1.1.5-1) ... 1016s Setting up libpaper-utils (2.2.5-0.3build1) ... 1016s Setting up libbibtex-parser-perl (1.93+dfsg-1) ... 1016s Setting up libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 1016s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 1016s Setting up pkgconf:ppc64el (1.8.1-4build1) ... 1016s Setting up libthai0:ppc64el (0.1.30-1) ... 1016s Setting up cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1016s Setting up libjs-jquery-ui (1.13.2+dfsg-1build1) ... 1016s Setting up libptexenc1:ppc64el (2025.20250727.75242+ds-5build1) ... 1016s Setting up pandoc (3.1.11.1+ds-4) ... 1016s Setting up liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 1016s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode 1016s Setting up libhdf5-310:ppc64el (1.14.6+repack-2) ... 1016s Setting up cpp-15 (15.2.0-12ubuntu1) ... 1016s Setting up libtiff6:ppc64el (4.7.0-3ubuntu3) ... 1016s Setting up libkadm5srv-mit12:ppc64el (1.22.1-2) ... 1016s Setting up libc6-dev:ppc64el (2.42-2ubuntu4) ... 1016s Setting up libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 1016s Setting up libhdf5-fortran-310:ppc64el (1.14.6+repack-2) ... 1016s Setting up libsm6:ppc64el (2:1.2.6-1build1) ... 1016s Setting up libicu-dev:ppc64el (78.2-1ubuntu1) ... 1016s Setting up cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1016s Setting up libbz2-dev:ppc64el (1.0.8-6build2) ... 1016s Setting up libhdf5-cpp-310:ppc64el (1.14.6+repack-2) ... 1016s Setting up libgnutls28-dev:ppc64el (3.8.10-3ubuntu1) ... 1016s Setting up libnghttp2-dev:ppc64el (1.64.0-1.1ubuntu1) ... 1016s Setting up libhdf5-hl-310:ppc64el (1.14.6+repack-2) ... 1016s Setting up fontconfig (2.17.1-3ubuntu1) ... 1018s Regenerating fonts cache... done. 1018s Setting up libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 1018s Setting up libxft2:ppc64el (2.3.6-1build2) ... 1018s Setting up libncurses-dev:ppc64el (6.6+20251231-1) ... 1018s Setting up libpcre2-dev:ppc64el (10.46-1) ... 1018s Setting up gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1018s Setting up libtk8.6:ppc64el (8.6.17-1) ... 1018s Setting up libpango-1.0-0:ppc64el (1.57.0-1) ... 1018s Setting up libreadline-dev:ppc64el (8.3-3) ... 1018s Setting up libcairo2:ppc64el (1.18.4-3) ... 1018s Setting up gcc-15 (15.2.0-12ubuntu1) ... 1018s Setting up libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 1018s Setting up gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1018s Setting up libxt6t64:ppc64el (1:1.2.1-1.3) ... 1018s Setting up comerr-dev:ppc64el (2.1-1.47.2-3ubuntu2) ... 1018s Setting up gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1018s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 1018s Setting up cpp (4:15.2.0-4ubuntu1) ... 1018s Setting up libboost1.90-dev:ppc64el (1.90.0-2ubuntu1) ... 1018s Setting up libboost-dev:ppc64el (1.90.0.0ubuntu3) ... 1018s Setting up libpangoft2-1.0-0:ppc64el (1.57.0-1) ... 1018s Setting up libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 1018s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 1018s Setting up libpangocairo-1.0-0:ppc64el (1.57.0-1) ... 1018s Setting up krb5-multidev:ppc64el (1.22.1-2) ... 1018s Setting up libhdf5-hl-cpp-310:ppc64el (1.14.6+repack-2) ... 1018s Setting up g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1018s Setting up libhdf5-hl-fortran-310:ppc64el (1.14.6+repack-2) ... 1018s Setting up libxmu6:ppc64el (2:1.1.3-4) ... 1018s Setting up libpng-dev:ppc64el (1.6.54-1) ... 1018s Setting up libjpeg-dev:ppc64el (8c-2ubuntu11) ... 1018s Setting up libxaw7:ppc64el (2:1.0.16-1build1) ... 1018s Setting up gcc (4:15.2.0-4ubuntu1) ... 1018s Setting up libkrb5-dev:ppc64el (1.22.1-2) ... 1018s Setting up gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1018s Setting up r-base-core (4.5.2-1ubuntu2) ... 1018s Creating config file /etc/R/Renviron with new version 1018s Setting up r-cran-crayon (1.5.3-1) ... 1018s Setting up librtmp-dev:ppc64el (2.4+20151223.gitfa8646d.1-3) ... 1018s Setting up r-cran-labeling (0.4.3-1) ... 1018s Setting up r-cran-sourcetools (0.1.7-1-1) ... 1018s Setting up r-cran-futile.options (1.0.1-3build2) ... 1018s Setting up r-cran-lattice (0.22-7-1) ... 1018s Setting up libssh2-1-dev:ppc64el (1.11.1-1build1) ... 1018s Setting up r-cran-ps (1.9.0-1) ... 1018s Setting up r-cran-farver (2.1.2-1) ... 1018s Setting up r-cran-formatr (1.14-2) ... 1018s Setting up r-cran-xml (3.99-0.20-1) ... 1018s Setting up r-cran-viridislite (0.4.3-1) ... 1018s Setting up texlive-binaries (2025.20250727.75242+ds-5build1) ... 1018s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 1018s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 1018s Setting up r-cran-lazyeval (0.2.2-1build2) ... 1018s Setting up r-cran-commonmark (1.9.5-1) ... 1018s Setting up r-cran-rjson (0.2.23-1) ... 1018s Setting up r-cran-r6 (2.6.1-1) ... 1018s Setting up r-cran-pkgkitten (0.2.4-1) ... 1018s Setting up texlive-base (2025.20260124-1) ... 1019s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 1019s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 1019s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 1020s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 1020s Setting up g++-15 (15.2.0-12ubuntu1) ... 1020s Setting up r-cran-magrittr (2.0.3-1) ... 1020s Setting up r-cran-rappdirs (0.3.3-1build1) ... 1020s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ... 1020s Setting up g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1020s Setting up r-cran-littler (0.3.22-1) ... 1020s Setting up r-cran-bh (1.84.0-1) ... 1020s Setting up r-cran-fs (1.6.5+dfsg-1) ... 1020s Setting up r-cran-rcpp (1.1.0-1) ... 1020s Setting up r-cran-curl (7.0.0+dfsg-1) ... 1020s Setting up r-cran-codetools (0.2-20-1build1) ... 1020s Setting up r-cran-brio (1.1.5-1) ... 1020s Setting up r-cran-diffobj (0.3.5-1build1) ... 1020s Setting up r-bioc-biocgenerics (0.52.0-2) ... 1020s Setting up r-cran-rlang (1.1.5-3) ... 1020s Setting up r-cran-matrixstats (1.5.0-1) ... 1020s Setting up r-cran-listenv (0.10.0+dfsg-1) ... 1020s Setting up r-bioc-matrixgenerics (1.18.1-1) ... 1020s Setting up r-cran-xfun (0.55+dfsg-1) ... 1020s Setting up r-cran-vgam (1.1-13-1) ... 1020s Setting up r-cran-sys (3.4.3-1) ... 1020s Setting up r-cran-plogr (0.2.0-3build2) ... 1020s Setting up r-cran-withr (3.0.2+dfsg-1) ... 1020s Setting up r-cran-processx (3.8.6-1) ... 1020s Setting up r-cran-mime (0.12-2) ... 1020s Setting up r-cran-praise (1.0.0-4build2) ... 1020s Setting up r-cran-base64enc (0.1-3-3build1) ... 1020s Setting up r-cran-abind (1.4-8-1build1) ... 1020s Setting up r-cran-digest (0.6.39-1) ... 1020s Setting up r-cran-yaml (2.3.10-1) ... 1020s Setting up r-cran-lambda.r (1.2.4-2build2) ... 1020s Setting up r-cran-evaluate (1.0.5-1) ... 1020s Setting up r-cran-dbi (1.2.3-1build1) ... 1020s Setting up r-cran-highr (0.11+dfsg-1) ... 1020s Setting up r-cran-mclust (6.1.1-1) ... 1020s Setting up r-cran-snow (1:0.4.4-2build1) ... 1020s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 1020s Setting up r-cran-glue (1.8.0-1) ... 1020s Setting up r-cran-bit (4.6.0+dfsg-1) ... 1020s Setting up r-cran-xtable (1:1.8-4-2build1) ... 1020s Setting up r-cran-cli (3.6.4-1) ... 1020s Setting up gfortran (4:15.2.0-4ubuntu1) ... 1020s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 1020s 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 1020s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 1020s 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 1020s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 1020s Setting up r-cran-bitops (1.0-9-1) ... 1020s Setting up r-bioc-biocversion (3.20.0-2) ... 1020s Setting up r-cran-rprojroot (2.1.1-1) ... 1020s Setting up r-cran-bit64 (4.6.0-1-4) ... 1020s Setting up r-cran-biocmanager (1.30.25+dfsg-1) ... 1020s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ... 1020s Setting up r-cran-askpass (1.2.1-1) ... 1020s Setting up r-cran-fastmap (1.2.0-1) ... 1020s Setting up r-cran-png (0.1-8-1build2) ... 1020s Setting up r-cran-r.methodss3 (1.8.2-1) ... 1020s Setting up r-bioc-biobase (2.66.0-2) ... 1020s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... 1020s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 1020s Setting up r-cran-getopt (1.20.4-1) ... 1020s Setting up r-cran-parallelly (1.42.0-1) ... 1020s Setting up texlive-latex-base (2025.20260124-1) ... 1020s Setting up r-cran-rex (1.2.1-1build1) ... 1020s Setting up r-cran-markdown (1.13-1) ... 1020s Setting up r-cran-s7 (0.2.0-1) ... 1020s Setting up libcurl4-openssl-dev:ppc64el (8.18.0-1ubuntu1) ... 1020s Setting up r-cran-cpp11 (0.5.3-1) ... 1020s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 1020s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ... 1020s Setting up r-cran-isoband (0.2.7-1) ... 1020s Setting up r-cran-futile.logger (1.4.3-4build2) ... 1020s Setting up r-cran-waldo (0.6.2-1) ... 1020s Setting up libhdf5-dev (1.14.6+repack-2) ... 1020s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/powerpc64le-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode 1020s Setting up r-cran-scales (1.4.0-1) ... 1020s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 1020s Setting up r-cran-later (1.4.1+dfsg-1) ... 1020s Setting up r-cran-matrix (1.7-4-1) ... 1020s Setting up r-cran-htmltools (0.5.8.1-1) ... 1020s Setting up r-cran-tinytex (0.58-1) ... 1020s Setting up r-cran-knitr (1.51+dfsg-1) ... 1020s Setting up g++ (4:15.2.0-4ubuntu1) ... 1020s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1020s Setting up r-bioc-dnacopy (1.80.0-2) ... 1020s Setting up r-cran-cachem (1.1.0-1) ... 1020s Setting up r-cran-sass (0.4.9+dfsg-1) ... 1020s Setting up build-essential (12.12ubuntu2) ... 1020s Setting up r-bioc-iranges (2.40.1-3) ... 1020s Setting up r-cran-globals (0.19.0-1) ... 1020s Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ... 1020s Setting up r-cran-restfulr (0.0.15-1) ... 1020s Setting up r-cran-optparse (1.7.5-1) ... 1020s Setting up r-cran-vctrs (0.6.5-1) ... 1020s Setting up r-cran-openssl (2.3.2+dfsg-1) ... 1020s Setting up r-base-dev (4.5.2-1ubuntu2) ... 1020s Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ... 1020s Setting up r-bioc-biocparallel (1.40.0-2) ... 1020s Setting up r-cran-callr (3.7.6-1) ... 1020s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 1020s Setting up r-bioc-rhtslib (3.2.0+dfsg-2) ... 1020s Setting up r-cran-desc (1.4.3-1) ... 1020s Setting up r-bioc-rhdf5lib (1.28.0+dfsg-3) ... 1020s Setting up r-cran-fontawesome (0.5.3-1) ... 1020s Setting up r-bioc-biocio (1.16.0+dfsg-2) ... 1020s Setting up r-cran-r.oo (1.27.1-1) ... 1020s Setting up r-bioc-rhdf5filters (1.18.1+dfsg-1) ... 1020s Setting up r-cran-future (1.34.0+dfsg-1) ... 1020s Setting up r-cran-jquerylib (0.1.4+dfsg-5) ... 1020s Setting up texlive-bibtex-extra (2025.20260124-1) ... 1020s Setting up r-cran-httr (1.4.7+dfsg-1) ... 1020s Setting up r-cran-gridextra (2.3-3build2) ... 1020s Setting up r-cran-memoise (2.0.1-1build1) ... 1020s Setting up r-cran-covr (3.6.4+dfsg-1) ... 1020s Setting up r-cran-promises (1.3.2+dfsg-1) ... 1020s Setting up r-cran-blob (1.3.0-1) ... 1020s Setting up pkg-r-autopkgtest (20250812) ... 1020s Setting up r-bioc-xvector (0.46.0-2) ... 1020s Setting up r-cran-pkgbuild (1.4.8-1) ... 1020s Setting up r-cran-rsqlite (2.3.9-1) ... 1020s Setting up r-cran-pkgload (1.4.1-1) ... 1020s Setting up r-cran-r.utils (2.13.0-1) ... 1020s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ... 1020s Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ... 1020s Setting up r-bioc-rhdf5 (2.50.2+dfsg-1build1) ... 1020s Setting up r-cran-httpuv (1.6.15+dfsg-1) ... 1020s Setting up r-cran-testthat (3.2.3-1) ... 1020s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ... 1020s Setting up r-cran-bslib (0.9.0+dfsg-3build1) ... 1020s Setting up r-bioc-aroma.light (3.36.0-2) ... 1020s Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ... 1020s Setting up r-cran-r.cache (0.17.0-1) ... 1020s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ... 1020s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ... 1020s Setting up r-cran-shiny (1.10.0+dfsg-2) ... 1020s Setting up r-cran-pscbs (0.68.0-1) ... 1020s Setting up r-cran-rmarkdown (2.30+dfsg-1) ... 1020s Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ... 1020s Setting up r-cran-bookdown (0.42+dfsg-1) ... 1020s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... 1020s Setting up r-bioc-keggrest (1.46.0+dfsg-3) ... 1020s Setting up r-bioc-annotationdbi (1.68.0-2) ... 1020s Setting up r-bioc-biocstyle (2.34.0+dfsg-1) ... 1020s Setting up r-bioc-genomicalignments (1.42.0-2) ... 1020s Setting up r-bioc-org.hs.eg.db (3.20.0-3) ... 1020s Setting up r-bioc-rtracklayer (1.66.0-3) ... 1020s Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ... 1020s Setting up r-bioc-bsgenome (1.74.0-2) ... 1020s Setting up r-bioc-variantannotation (1.52.0-2) ... 1020s Setting up r-bioc-purecn (2.12.0+dfsg-2) ... 1020s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1021s Processing triggers for man-db (2.13.1-1build1) ... 1023s Processing triggers for install-info (7.2-5) ... 1023s Processing triggers for tex-common (6.20) ... 1023s Running updmap-sys. This may take some time... done. 1023s Running mktexlsr /var/lib/texmf ... done. 1023s Building format(s) --all. 1059s This may take some time... done. 1060s autopkgtest [23:17:36]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1060s autopkgtest [23:17:36]: test pkg-r-autopkgtest: [----------------------- 1060s Test: Try to load the R library PureCN 1060s 1060s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1060s Copyright (C) 2025 The R Foundation for Statistical Computing 1060s Platform: powerpc64le-unknown-linux-gnu 1060s 1060s R is free software and comes with ABSOLUTELY NO WARRANTY. 1060s You are welcome to redistribute it under certain conditions. 1060s Type 'license()' or 'licence()' for distribution details. 1060s 1060s R is a collaborative project with many contributors. 1060s Type 'contributors()' for more information and 1060s 'citation()' on how to cite R or R packages in publications. 1060s 1060s Type 'demo()' for some demos, 'help()' for on-line help, or 1060s 'help.start()' for an HTML browser interface to help. 1060s Type 'q()' to quit R. 1060s 1060s > library('PureCN') 1060s Loading required package: DNAcopy 1060s Loading required package: VariantAnnotation 1060s Loading required package: BiocGenerics 1060s 1060s Attaching package: ‘BiocGenerics’ 1060s 1060s The following objects are masked from ‘package:stats’: 1060s 1060s IQR, mad, sd, var, xtabs 1060s 1060s The following objects are masked from ‘package:base’: 1060s 1060s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 1060s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 1060s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 1060s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 1060s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 1060s table, tapply, union, unique, unsplit, which.max, which.min 1060s 1060s Loading required package: MatrixGenerics 1060s Loading required package: matrixStats 1061s 1061s Attaching package: ‘MatrixGenerics’ 1061s 1061s The following objects are masked from ‘package:matrixStats’: 1061s 1061s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 1061s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 1061s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 1061s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 1061s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 1061s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 1061s colWeightedMeans, colWeightedMedians, colWeightedSds, 1061s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 1061s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 1061s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 1061s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 1061s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 1061s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 1061s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 1061s rowWeightedSds, rowWeightedVars 1061s 1061s Loading required package: GenomeInfoDb 1061s Loading required package: S4Vectors 1061s Loading required package: stats4 1061s 1061s Attaching package: ‘S4Vectors’ 1061s 1061s The following object is masked from ‘package:utils’: 1061s 1061s findMatches 1061s 1061s The following objects are masked from ‘package:base’: 1061s 1061s expand.grid, I, unname 1061s 1061s Loading required package: IRanges 1062s Loading required package: GenomicRanges 1063s Loading required package: SummarizedExperiment 1063s Loading required package: Biobase 1063s Welcome to Bioconductor 1063s 1063s Vignettes contain introductory material; view with 1063s 'browseVignettes()'. To cite Bioconductor, see 1063s 'citation("Biobase")', and for packages 'citation("pkgname")'. 1063s 1063s 1063s Attaching package: ‘Biobase’ 1063s 1063s The following object is masked from ‘package:MatrixGenerics’: 1063s 1063s rowMedians 1063s 1063s The following objects are masked from ‘package:matrixStats’: 1063s 1063s anyMissing, rowMedians 1063s 1066s Loading required package: Rsamtools 1066s Loading required package: Biostrings 1066s Loading required package: XVector 1066s 1066s Attaching package: ‘Biostrings’ 1066s 1066s The following object is masked from ‘package:base’: 1066s 1066s strsplit 1066s 1071s 1071s Attaching package: ‘VariantAnnotation’ 1071s 1071s The following object is masked from ‘package:base’: 1071s 1071s tabulate 1071s 1073s > 1073s + cd tests 1073s + 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 1073s + rm -f testthat/test_setMappingBiasVcf.R 1073s + rm -f testthat/test_processMultipleSamples.R 1073s + grep -Rl TxDb.Hsapiens.UCSC.hg19.knownGene testthat testthat.R 1073s BEGIN TEST testthat.R 1073s + rm -f testthat/test_annotateTargets.R 1073s + 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 1073s + rm -f testthat/test_runAbsoluteCN.R 1073s + rm -f testthat/test_calculatePowerDetectSomatic.R 1073s + rm -f testthat/test_callAmplificationsInLowPurity.R 1073s + rm -f testthat/test_callMutationBurden.R 1073s + rm -f testthat/test_correctCoverageBias.R 1073s + rm -f testthat/test_createCurationFile.R 1073s + rm -f testthat/test_createNormalDatabase.R 1073s + rm -f testthat/test_getSexFromVcf.R 1073s + rm -f testthat/test_plotAbs.R 1073s + rm -f testthat/test_poolCoverage.R 1073s + rm -f testthat/test_readLogRatioFile.R 1073s + rm -f testthat/test_preprocessIntervals.R 1073s + ln -s /usr/lib/R/site-library/PureCN/extdata 1073s + echo BEGIN TEST testthat.R 1073s + LC_ALL=C.UTF-8 R --no-save 1073s 1073s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1073s Copyright (C) 2025 The R Foundation for Statistical Computing 1073s Platform: powerpc64le-unknown-linux-gnu 1073s 1073s R is free software and comes with ABSOLUTELY NO WARRANTY. 1073s You are welcome to redistribute it under certain conditions. 1073s Type 'license()' or 'licence()' for distribution details. 1073s 1073s R is a collaborative project with many contributors. 1073s Type 'contributors()' for more information and 1073s 'citation()' on how to cite R or R packages in publications. 1073s 1073s Type 'demo()' for some demos, 'help()' for on-line help, or 1073s 'help.start()' for an HTML browser interface to help. 1073s Type 'q()' to quit R. 1073s 1073s > library(testthat) 1073s > Loading required package: DNAcopy 1073s library(PureCN) 1073s Loading required package: VariantAnnotation 1073s Loading required package: BiocGenerics 1074s 1074s Attaching package: ‘BiocGenerics’ 1074s 1074s The following objects are masked from ‘package:stats’: 1074s 1074s IQR, mad, sd, var, xtabs 1074s 1074s The following objects are masked from ‘package:base’: 1074s 1074s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 1074s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 1074s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 1074s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 1074s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 1074s table, tapply, union, unique, unsplit, which.max, which.min 1074s 1074s Loading required package: MatrixGenerics 1074s Loading required package: matrixStats 1074s 1074s Attaching package: ‘MatrixGenerics’ 1074s 1074s The following objects are masked from ‘package:matrixStats’: 1074s 1074s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 1074s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 1074s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 1074s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 1074s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 1074s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 1074s colWeightedMeans, colWeightedMedians, colWeightedSds, 1074s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 1074s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 1074s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 1074s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 1074s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 1074s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 1074s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 1074s rowWeightedSds, rowWeightedVars 1074s 1074s Loading required package: GenomeInfoDb 1074s Loading required package: S4Vectors 1074s Loading required package: stats4 1074s 1074s Attaching package: ‘S4Vectors’ 1074s 1074s The following object is masked from ‘package:utils’: 1074s 1074s findMatches 1074s 1074s The following objects are masked from ‘package:base’: 1074s 1074s expand.grid, I, unname 1074s 1074s Loading required package: IRanges 1075s Loading required package: GenomicRanges 1076s Loading required package: SummarizedExperiment 1076s Loading required package: Biobase 1076s Welcome to Bioconductor 1076s 1076s Vignettes contain introductory material; view with 1076s 'browseVignettes()'. To cite Bioconductor, see 1076s 'citation("Biobase")', and for packages 'citation("pkgname")'. 1076s 1076s 1076s Attaching package: ‘Biobase’ 1076s 1076s The following object is masked from ‘package:MatrixGenerics’: 1076s 1076s rowMedians 1076s 1076s The following objects are masked from ‘package:matrixStats’: 1076s 1076s anyMissing, rowMedians 1076s 1079s Loading required package: Rsamtools 1079s Loading required package: Biostrings 1079s Loading required package: XVector 1079s 1079s Attaching package: ‘Biostrings’ 1079s 1079s The following object is masked from ‘package:base’: 1079s 1079s strsplit 1079s 1084s 1084s Attaching package: ‘VariantAnnotation’ 1084s 1084s The following object is masked from ‘package:base’: 1084s 1084s tabulate 1084s 1085s > 1085s > test_check("PureCN") 1088s FATAL [2026-02-09 23:18:02] tumor.coverage.file and interval.file do not align. 1088s 1088s FATAL [2026-02-09 23:18:02] 1088s 1088s FATAL [2026-02-09 23:18:02] This is most likely a user error due to invalid input data or 1088s 1088s FATAL [2026-02-09 23:18:02] parameters (PureCN 2.12.0). 1088s 1088s WARN [2026-02-09 23:18:03] Cannot find all contig lengths while exporting interval file. 1089s INFO [2026-02-09 23:18:04] Processing seq1:1-21 (1/3)... 1089s INFO [2026-02-09 23:18:04] Processing seq1:1227-1247 (2/3)... 1090s INFO [2026-02-09 23:18:04] Processing seq2:594-614 (3/3)... 1091s WARN [2026-02-09 23:18:05] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 1095s INFO [2026-02-09 23:18:09] ------------------------------------------------------------ 1095s INFO [2026-02-09 23:18:09] PureCN 2.12.0 1095s INFO [2026-02-09 23:18:09] ------------------------------------------------------------ 1095s INFO [2026-02-09 23:18:09] Loading coverage files... 1095s INFO [2026-02-09 23:18:09] Mean target coverages: 112X (tumor) 99X (normal). 1095s WARN [2026-02-09 23:18:10] Allosome coverage missing, cannot determine sex. 1095s WARN [2026-02-09 23:18:10] Allosome coverage missing, cannot determine sex. 1095s INFO [2026-02-09 23:18:10] Removing 228 intervals with missing log.ratio. 1095s INFO [2026-02-09 23:18:10] Removing 22 small (< 5bp) intervals. 1095s INFO [2026-02-09 23:18:10] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 1095s WARN [2026-02-09 23:18:10] No normalDB provided. Provide one for better results. 1095s INFO [2026-02-09 23:18:10] Removing 1724 low count (< 100 total reads) intervals. 1095s INFO [2026-02-09 23:18:10] Removing 6 low coverage (< 15.0000X) intervals. 1095s INFO [2026-02-09 23:18:10] Using 8050 intervals (8050 on-target, 0 off-target). 1095s INFO [2026-02-09 23:18:10] No off-target intervals. If this is hybrid-capture data, consider adding them. 1095s INFO [2026-02-09 23:18:10] No interval.file provided. Cannot check for any GC-biases. 1095s INFO [2026-02-09 23:18:10] Loading VCF... 1095s INFO [2026-02-09 23:18:10] Found 127 variants in VCF file. 1095s INFO [2026-02-09 23:18:10] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1095s INFO [2026-02-09 23:18:10] LIB-02240e4 is tumor in VCF file. 1095s INFO [2026-02-09 23:18:10] No homozygous variants in VCF, provide unfiltered VCF. 1095s INFO [2026-02-09 23:18:10] Removing 1 non heterozygous (in matched normal) germline SNPs. 1095s INFO [2026-02-09 23:18:10] Removing 0 low quality variants with non-offset BQ < 25. 1095s INFO [2026-02-09 23:18:10] Base quality scores range from 29 to 35 (offset by 1) 1095s INFO [2026-02-09 23:18:10] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 1096s INFO [2026-02-09 23:18:10] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1096s INFO [2026-02-09 23:18:10] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 1096s INFO [2026-02-09 23:18:11] 1.2% of targets contain variants. 1096s INFO [2026-02-09 23:18:11] Removing 4 variants outside intervals. 1096s INFO [2026-02-09 23:18:11] Found SOMATIC annotation in VCF. 1096s INFO [2026-02-09 23:18:11] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1096s INFO [2026-02-09 23:18:11] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 1096s INFO [2026-02-09 23:18:11] Excluding 0 novel or poor quality variants from segmentation. 1096s INFO [2026-02-09 23:18:11] Sample sex: ? 1096s INFO [2026-02-09 23:18:11] Segmenting data... 1096s INFO [2026-02-09 23:18:11] Loading pre-computed boundaries for DNAcopy... 1096s INFO [2026-02-09 23:18:11] Setting undo.SD parameter to 1.000000. 1097s INFO [2026-02-09 23:18:12] Setting prune.hclust.h parameter to 0.200000. 1097s INFO [2026-02-09 23:18:12] Found 59 segments with median size of 17.67Mb. 1097s INFO [2026-02-09 23:18:12] Using 121 variants. 1097s INFO [2026-02-09 23:18:12] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 1097s INFO [2026-02-09 23:18:12] 2D-grid search of purity and ploidy... 1099s INFO [2026-02-09 23:18:14] Local optima: 0.63/1.9, 0.5/2 1099s INFO [2026-02-09 23:18:14] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... 1100s INFO [2026-02-09 23:18:15] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... 1101s INFO [2026-02-09 23:18:16] Skipping 1 solutions that converged to the same optima. 1101s INFO [2026-02-09 23:18:16] Fitting variants with beta model for local optimum 1/2... 1101s INFO [2026-02-09 23:18:16] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 1104s INFO [2026-02-09 23:18:19] Optimized purity: 0.65 1104s INFO [2026-02-09 23:18:19] Done. 1104s INFO [2026-02-09 23:18:19] ------------------------------------------------------------ 1105s INFO [2026-02-09 23:18:19] Removing 22 non heterozygous (in matched normal) germline SNPs. 1105s INFO [2026-02-09 23:18:19] Removing 19 low quality variants with non-offset BQ < 25. 1105s INFO [2026-02-09 23:18:19] Base quality scores range from 24 to 35 (offset by 1) 1105s INFO [2026-02-09 23:18:20] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1105s INFO [2026-02-09 23:18:20] Initial testing for significant sample cross-contamination: unlikely 1105s INFO [2026-02-09 23:18:20] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1105s INFO [2026-02-09 23:18:20] Removing 22 non heterozygous (in matched normal) germline SNPs. 1105s INFO [2026-02-09 23:18:20] Removing 19 low quality variants with non-offset BQ < 25. 1105s INFO [2026-02-09 23:18:20] Base quality scores range from 24 to 35 (offset by 1) 1105s INFO [2026-02-09 23:18:20] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1106s INFO [2026-02-09 23:18:21] Initial testing for significant sample cross-contamination: unlikely 1106s INFO [2026-02-09 23:18:21] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1106s INFO [2026-02-09 23:18:21] Removing 6 blacklisted variants. 1106s INFO [2026-02-09 23:18:21] Removing 22 non heterozygous (in matched normal) germline SNPs. 1106s INFO [2026-02-09 23:18:21] Removing 19 low quality variants with non-offset BQ < 25. 1106s INFO [2026-02-09 23:18:21] Base quality scores range from 24 to 35 (offset by 1) 1106s INFO [2026-02-09 23:18:21] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1107s INFO [2026-02-09 23:18:21] Initial testing for significant sample cross-contamination: unlikely 1107s INFO [2026-02-09 23:18:22] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1107s WARN [2026-02-09 23:18:22] MuTect stats file lacks contig and position columns. 1107s INFO [2026-02-09 23:18:22] Removing 22 non heterozygous (in matched normal) germline SNPs. 1107s INFO [2026-02-09 23:18:22] Removing 19 low quality variants with non-offset BQ < 25. 1107s INFO [2026-02-09 23:18:22] Base quality scores range from 24 to 35 (offset by 1) 1107s INFO [2026-02-09 23:18:22] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1107s INFO [2026-02-09 23:18:22] Initial testing for significant sample cross-contamination: unlikely 1107s INFO [2026-02-09 23:18:22] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1108s WARN [2026-02-09 23:18:22] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. 1108s WARN [2026-02-09 23:18:22] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. 1108s INFO [2026-02-09 23:18:22] Removing 0 non heterozygous (in matched normal) germline SNPs. 1108s INFO [2026-02-09 23:18:23] Removing 0 low quality variants with non-offset BQ < 25. 1108s INFO [2026-02-09 23:18:23] Base quality scores range from 31 to 33 (offset by 1) 1108s INFO [2026-02-09 23:18:23] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. 1108s INFO [2026-02-09 23:18:23] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1108s INFO [2026-02-09 23:18:23] Removing 22 non heterozygous (in matched normal) germline SNPs. 1108s INFO [2026-02-09 23:18:23] Base quality scores range from 7 to 35 (offset by 1) 1108s INFO [2026-02-09 23:18:23] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 1109s INFO [2026-02-09 23:18:23] Initial testing for significant sample cross-contamination: unlikely 1109s INFO [2026-02-09 23:18:24] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1109s INFO [2026-02-09 23:18:24] Removing 22 non heterozygous (in matched normal) germline SNPs. 1109s INFO [2026-02-09 23:18:24] Base quality scores range from 7 to 35 (offset by 1) 1109s INFO [2026-02-09 23:18:24] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 1109s INFO [2026-02-09 23:18:24] Initial testing for significant sample cross-contamination: unlikely 1109s INFO [2026-02-09 23:18:24] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1109s INFO [2026-02-09 23:18:24] Removing 22 non heterozygous (in matched normal) germline SNPs. 1110s WARN [2026-02-09 23:18:24] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. 1110s FATAL [2026-02-09 23:18:24] No variants passed filter BQ. 1110s 1110s FATAL [2026-02-09 23:18:24] 1110s 1110s FATAL [2026-02-09 23:18:24] This is most likely a user error due to invalid input data or 1110s 1110s FATAL [2026-02-09 23:18:24] parameters (PureCN 2.12.0). 1110s 1110s INFO [2026-02-09 23:18:25] Found 11 variants in VCF file. 1110s WARN [2026-02-09 23:18:25] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 1110s INFO [2026-02-09 23:18:25] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1112s INFO [2026-02-09 23:18:27] Found 11 variants in VCF file. 1112s WARN [2026-02-09 23:18:27] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 1112s INFO [2026-02-09 23:18:27] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1113s INFO [2026-02-09 23:18:28] Found 11 variants in VCF file. 1113s WARN [2026-02-09 23:18:28] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. 1113s INFO [2026-02-09 23:18:28] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1113s INFO [2026-02-09 23:18:28] Found 1000 variants in VCF file. 1113s INFO [2026-02-09 23:18:28] Removing 2 triallelic sites. 1113s WARN [2026-02-09 23:18:28] Having trouble guessing SOMATIC status... 1114s WARN [2026-02-09 23:18:28] DP FORMAT field contains NAs. Removing 44 variants. 1114s INFO [2026-02-09 23:18:28] 954 (100.0%) variants annotated as likely germline (DB INFO flag). 1115s INFO [2026-02-09 23:18:30] Found 12 variants in VCF file. 1115s INFO [2026-02-09 23:18:30] Removing 1 triallelic sites. 1115s WARN [2026-02-09 23:18:30] DP FORMAT field contains NAs. Removing 1 variants. 1115s WARN [2026-02-09 23:18:30] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. 1115s INFO [2026-02-09 23:18:30] 8 (80.0%) variants annotated as likely germline (DB INFO flag). 1116s WARN [2026-02-09 23:18:30] BQ FORMAT field contains NAs. 1116s INFO [2026-02-09 23:18:31] Found 2331 variants in VCF file. 1116s INFO [2026-02-09 23:18:31] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1116s INFO [2026-02-09 23:18:31] Found 2331 variants in VCF file. 1117s INFO [2026-02-09 23:18:31] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1117s WARN [2026-02-09 23:18:32] Did not find base quality scores, will use global error rate of 0.0010 instead. 1117s INFO [2026-02-09 23:18:32] Removing 21 low quality variants with non-offset BQ < 25. 1117s INFO [2026-02-09 23:18:32] Base quality scores range from 24 to 35 (offset by 1) 1118s INFO [2026-02-09 23:18:32] Initial testing for significant sample cross-contamination: unlikely 1118s INFO [2026-02-09 23:18:33] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. 1118s INFO [2026-02-09 23:18:33] Found 2331 variants in VCF file. 1118s INFO [2026-02-09 23:18:33] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1118s WARN [2026-02-09 23:18:33] BQ FORMAT field contains NAs. 1119s WARN [2026-02-09 23:18:34] Allosome coverage missing, cannot determine sex. 1119s WARN [2026-02-09 23:18:34] Allosome coverage missing, cannot determine sex. 1119s INFO [2026-02-09 23:18:34] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. 1119s INFO [2026-02-09 23:18:34] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. 1119s INFO [2026-02-09 23:18:34] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. 1120s INFO [2026-02-09 23:18:35] Found 20 variants in VCF file. 1121s INFO [2026-02-09 23:18:35] 20 (100.0%) variants annotated as likely germline (DB INFO flag). 1121s WARN [2026-02-09 23:18:36] Did not find base quality scores, will use global error rate of 0.0010 instead. 1122s INFO [2026-02-09 23:18:36] Found 127 variants in VCF file. 1122s INFO [2026-02-09 23:18:37] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1122s WARN [2026-02-09 23:18:37] Did not find base quality scores, will use global error rate of 0.0010 instead. 1122s INFO [2026-02-09 23:18:37] ------------------------------------------------------------ 1122s INFO [2026-02-09 23:18:37] PureCN 2.12.0 1122s INFO [2026-02-09 23:18:37] ------------------------------------------------------------ 1122s INFO [2026-02-09 23:18:37] Loading coverage files... 1122s INFO [2026-02-09 23:18:37] Mean target coverages: 112X (tumor) 99X (normal). 1122s WARN [2026-02-09 23:18:37] Allosome coverage missing, cannot determine sex. 1122s WARN [2026-02-09 23:18:37] Allosome coverage missing, cannot determine sex. 1123s INFO [2026-02-09 23:18:37] Removing 228 intervals with missing log.ratio. 1123s INFO [2026-02-09 23:18:37] Removing 22 small (< 5bp) intervals. 1123s INFO [2026-02-09 23:18:37] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 1123s WARN [2026-02-09 23:18:37] No normalDB provided. Provide one for better results. 1123s INFO [2026-02-09 23:18:37] Removing 1724 low count (< 100 total reads) intervals. 1123s INFO [2026-02-09 23:18:37] Removing 6 low coverage (< 15.0000X) intervals. 1123s INFO [2026-02-09 23:18:37] Using 8050 intervals (8050 on-target, 0 off-target). 1123s INFO [2026-02-09 23:18:37] No off-target intervals. If this is hybrid-capture data, consider adding them. 1123s INFO [2026-02-09 23:18:37] No interval.file provided. Cannot check for any GC-biases. 1123s INFO [2026-02-09 23:18:37] Loading VCF... 1123s INFO [2026-02-09 23:18:37] Found 127 variants in VCF file. 1123s INFO [2026-02-09 23:18:38] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1123s INFO [2026-02-09 23:18:38] LIB-02240e4 is tumor in VCF file. 1123s INFO [2026-02-09 23:18:38] No homozygous variants in VCF, provide unfiltered VCF. 1123s INFO [2026-02-09 23:18:38] Removing 1 non heterozygous (in matched normal) germline SNPs. 1123s INFO [2026-02-09 23:18:38] Removing 0 low quality variants with non-offset BQ < 25. 1123s INFO [2026-02-09 23:18:38] Base quality scores range from 29 to 35 (offset by 1) 1123s INFO [2026-02-09 23:18:38] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 1123s INFO [2026-02-09 23:18:38] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1123s INFO [2026-02-09 23:18:38] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 1124s INFO [2026-02-09 23:18:38] 1.2% of targets contain variants. 1124s INFO [2026-02-09 23:18:38] Removing 4 variants outside intervals. 1124s INFO [2026-02-09 23:18:39] Found SOMATIC annotation in VCF. 1124s INFO [2026-02-09 23:18:39] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1124s INFO [2026-02-09 23:18:39] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 1124s INFO [2026-02-09 23:18:39] Excluding 0 novel or poor quality variants from segmentation. 1124s INFO [2026-02-09 23:18:39] Sample sex: ? 1124s INFO [2026-02-09 23:18:39] Segmenting data... 1124s INFO [2026-02-09 23:18:39] Loading pre-computed boundaries for DNAcopy... 1124s INFO [2026-02-09 23:18:39] Setting undo.SD parameter to 1.000000. 1125s INFO [2026-02-09 23:18:40] Setting prune.hclust.h parameter to 0.200000. 1125s INFO [2026-02-09 23:18:40] Found 59 segments with median size of 17.67Mb. 1125s INFO [2026-02-09 23:18:40] Using 121 variants. 1125s INFO [2026-02-09 23:18:40] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 1125s INFO [2026-02-09 23:18:40] 2D-grid search of purity and ploidy... 1125s INFO [2026-02-09 23:18:40] Local optima: 0.65/1.8, 0.52/2 1125s INFO [2026-02-09 23:18:40] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... 1126s INFO [2026-02-09 23:18:41] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... 1127s INFO [2026-02-09 23:18:42] Skipping 1 solutions that converged to the same optima. 1127s INFO [2026-02-09 23:18:42] Fitting variants with beta model for local optimum 1/2... 1127s INFO [2026-02-09 23:18:42] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 1130s INFO [2026-02-09 23:18:45] Optimized purity: 0.65 1130s INFO [2026-02-09 23:18:45] Done. 1130s INFO [2026-02-09 23:18:45] ------------------------------------------------------------ 1131s INFO [2026-02-09 23:18:46] Loaded provided segmentation file example_seg.txt (format DNAcopy). 1131s INFO [2026-02-09 23:18:46] Re-centering provided segment means (offset -0.0033). 1131s INFO [2026-02-09 23:18:46] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). 1131s WARN [2026-02-09 23:18:46] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. 1131s INFO [2026-02-09 23:18:46] Re-centering provided segment means (offset -0.0037). 1134s sh: 1: gatk: not found 1134s WARN [2026-02-09 23:18:49] Cannot find gatk binary in path. 1134s INFO [2026-02-09 23:18:49] ------------------------------------------------------------ 1134s INFO [2026-02-09 23:18:49] PureCN 2.12.0 1134s INFO [2026-02-09 23:18:49] ------------------------------------------------------------ 1134s INFO [2026-02-09 23:18:49] Loading coverage files... 1135s INFO [2026-02-09 23:18:49] Mean target coverages: 109X (tumor) 102X (normal). 1135s WARN [2026-02-09 23:18:49] Allosome coverage missing, cannot determine sex. 1135s WARN [2026-02-09 23:18:49] Allosome coverage missing, cannot determine sex. 1135s INFO [2026-02-09 23:18:50] Removing 9 intervals with missing log.ratio. 1135s INFO [2026-02-09 23:18:50] Removing 1 small (< 5bp) intervals. 1135s INFO [2026-02-09 23:18:50] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 1135s WARN [2026-02-09 23:18:50] No normalDB provided. Provide one for better results. 1135s INFO [2026-02-09 23:18:50] Removing 73 low count (< 100 total reads) intervals. 1135s INFO [2026-02-09 23:18:50] Removing 1 low coverage (< 15.0000X) intervals. 1135s INFO [2026-02-09 23:18:50] Using 411 intervals (411 on-target, 0 off-target). 1135s INFO [2026-02-09 23:18:50] No off-target intervals. If this is hybrid-capture data, consider adding them. 1135s INFO [2026-02-09 23:18:50] No interval.file provided. Cannot check for any GC-biases. 1135s INFO [2026-02-09 23:18:50] Sample sex: ? 1135s INFO [2026-02-09 23:18:50] Segmenting data... 1135s FATAL [2026-02-09 23:18:50] segmentationHclust requires an input segmentation. 1135s 1135s FATAL [2026-02-09 23:18:50] 1135s 1135s FATAL [2026-02-09 23:18:50] This is most likely a user error due to invalid input data or 1135s 1135s FATAL [2026-02-09 23:18:50] parameters (PureCN 2.12.0). 1135s 1135s INFO [2026-02-09 23:18:50] Loaded provided segmentation file example_seg.txt (format DNAcopy). 1135s INFO [2026-02-09 23:18:50] Re-centering provided segment means (offset -0.0033). 1135s INFO [2026-02-09 23:18:50] ------------------------------------------------------------ 1135s INFO [2026-02-09 23:18:50] PureCN 2.12.0 1135s INFO [2026-02-09 23:18:50] ------------------------------------------------------------ 1135s INFO [2026-02-09 23:18:50] Loading coverage files... 1135s INFO [2026-02-09 23:18:50] Mean target coverages: 109X (tumor) 102X (normal). 1135s WARN [2026-02-09 23:18:50] Allosome coverage missing, cannot determine sex. 1135s WARN [2026-02-09 23:18:50] Allosome coverage missing, cannot determine sex. 1135s INFO [2026-02-09 23:18:50] Removing 9 intervals with missing log.ratio. 1135s INFO [2026-02-09 23:18:50] Removing 1 small (< 5bp) intervals. 1135s INFO [2026-02-09 23:18:50] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 1135s WARN [2026-02-09 23:18:50] No normalDB provided. Provide one for better results. 1135s INFO [2026-02-09 23:18:50] Removing 73 low count (< 100 total reads) intervals. 1135s INFO [2026-02-09 23:18:50] Removing 1 low coverage (< 15.0000X) intervals. 1135s INFO [2026-02-09 23:18:50] Using 411 intervals (411 on-target, 0 off-target). 1135s INFO [2026-02-09 23:18:50] No off-target intervals. If this is hybrid-capture data, consider adding them. 1135s INFO [2026-02-09 23:18:50] No interval.file provided. Cannot check for any GC-biases. 1135s INFO [2026-02-09 23:18:50] Sample sex: ? 1135s INFO [2026-02-09 23:18:50] Segmenting data... 1136s INFO [2026-02-09 23:18:51] Found SOMATIC annotation in VCF. 1136s INFO [2026-02-09 23:18:51] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1136s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 1136s 1136s ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ 1136s • gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4' 1136s 1136s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 1136s > 1136s + cd .. 1136s + find tests -type f -iname *.R 1136s + wc -l 1136s Test: Run tests for PureCN 1136s Start: testthat.R 1136s + NBTEST=18 1136s + [ 18 -gt 0 ] 1136s + echo Test: Run tests for PureCN 1136s + cd tests 1136s + echo Start: testthat.R 1136s + R --no-save 1136s 1136s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1136s Copyright (C) 2025 The R Foundation for Statistical Computing 1136s Platform: powerpc64le-unknown-linux-gnu 1136s 1136s R is free software and comes with ABSOLUTELY NO WARRANTY. 1136s You are welcome to redistribute it under certain conditions. 1136s Type 'license()' or 'licence()' for distribution details. 1136s 1136s R is a collaborative project with many contributors. 1136s Type 'contributors()' for more information and 1136s 'citation()' on how to cite R or R packages in publications. 1136s 1136s Type 'demo()' for some demos, 'help()' for on-line help, or 1136s 'help.start()' for an HTML browser interface to help. 1136s Type 'q()' to quit R. 1136s 1136s > library(testthat) 1136s > library(PureCN) 1136s Loading required package: DNAcopy 1136s Loading required package: VariantAnnotation 1136s Loading required package: BiocGenerics 1136s 1136s Attaching package: ‘BiocGenerics’ 1136s 1136s The following objects are masked from ‘package:stats’: 1136s 1136s IQR, mad, sd, var, xtabs 1136s 1136s The following objects are masked from ‘package:base’: 1136s 1136s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 1136s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 1136s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 1136s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 1136s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 1136s table, tapply, union, unique, unsplit, which.max, which.min 1136s 1136s Loading required package: MatrixGenerics 1136s Loading required package: matrixStats 1136s 1136s Attaching package: ‘MatrixGenerics’ 1136s 1136s The following objects are masked from ‘package:matrixStats’: 1136s 1136s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 1136s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 1136s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 1136s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 1136s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 1136s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 1136s colWeightedMeans, colWeightedMedians, colWeightedSds, 1136s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 1136s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 1136s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 1136s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 1136s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 1136s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 1136s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 1136s rowWeightedSds, rowWeightedVars 1136s 1136s Loading required package: GenomeInfoDb 1137s Loading required package: S4Vectors 1137s Loading required package: stats4 1137s 1137s Attaching package: ‘S4Vectors’ 1137s 1137s The following object is masked from ‘package:utils’: 1137s 1137s findMatches 1137s 1137s The following objects are masked from ‘package:base’: 1137s 1137s expand.grid, I, unname 1137s 1137s Loading required package: IRanges 1138s Loading required package: GenomicRanges 1138s Loading required package: SummarizedExperiment 1138s Loading required package: Biobase 1139s Welcome to Bioconductor 1139s 1139s Vignettes contain introductory material; view with 1139s 'browseVignettes()'. To cite Bioconductor, see 1139s 'citation("Biobase")', and for packages 'citation("pkgname")'. 1139s 1139s 1139s Attaching package: ‘Biobase’ 1139s 1139s The following object is masked from ‘package:MatrixGenerics’: 1139s 1139s rowMedians 1139s 1139s The following objects are masked from ‘package:matrixStats’: 1139s 1139s anyMissing, rowMedians 1139s 1142s Loading required package: Rsamtools 1142s Loading required package: Biostrings 1142s Loading required package: XVector 1142s 1142s Attaching package: ‘Biostrings’ 1142s 1142s The following object is masked from ‘package:base’: 1142s 1142s strsplit 1142s 1146s 1146s Attaching package: ‘VariantAnnotation’ 1146s 1146s The following object is masked from ‘package:base’: 1146s 1146s tabulate 1146s 1148s > 1148s > test_check("PureCN") 1150s FATAL [2026-02-09 23:19:05] tumor.coverage.file and interval.file do not align. 1150s 1150s FATAL [2026-02-09 23:19:05] 1150s 1150s FATAL [2026-02-09 23:19:05] This is most likely a user error due to invalid input data or 1150s 1150s FATAL [2026-02-09 23:19:05] parameters (PureCN 2.12.0). 1150s 1150s WARN [2026-02-09 23:19:05] Cannot find all contig lengths while exporting interval file. 1152s INFO [2026-02-09 23:19:06] Processing seq1:1-21 (1/3)... 1152s INFO [2026-02-09 23:19:07] Processing seq1:1227-1247 (2/3)... 1152s INFO [2026-02-09 23:19:07] Processing seq2:594-614 (3/3)... 1153s WARN [2026-02-09 23:19:08] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 1157s INFO [2026-02-09 23:19:12] ------------------------------------------------------------ 1157s INFO [2026-02-09 23:19:12] PureCN 2.12.0 1157s INFO [2026-02-09 23:19:12] ------------------------------------------------------------ 1157s INFO [2026-02-09 23:19:12] Loading coverage files... 1157s INFO [2026-02-09 23:19:12] Mean target coverages: 112X (tumor) 99X (normal). 1157s WARN [2026-02-09 23:19:12] Allosome coverage missing, cannot determine sex. 1157s WARN [2026-02-09 23:19:12] Allosome coverage missing, cannot determine sex. 1157s INFO [2026-02-09 23:19:12] Removing 228 intervals with missing log.ratio. 1158s INFO [2026-02-09 23:19:12] Removing 22 small (< 5bp) intervals. 1158s INFO [2026-02-09 23:19:12] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 1158s WARN [2026-02-09 23:19:12] No normalDB provided. Provide one for better results. 1158s INFO [2026-02-09 23:19:12] Removing 1724 low count (< 100 total reads) intervals. 1158s INFO [2026-02-09 23:19:12] Removing 6 low coverage (< 15.0000X) intervals. 1158s INFO [2026-02-09 23:19:12] Using 8050 intervals (8050 on-target, 0 off-target). 1158s INFO [2026-02-09 23:19:12] No off-target intervals. If this is hybrid-capture data, consider adding them. 1158s INFO [2026-02-09 23:19:12] No interval.file provided. Cannot check for any GC-biases. 1158s INFO [2026-02-09 23:19:12] Loading VCF... 1158s INFO [2026-02-09 23:19:12] Found 127 variants in VCF file. 1158s INFO [2026-02-09 23:19:13] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1158s INFO [2026-02-09 23:19:13] LIB-02240e4 is tumor in VCF file. 1158s INFO [2026-02-09 23:19:13] No homozygous variants in VCF, provide unfiltered VCF. 1158s INFO [2026-02-09 23:19:13] Removing 1 non heterozygous (in matched normal) germline SNPs. 1158s INFO [2026-02-09 23:19:13] Removing 0 low quality variants with non-offset BQ < 25. 1158s INFO [2026-02-09 23:19:13] Base quality scores range from 29 to 35 (offset by 1) 1158s INFO [2026-02-09 23:19:13] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 1158s INFO [2026-02-09 23:19:13] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1158s INFO [2026-02-09 23:19:13] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 1159s INFO [2026-02-09 23:19:14] 1.2% of targets contain variants. 1159s INFO [2026-02-09 23:19:14] Removing 4 variants outside intervals. 1159s INFO [2026-02-09 23:19:14] Found SOMATIC annotation in VCF. 1159s INFO [2026-02-09 23:19:14] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1159s INFO [2026-02-09 23:19:14] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 1159s INFO [2026-02-09 23:19:14] Excluding 0 novel or poor quality variants from segmentation. 1159s INFO [2026-02-09 23:19:14] Sample sex: ? 1159s INFO [2026-02-09 23:19:14] Segmenting data... 1159s INFO [2026-02-09 23:19:14] Loading pre-computed boundaries for DNAcopy... 1159s INFO [2026-02-09 23:19:14] Setting undo.SD parameter to 1.000000. 1160s INFO [2026-02-09 23:19:15] Setting prune.hclust.h parameter to 0.200000. 1160s INFO [2026-02-09 23:19:15] Found 59 segments with median size of 17.67Mb. 1160s INFO [2026-02-09 23:19:15] Using 121 variants. 1160s INFO [2026-02-09 23:19:15] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 1160s INFO [2026-02-09 23:19:15] 2D-grid search of purity and ploidy... 1162s INFO [2026-02-09 23:19:17] Local optima: 0.63/1.9, 0.5/2 1162s INFO [2026-02-09 23:19:17] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... 1163s INFO [2026-02-09 23:19:18] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... 1164s INFO [2026-02-09 23:19:19] Skipping 1 solutions that converged to the same optima. 1164s INFO [2026-02-09 23:19:19] Fitting variants with beta model for local optimum 1/2... 1164s INFO [2026-02-09 23:19:19] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 1167s INFO [2026-02-09 23:19:22] Optimized purity: 0.65 1167s INFO [2026-02-09 23:19:22] Done. 1167s INFO [2026-02-09 23:19:22] ------------------------------------------------------------ 1168s INFO [2026-02-09 23:19:22] Removing 22 non heterozygous (in matched normal) germline SNPs. 1168s INFO [2026-02-09 23:19:22] Removing 19 low quality variants with non-offset BQ < 25. 1168s INFO [2026-02-09 23:19:22] Base quality scores range from 24 to 35 (offset by 1) 1168s INFO [2026-02-09 23:19:22] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1168s INFO [2026-02-09 23:19:23] Initial testing for significant sample cross-contamination: unlikely 1168s INFO [2026-02-09 23:19:23] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1168s INFO [2026-02-09 23:19:23] Removing 22 non heterozygous (in matched normal) germline SNPs. 1168s INFO [2026-02-09 23:19:23] Removing 19 low quality variants with non-offset BQ < 25. 1168s INFO [2026-02-09 23:19:23] Base quality scores range from 24 to 35 (offset by 1) 1168s INFO [2026-02-09 23:19:23] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1169s INFO [2026-02-09 23:19:24] Initial testing for significant sample cross-contamination: unlikely 1169s INFO [2026-02-09 23:19:24] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1169s INFO [2026-02-09 23:19:24] Removing 6 blacklisted variants. 1169s INFO [2026-02-09 23:19:24] Removing 22 non heterozygous (in matched normal) germline SNPs. 1169s INFO [2026-02-09 23:19:24] Removing 19 low quality variants with non-offset BQ < 25. 1169s INFO [2026-02-09 23:19:24] Base quality scores range from 24 to 35 (offset by 1) 1169s INFO [2026-02-09 23:19:24] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1170s INFO [2026-02-09 23:19:24] Initial testing for significant sample cross-contamination: unlikely 1170s INFO [2026-02-09 23:19:25] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1170s WARN [2026-02-09 23:19:25] MuTect stats file lacks contig and position columns. 1170s INFO [2026-02-09 23:19:25] Removing 22 non heterozygous (in matched normal) germline SNPs. 1170s INFO [2026-02-09 23:19:25] Removing 19 low quality variants with non-offset BQ < 25. 1170s INFO [2026-02-09 23:19:25] Base quality scores range from 24 to 35 (offset by 1) 1170s INFO [2026-02-09 23:19:25] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 1170s INFO [2026-02-09 23:19:25] Initial testing for significant sample cross-contamination: unlikely 1170s INFO [2026-02-09 23:19:25] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1171s WARN [2026-02-09 23:19:25] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. 1171s WARN [2026-02-09 23:19:25] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. 1171s INFO [2026-02-09 23:19:25] Removing 0 non heterozygous (in matched normal) germline SNPs. 1171s INFO [2026-02-09 23:19:26] Removing 0 low quality variants with non-offset BQ < 25. 1171s INFO [2026-02-09 23:19:26] Base quality scores range from 31 to 33 (offset by 1) 1171s INFO [2026-02-09 23:19:26] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. 1171s INFO [2026-02-09 23:19:26] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1171s INFO [2026-02-09 23:19:26] Removing 22 non heterozygous (in matched normal) germline SNPs. 1171s INFO [2026-02-09 23:19:26] Base quality scores range from 7 to 35 (offset by 1) 1171s INFO [2026-02-09 23:19:26] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 1172s INFO [2026-02-09 23:19:26] Initial testing for significant sample cross-contamination: unlikely 1172s INFO [2026-02-09 23:19:27] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1172s INFO [2026-02-09 23:19:27] Removing 22 non heterozygous (in matched normal) germline SNPs. 1172s INFO [2026-02-09 23:19:27] Base quality scores range from 7 to 35 (offset by 1) 1172s INFO [2026-02-09 23:19:27] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 1172s INFO [2026-02-09 23:19:27] Initial testing for significant sample cross-contamination: unlikely 1172s INFO [2026-02-09 23:19:27] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1173s INFO [2026-02-09 23:19:27] Removing 22 non heterozygous (in matched normal) germline SNPs. 1173s WARN [2026-02-09 23:19:27] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. 1173s FATAL [2026-02-09 23:19:27] No variants passed filter BQ. 1173s 1173s FATAL [2026-02-09 23:19:27] 1173s 1173s FATAL [2026-02-09 23:19:27] This is most likely a user error due to invalid input data or 1173s 1173s FATAL [2026-02-09 23:19:27] parameters (PureCN 2.12.0). 1173s 1173s INFO [2026-02-09 23:19:28] Found 11 variants in VCF file. 1173s WARN [2026-02-09 23:19:28] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 1173s INFO [2026-02-09 23:19:28] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1175s INFO [2026-02-09 23:19:30] Found 11 variants in VCF file. 1175s WARN [2026-02-09 23:19:30] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 1175s INFO [2026-02-09 23:19:30] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1176s INFO [2026-02-09 23:19:31] Found 11 variants in VCF file. 1176s WARN [2026-02-09 23:19:31] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. 1176s INFO [2026-02-09 23:19:31] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 1176s INFO [2026-02-09 23:19:31] Found 1000 variants in VCF file. 1176s INFO [2026-02-09 23:19:31] Removing 2 triallelic sites. 1176s WARN [2026-02-09 23:19:31] Having trouble guessing SOMATIC status... 1177s WARN [2026-02-09 23:19:31] DP FORMAT field contains NAs. Removing 44 variants. 1177s INFO [2026-02-09 23:19:31] 954 (100.0%) variants annotated as likely germline (DB INFO flag). 1178s INFO [2026-02-09 23:19:33] Found 12 variants in VCF file. 1178s INFO [2026-02-09 23:19:33] Removing 1 triallelic sites. 1178s WARN [2026-02-09 23:19:33] DP FORMAT field contains NAs. Removing 1 variants. 1178s WARN [2026-02-09 23:19:33] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. 1178s INFO [2026-02-09 23:19:33] 8 (80.0%) variants annotated as likely germline (DB INFO flag). 1179s WARN [2026-02-09 23:19:33] BQ FORMAT field contains NAs. 1179s INFO [2026-02-09 23:19:34] Found 2331 variants in VCF file. 1179s INFO [2026-02-09 23:19:34] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1180s INFO [2026-02-09 23:19:34] Found 2331 variants in VCF file. 1180s INFO [2026-02-09 23:19:34] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1180s WARN [2026-02-09 23:19:35] Did not find base quality scores, will use global error rate of 0.0010 instead. 1180s INFO [2026-02-09 23:19:35] Removing 21 low quality variants with non-offset BQ < 25. 1180s INFO [2026-02-09 23:19:35] Base quality scores range from 24 to 35 (offset by 1) 1181s INFO [2026-02-09 23:19:35] Initial testing for significant sample cross-contamination: unlikely 1181s INFO [2026-02-09 23:19:36] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. 1181s INFO [2026-02-09 23:19:36] Found 2331 variants in VCF file. 1181s INFO [2026-02-09 23:19:36] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 1181s WARN [2026-02-09 23:19:36] BQ FORMAT field contains NAs. 1182s WARN [2026-02-09 23:19:37] Allosome coverage missing, cannot determine sex. 1182s WARN [2026-02-09 23:19:37] Allosome coverage missing, cannot determine sex. 1182s INFO [2026-02-09 23:19:37] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. 1182s INFO [2026-02-09 23:19:37] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. 1182s INFO [2026-02-09 23:19:37] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. 1183s INFO [2026-02-09 23:19:38] Found 20 variants in VCF file. 1184s INFO [2026-02-09 23:19:38] 20 (100.0%) variants annotated as likely germline (DB INFO flag). 1184s WARN [2026-02-09 23:19:39] Did not find base quality scores, will use global error rate of 0.0010 instead. 1185s INFO [2026-02-09 23:19:39] Found 127 variants in VCF file. 1185s INFO [2026-02-09 23:19:40] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1185s WARN [2026-02-09 23:19:40] Did not find base quality scores, will use global error rate of 0.0010 instead. 1185s INFO [2026-02-09 23:19:40] ------------------------------------------------------------ 1185s INFO [2026-02-09 23:19:40] PureCN 2.12.0 1185s INFO [2026-02-09 23:19:40] ------------------------------------------------------------ 1185s INFO [2026-02-09 23:19:40] Loading coverage files... 1185s INFO [2026-02-09 23:19:40] Mean target coverages: 112X (tumor) 99X (normal). 1185s WARN [2026-02-09 23:19:40] Allosome coverage missing, cannot determine sex. 1185s WARN [2026-02-09 23:19:40] Allosome coverage missing, cannot determine sex. 1186s INFO [2026-02-09 23:19:40] Removing 228 intervals with missing log.ratio. 1186s INFO [2026-02-09 23:19:40] Removing 22 small (< 5bp) intervals. 1186s INFO [2026-02-09 23:19:40] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 1186s WARN [2026-02-09 23:19:40] No normalDB provided. Provide one for better results. 1186s INFO [2026-02-09 23:19:40] Removing 1724 low count (< 100 total reads) intervals. 1186s INFO [2026-02-09 23:19:40] Removing 6 low coverage (< 15.0000X) intervals. 1186s INFO [2026-02-09 23:19:40] Using 8050 intervals (8050 on-target, 0 off-target). 1186s INFO [2026-02-09 23:19:40] No off-target intervals. If this is hybrid-capture data, consider adding them. 1186s INFO [2026-02-09 23:19:40] No interval.file provided. Cannot check for any GC-biases. 1186s INFO [2026-02-09 23:19:40] Loading VCF... 1186s INFO [2026-02-09 23:19:40] Found 127 variants in VCF file. 1186s INFO [2026-02-09 23:19:41] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 1186s INFO [2026-02-09 23:19:41] LIB-02240e4 is tumor in VCF file. 1186s INFO [2026-02-09 23:19:41] No homozygous variants in VCF, provide unfiltered VCF. 1186s INFO [2026-02-09 23:19:41] Removing 1 non heterozygous (in matched normal) germline SNPs. 1186s INFO [2026-02-09 23:19:41] Removing 0 low quality variants with non-offset BQ < 25. 1186s INFO [2026-02-09 23:19:41] Base quality scores range from 29 to 35 (offset by 1) 1186s INFO [2026-02-09 23:19:41] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 1186s INFO [2026-02-09 23:19:41] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 1186s INFO [2026-02-09 23:19:41] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 1187s INFO [2026-02-09 23:19:41] 1.2% of targets contain variants. 1187s INFO [2026-02-09 23:19:41] Removing 4 variants outside intervals. 1187s INFO [2026-02-09 23:19:42] Found SOMATIC annotation in VCF. 1187s INFO [2026-02-09 23:19:42] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1187s INFO [2026-02-09 23:19:42] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 1187s INFO [2026-02-09 23:19:42] Excluding 0 novel or poor quality variants from segmentation. 1187s INFO [2026-02-09 23:19:42] Sample sex: ? 1187s INFO [2026-02-09 23:19:42] Segmenting data... 1187s INFO [2026-02-09 23:19:42] Loading pre-computed boundaries for DNAcopy... 1187s INFO [2026-02-09 23:19:42] Setting undo.SD parameter to 1.000000. 1188s INFO [2026-02-09 23:19:43] Setting prune.hclust.h parameter to 0.200000. 1188s INFO [2026-02-09 23:19:43] Found 59 segments with median size of 17.67Mb. 1188s INFO [2026-02-09 23:19:43] Using 121 variants. 1188s INFO [2026-02-09 23:19:43] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 1188s INFO [2026-02-09 23:19:43] 2D-grid search of purity and ploidy... 1188s INFO [2026-02-09 23:19:43] Local optima: 0.65/1.8, 0.52/2 1188s INFO [2026-02-09 23:19:43] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... 1189s INFO [2026-02-09 23:19:44] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... 1190s INFO [2026-02-09 23:19:45] Skipping 1 solutions that converged to the same optima. 1190s INFO [2026-02-09 23:19:45] Fitting variants with beta model for local optimum 1/2... 1190s INFO [2026-02-09 23:19:45] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 1193s INFO [2026-02-09 23:19:48] Optimized purity: 0.65 1193s INFO [2026-02-09 23:19:48] Done. 1193s INFO [2026-02-09 23:19:48] ------------------------------------------------------------ 1194s INFO [2026-02-09 23:19:49] Loaded provided segmentation file example_seg.txt (format DNAcopy). 1194s INFO [2026-02-09 23:19:49] Re-centering provided segment means (offset -0.0033). 1194s INFO [2026-02-09 23:19:49] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). 1194s WARN [2026-02-09 23:19:49] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. 1194s INFO [2026-02-09 23:19:49] Re-centering provided segment means (offset -0.0037). 1197s WARN [2026-02-09 23:19:52] Cannot find gatk binary in path. 1197s sh: 1: gatk: not found 1197s INFO [2026-02-09 23:19:52] ------------------------------------------------------------ 1197s INFO [2026-02-09 23:19:52] PureCN 2.12.0 1197s INFO [2026-02-09 23:19:52] ------------------------------------------------------------ 1197s INFO [2026-02-09 23:19:52] Loading coverage files... 1198s INFO [2026-02-09 23:19:52] Mean target coverages: 109X (tumor) 102X (normal). 1198s WARN [2026-02-09 23:19:52] Allosome coverage missing, cannot determine sex. 1198s WARN [2026-02-09 23:19:52] Allosome coverage missing, cannot determine sex. 1198s INFO [2026-02-09 23:19:53] Removing 9 intervals with missing log.ratio. 1198s INFO [2026-02-09 23:19:53] Removing 1 small (< 5bp) intervals. 1198s INFO [2026-02-09 23:19:53] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 1198s WARN [2026-02-09 23:19:53] No normalDB provided. Provide one for better results. 1198s INFO [2026-02-09 23:19:53] Removing 73 low count (< 100 total reads) intervals. 1198s INFO [2026-02-09 23:19:53] Removing 1 low coverage (< 15.0000X) intervals. 1198s INFO [2026-02-09 23:19:53] Using 411 intervals (411 on-target, 0 off-target). 1198s INFO [2026-02-09 23:19:53] No off-target intervals. If this is hybrid-capture data, consider adding them. 1198s INFO [2026-02-09 23:19:53] No interval.file provided. Cannot check for any GC-biases. 1198s INFO [2026-02-09 23:19:53] Sample sex: ? 1198s INFO [2026-02-09 23:19:53] Segmenting data... 1198s FATAL [2026-02-09 23:19:53] segmentationHclust requires an input segmentation. 1198s 1198s FATAL [2026-02-09 23:19:53] 1198s 1198s FATAL [2026-02-09 23:19:53] This is most likely a user error due to invalid input data or 1198s 1198s FATAL [2026-02-09 23:19:53] parameters (PureCN 2.12.0). 1198s 1198s INFO [2026-02-09 23:19:53] Loaded provided segmentation file example_seg.txt (format DNAcopy). 1198s INFO [2026-02-09 23:19:53] Re-centering provided segment means (offset -0.0033). 1198s INFO [2026-02-09 23:19:53] ------------------------------------------------------------ 1198s INFO [2026-02-09 23:19:53] PureCN 2.12.0 1198s INFO [2026-02-09 23:19:53] ------------------------------------------------------------ 1198s INFO [2026-02-09 23:19:53] Loading coverage files... 1198s INFO [2026-02-09 23:19:53] Mean target coverages: 109X (tumor) 102X (normal). 1198s WARN [2026-02-09 23:19:53] Allosome coverage missing, cannot determine sex. 1198s WARN [2026-02-09 23:19:53] Allosome coverage missing, cannot determine sex. 1198s INFO [2026-02-09 23:19:53] Removing 9 intervals with missing log.ratio. 1198s INFO [2026-02-09 23:19:53] Removing 1 small (< 5bp) intervals. 1198s INFO [2026-02-09 23:19:53] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 1198s WARN [2026-02-09 23:19:53] No normalDB provided. Provide one for better results. 1198s INFO [2026-02-09 23:19:53] Removing 73 low count (< 100 total reads) intervals. 1198s INFO [2026-02-09 23:19:53] Removing 1 low coverage (< 15.0000X) intervals. 1198s INFO [2026-02-09 23:19:53] Using 411 intervals (411 on-target, 0 off-target). 1198s INFO [2026-02-09 23:19:53] No off-target intervals. If this is hybrid-capture data, consider adding them. 1198s INFO [2026-02-09 23:19:53] No interval.file provided. Cannot check for any GC-biases. 1198s INFO [2026-02-09 23:19:53] Sample sex: ? 1198s INFO [2026-02-09 23:19:53] Segmenting data... 1199s INFO [2026-02-09 23:19:54] Found SOMATIC annotation in VCF. 1199s INFO [2026-02-09 23:19:54] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 1199s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 1199s 1199s ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ 1199s • gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4' 1199s 1199s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 1199s > 1199s + exit 0 1199s autopkgtest [23:19:55]: test pkg-r-autopkgtest: -----------------------] 1200s pkg-r-autopkgtest PASS 1200s autopkgtest [23:19:56]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1200s autopkgtest [23:19:56]: @@@@@@@@@@@@@@@@@@@@ summary 1200s pkg-r-autopkgtest PASS