0s autopkgtest [21:40:58]: starting date: 2024-03-07 0s autopkgtest [21:40:58]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [21:40:58]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o7lt4p4c/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:wget,src:libpsl,src:openssl --apt-upgrade pique --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=wget/1.21.4-1ubuntu2 libpsl/0.21.2-1.1 openssl/3.0.10-1ubuntu5' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-25.secgroup --name adt-noble-arm64-pique-20240307-214057-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 102s autopkgtest [21:42:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 103s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 103s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [23.8 kB] 103s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [321 kB] 103s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [1813 kB] 104s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [443 kB] 104s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 104s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 104s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 104s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2170 kB] 104s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 104s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [21.5 kB] 104s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 105s Fetched 4945 kB in 1s (3699 kB/s) 105s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s Calculating upgrade... 110s The following packages will be REMOVED: 110s libpsl5 libssl3 110s The following NEW packages will be installed: 110s libpsl5t64 libssl3t64 110s The following packages will be upgraded: 110s libproc2-0 openssl pci.ids procps wget 110s 5 upgraded, 2 newly installed, 2 to remove and 0 not upgraded. 110s Need to get 4172 kB of archives. 110s After this operation, 94.2 kB of additional disk space will be used. 110s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 wget arm64 1.21.4-1ubuntu2 [330 kB] 110s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 110s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.10-1ubuntu5 [982 kB] 110s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.10-1ubuntu5 [1763 kB] 111s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libproc2-0 arm64 2:4.0.4-4ubuntu1 [58.4 kB] 111s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 procps arm64 2:4.0.4-4ubuntu1 [708 kB] 111s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 pci.ids all 0.0~2024.02.02-1 [273 kB] 111s Fetched 4172 kB in 1s (5040 kB/s) 111s (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 ... 74662 files and directories currently installed.) 111s Preparing to unpack .../wget_1.21.4-1ubuntu2_arm64.deb ... 111s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ... 111s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 111s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 111s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 111s 111s (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 ... 74662 files and directories currently installed.) 111s Removing libpsl5:arm64 (0.21.2-1build1) ... 111s Selecting previously unselected package libpsl5t64:arm64. 111s (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 ... 74657 files and directories currently installed.) 111s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 111s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 112s Preparing to unpack .../openssl_3.0.10-1ubuntu5_arm64.deb ... 112s Unpacking openssl (3.0.10-1ubuntu5) over (3.0.10-1ubuntu4) ... 112s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 112s u-boot-tools depends on libssl3 (>= 3.0.0). 112s tnftp depends on libssl3 (>= 3.0.0). 112s tcpdump depends on libssl3 (>= 3.0.0). 112s systemd-resolved depends on libssl3 (>= 3.0.0). 112s systemd depends on libssl3 (>= 3.0.0). 112s sudo depends on libssl3 (>= 3.0.0). 112s sbsigntool depends on libssl3 (>= 3.0.0). 112s rsync depends on libssl3 (>= 3.0.0). 112s python3-cryptography depends on libssl3 (>= 3.0.0). 112s openssh-server depends on libssl3 (>= 3.0.10). 112s openssh-client depends on libssl3 (>= 3.0.10). 112s mtd-utils depends on libssl3 (>= 3.0.0). 112s mokutil depends on libssl3 (>= 3.0.0). 112s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 112s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 112s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 112s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 112s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 112s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 112s libnvme1 depends on libssl3 (>= 3.0.0). 112s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 112s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 112s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 112s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 112s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 112s kmod depends on libssl3 (>= 3.0.0). 112s dhcpcd-base depends on libssl3 (>= 3.0.0). 112s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 112s 112s (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 ... 74663 files and directories currently installed.) 112s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 112s Selecting previously unselected package libssl3t64:arm64. 112s (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 ... 74652 files and directories currently installed.) 112s Preparing to unpack .../libssl3t64_3.0.10-1ubuntu5_arm64.deb ... 112s Unpacking libssl3t64:arm64 (3.0.10-1ubuntu5) ... 112s Preparing to unpack .../libproc2-0_2%3a4.0.4-4ubuntu1_arm64.deb ... 112s Unpacking libproc2-0:arm64 (2:4.0.4-4ubuntu1) over (2:4.0.4-2ubuntu1) ... 112s Preparing to unpack .../procps_2%3a4.0.4-4ubuntu1_arm64.deb ... 112s Unpacking procps (2:4.0.4-4ubuntu1) over (2:4.0.4-2ubuntu1) ... 112s Preparing to unpack .../pci.ids_0.0~2024.02.02-1_all.deb ... 112s Unpacking pci.ids (0.0~2024.02.02-1) over (0.0~2023.11.11-1) ... 112s Setting up pci.ids (0.0~2024.02.02-1) ... 112s Setting up libssl3t64:arm64 (3.0.10-1ubuntu5) ... 112s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 112s Setting up libproc2-0:arm64 (2:4.0.4-4ubuntu1) ... 112s Setting up procps (2:4.0.4-4ubuntu1) ... 112s Setting up openssl (3.0.10-1ubuntu5) ... 112s Setting up wget (1.21.4-1ubuntu2) ... 112s Processing triggers for man-db (2.12.0-3) ... 114s Processing triggers for install-info (7.1-3) ... 114s Processing triggers for libc-bin (2.39-0ubuntu2) ... 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s sh: Attempting to set up Debian/Ubuntu apt sources automatically 117s sh: Distribution appears to be Ubuntu 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s eatmydata is already the newest version (131-1). 118s dbus is already the newest version (1.14.10-4ubuntu1). 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s rng-tools-debian is already the newest version (2.4). 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s haveged is already the newest version (1.9.14-1ubuntu1). 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s The following packages will be REMOVED: 121s cloud-init* python3-configobj* python3-debconf* 122s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 122s After this operation, 3248 kB disk space will be freed. 122s (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 ... 74665 files and directories currently installed.) 122s Removing cloud-init (24.1-0ubuntu1) ... 122s Removing python3-configobj (5.0.8-3) ... 123s Removing python3-debconf (1.5.86) ... 123s Processing triggers for man-db (2.12.0-3) ... 124s (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 ... 74276 files and directories currently installed.) 124s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 124s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 124s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s linux-generic is already the newest version (6.8.0-11.11+1). 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 126s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 126s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 126s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 127s Reading package lists... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 128s Calculating upgrade... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s autopkgtest [21:43:07]: rebooting testbed after setup commands that affected boot 284s autopkgtest [21:45:42]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 285s autopkgtest [21:45:43]: testbed dpkg architecture: arm64 286s autopkgtest [21:45:44]: @@@@@@@@@@@@@@@@@@@@ apt-source pique 288s Get:1 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (dsc) [2005 B] 288s Get:2 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (tar) [2017 kB] 288s Get:3 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (diff) [5236 B] 289s gpgv: Signature made Tue Dec 12 20:17:37 2023 UTC 289s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 289s gpgv: issuer "tille@debian.org" 289s gpgv: Can't check signature: No public key 289s dpkg-source: warning: cannot verify inline signature for ./pique_1.0-7.dsc: no acceptable signature found 289s autopkgtest [21:45:47]: testing package pique version 1.0-7 289s autopkgtest [21:45:47]: build not needed 289s autopkgtest [21:45:47]: test run-unit-test: preparing testbed 295s Reading package lists... 295s Building dependency tree... 295s Reading state information... 295s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 295s Done 296s Starting pkgProblemResolver with broken count: 0 296s Starting 2 pkgProblemResolver with broken count: 0 296s Done 296s The following additional packages will be installed: 296s eigensoft emmax fontconfig fontconfig-config fonts-dejavu-core 296s fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings 296s fonts-mathjax javascript-common libb-hooks-op-check-perl libblas3 libcairo2 296s libclass-method-modifiers-perl libclass-xsaccessor-perl libdatrie1 296s libdeflate0 libdevel-callchecker-perl libdynaloader-functions-perl 296s libfile-slurp-perl libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 296s libgsl27 libgslcblas0 libharfbuzz0b libice6 libimport-into-perl libjbig0 296s libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3 296s libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables 296s libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax 296s libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify 296s libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 liblapacke 296s liblerc4 liblua5.4-0 libmodule-runtime-perl libmoo-perl libpango-1.0-0 296s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 296s libparallel-forkmanager-perl libparams-classify-perl libpixman-1-0 296s libreadonly-perl librole-tiny-perl libsharpyuv0 libsm6 libsub-quote-perl 296s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtmglib3 libwebp7 296s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 littler 296s node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data 296s pique pique-doc plink r-base-core r-bioc-biobase r-bioc-biocgenerics 296s r-bioc-multtest r-cran-acepack r-cran-backports r-cran-base64enc 296s r-cran-bslib r-cran-cachem r-cran-checkmate r-cran-chron r-cran-cli 296s r-cran-cluster r-cran-colorspace r-cran-commonmark r-cran-cpp11 296s r-cran-crayon r-cran-curl r-cran-data.table r-cran-deldir r-cran-digest 296s r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 296s r-cran-fastmap r-cran-fontawesome r-cran-forecast r-cran-foreign 296s r-cran-formula r-cran-fracdiff r-cran-fs r-cran-generics r-cran-getopt 296s r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-highr 296s r-cran-hmisc r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets 296s r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg r-cran-jquerylib 296s r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later r-cran-lattice 296s r-cran-latticeextra r-cran-lifecycle r-cran-littler r-cran-lmtest 296s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-memoise r-cran-mgcv 296s r-cran-mime r-cran-munsell r-cran-nlme r-cran-nnet r-cran-optparse 296s r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-png r-cran-promises 296s r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 r-cran-rappdirs 296s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen 296s r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass 296s r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr 296s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timedate 296s r-cran-tinytex r-cran-tseries r-cran-ttr r-cran-urca r-cran-uroot 296s r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr 296s r-cran-xfun r-cran-xtable r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common 296s xdg-utils zip 296s Suggested packages: 296s apache2 | lighttpd | httpd gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info 296s | gsl-ref-html libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix 296s libjs-mathjax-doc libscalar-number-perl libxstring-perl tcl8.6 tk8.6 nodejs 296s texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc 296s texlive-latex-extra context wkhtmltopdf librsvg2-bin groff ghc php python 296s ruby libjs-katex citation-style-language-styles elpa-ess r-doc-info 296s | r-doc-pdf r-mathlib r-base-html r-bioc-all r-cran-runit r-bioc-biocstyle 296s r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray 296s r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy 296s r-bioc-deseq2 r-bioc-annotate r-cran-snow r-cran-kernsmooth r-cran-kernlab 296s r-cran-mvtnorm r-cran-vcd r-cran-shinyjs r-cran-polyclip r-cran-covr 296s r-cran-markdown r-cran-sp r-cran-scatterplot3d r-cran-magick r-cran-sf 296s r-cran-testthat r-cran-httr r-cran-bit64 r-cran-dbi r-cran-formattable 296s r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-vdiffr 296s r-cran-roxygen2 r-cran-inline r-cran-bench r-cran-blob r-cran-brio 296s r-cran-callr r-cran-here r-cran-hms r-cran-pkgbuild r-cran-pkgload 296s r-cran-plm 296s Recommended packages: 296s gnuplot node-jquery libnamespace-clean-perl med-config r-recommended 296s r-base-dev r-doc-html r-cran-testthat r-cran-thematic r-cran-fastmatch 296s r-cran-devtools r-cran-tinytest r-cran-callr r-cran-covr r-cran-mockery 296s r-cran-processx r-cran-ps r-cran-rprojroot r-cran-whoami r-cran-xml2 296s r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr 296s r-cran-progress r-cran-spelling r-cran-webutils r-cran-bit64 r-cran-bit 296s r-cran-r.utils r-cran-nanotime r-cran-broom r-cran-dbi r-cran-dbplyr 296s r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite r-cran-unitizer r-cran-rsvg 296s r-cran-pkgload r-cran-hexbin r-cran-mapproj r-cran-maps r-cran-multcomp 296s r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-sf r-cran-svglite 296s r-cran-vdiffr r-cran-waldo r-cran-testit r-cran-cairo r-cran-markdown 296s r-cran-httr r-cran-r.rsp r-cran-codetools r-cran-formatr r-cran-gridsvg 296s r-cran-magick r-cran-reticulate r-cran-rgl r-cran-tikzdevice r-cran-webshot 296s node-highlight.js r-cran-lintr r-cran-tidyverse r-cran-lubridate 296s r-cran-future r-cran-usethis r-cran-dygraphs r-cran-rsconnect r-cran-downlit 296s r-cran-dichromat r-cran-hms r-cran-mockr r-cran-formattable r-cran-readr 296s r-cran-pkgdown r-cran-zeallot r-cran-remotes r-cran-renv r-cran-timeseries 296s r-cran-runit libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl 296s x11-utils x11-xserver-utils 297s The following NEW packages will be installed: 297s eigensoft emmax fontconfig fontconfig-config fonts-dejavu-core 297s fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings 297s fonts-mathjax javascript-common libb-hooks-op-check-perl libblas3 libcairo2 297s libclass-method-modifiers-perl libclass-xsaccessor-perl libdatrie1 297s libdeflate0 libdevel-callchecker-perl libdynaloader-functions-perl 297s libfile-slurp-perl libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 297s libgsl27 libgslcblas0 libharfbuzz0b libice6 libimport-into-perl libjbig0 297s libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3 297s libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables 297s libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax 297s libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify 297s libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 liblapacke 297s liblerc4 liblua5.4-0 libmodule-runtime-perl libmoo-perl libpango-1.0-0 297s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 297s libparallel-forkmanager-perl libparams-classify-perl libpixman-1-0 297s libreadonly-perl librole-tiny-perl libsharpyuv0 libsm6 libsub-quote-perl 297s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtmglib3 libwebp7 297s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 littler 297s node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data 297s pique pique-doc plink r-base-core r-bioc-biobase r-bioc-biocgenerics 297s r-bioc-multtest r-cran-acepack r-cran-backports r-cran-base64enc 297s r-cran-bslib r-cran-cachem r-cran-checkmate r-cran-chron r-cran-cli 297s r-cran-cluster r-cran-colorspace r-cran-commonmark r-cran-cpp11 297s r-cran-crayon r-cran-curl r-cran-data.table r-cran-deldir r-cran-digest 297s r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 297s r-cran-fastmap r-cran-fontawesome r-cran-forecast r-cran-foreign 297s r-cran-formula r-cran-fracdiff r-cran-fs r-cran-generics r-cran-getopt 297s r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-highr 297s r-cran-hmisc r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets 297s r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg r-cran-jquerylib 297s r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later r-cran-lattice 297s r-cran-latticeextra r-cran-lifecycle r-cran-littler r-cran-lmtest 297s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-memoise r-cran-mgcv 297s r-cran-mime r-cran-munsell r-cran-nlme r-cran-nnet r-cran-optparse 297s r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-png r-cran-promises 297s r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 r-cran-rappdirs 297s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen 297s r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass 297s r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr 297s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timedate 297s r-cran-tinytex r-cran-tseries r-cran-ttr r-cran-urca r-cran-uroot 297s r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr 297s r-cran-xfun r-cran-xtable r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common 297s xdg-utils zip 297s 0 upgraded, 206 newly installed, 0 to remove and 0 not upgraded. 297s 1 not fully installed or removed. 297s Need to get 172 MB of archives. 297s After this operation, 539 MB of additional disk space will be used. 297s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 297s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 297s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 297s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 297s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 297s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 297s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 297s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 297s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 297s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 297s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 297s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 297s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 297s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 297s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 297s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 297s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 297s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 297s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 297s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 297s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 297s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 297s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 297s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 297s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 297s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 297s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 297s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 297s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 297s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 297s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 297s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 297s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 297s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 297s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 297s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 297s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 298s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 298s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 298s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 298s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 298s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 298s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 298s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 298s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libtmglib3 arm64 3.12.0-3 [112 kB] 298s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 liblapacke arm64 3.12.0-3 [427 kB] 298s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 emmax arm64 0~beta.20100307-5 [29.9 kB] 298s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 plink arm64 1.07+dfsg-4 [1005 kB] 298s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 298s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 298s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 eigensoft arm64 8.0.0+dfsg-2 [318 kB] 298s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 libreadonly-perl all 2.050-3 [19.9 kB] 298s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libclass-method-modifiers-perl all 2.15-1 [16.1 kB] 298s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libclass-xsaccessor-perl arm64 1.19-4build2 [33.1 kB] 298s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libb-hooks-op-check-perl arm64 0.22-2build2 [9220 B] 298s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libdynaloader-functions-perl all 0.003-3 [12.1 kB] 298s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libdevel-callchecker-perl arm64 0.008-2build1 [13.7 kB] 298s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libparams-classify-perl arm64 0.015-2build3 [19.6 kB] 298s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libmodule-runtime-perl all 0.016-2 [16.4 kB] 298s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libimport-into-perl all 1.002005-2 [10.7 kB] 298s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 librole-tiny-perl all 2.002004-1 [16.3 kB] 298s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-quote-perl all 2.006008-1ubuntu1 [20.7 kB] 298s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libmoo-perl all 2.005005-1 [47.4 kB] 298s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 libparallel-forkmanager-perl all 2.02-1 [27.7 kB] 299s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 libfile-slurp-perl all 9999.32-2 [21.7 kB] 299s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-getopt all 1.20.4-1 [38.4 kB] 299s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB] 299s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fracdiff arm64 1.5-3-1 [108 kB] 299s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 299s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 299s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 299s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 299s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 299s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 299s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 299s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 299s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 299s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 299s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 299s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 299s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB] 299s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 299s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] 299s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 299s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 299s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 299s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 299s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 299s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 299s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 299s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 299s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 299s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 299s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 299s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 299s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 299s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-zoo arm64 1.8-12-2 [984 kB] 299s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lmtest arm64 0.9.40-1 [396 kB] 299s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nnet arm64 7.3-19-2 [111 kB] 299s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 299s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 299s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 300s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 300s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-timedate arm64 4032.109-1 [1229 kB] 300s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-quadprog arm64 1.5-8-1build1 [29.8 kB] 300s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xts arm64 0.13.2-1 [770 kB] 300s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-curl arm64 5.2.0+dfsg-1 [189 kB] 300s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ttr arm64 0.24.4-1 [509 kB] 300s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB] 300s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-quantmod all 0.4.26-1 [1027 kB] 300s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tseries arm64 0.10-55-1 [367 kB] 300s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-urca arm64 1.3-3-1 [1071 kB] 300s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpparmadillo arm64 0.12.8.0.0-1 [859 kB] 300s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-forecast arm64 8.21.1-1 [1547 kB] 300s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocgenerics all 0.48.1-2 [595 kB] 300s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biobase arm64 2.62.0-1 [2136 kB] 300s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 301s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-multtest arm64 2.58.0-1 [836 kB] 301s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-optparse all 1.7.4-1 [81.6 kB] 301s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-uroot all 2.1-3-1 [1927 kB] 301s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 pique all 1.0-7 [21.3 kB] 301s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 pique-doc all 1.0-7 [1931 kB] 301s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cluster arm64 2.1.6-1 [552 kB] 301s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB] 301s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreign arm64 0.8.86-1 [240 kB] 301s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gridextra all 2.3-3build1 [1024 kB] 301s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-data.table arm64 1.14.10+dfsg-1 [1844 kB] 301s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB] 301s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 301s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB] 301s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xfun arm64 0.41+dfsg-1 [415 kB] 301s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 301s Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 301s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-highr all 0.10+dfsg-1 [38.3 kB] 301s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-yaml arm64 2.3.8-1 [107 kB] 301s Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 301s Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 301s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 301s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 301s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 301s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 301s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-knitr all 1.45+dfsg-1 [917 kB] 301s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-backports arm64 1.4.1-1 [101 kB] 301s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-checkmate arm64 2.3.1-1 [711 kB] 301s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-base64enc arm64 0.1-3-3 [27.4 kB] 301s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB] 301s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 301s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fastmap arm64 1.1.1-1 [69.6 kB] 301s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmltools arm64 0.5.7-1 [369 kB] 301s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cachem arm64 1.0.8-1 [72.3 kB] 301s Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB] 301s Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB] 301s Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mime arm64 0.12-1 [35.8 kB] 301s Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fs arm64 1.6.3+dfsg-1 [227 kB] 301s Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rappdirs arm64 0.3.3-1 [47.5 kB] 301s Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sass arm64 0.4.8+dfsg-1 [952 kB] 301s Get:157 http://ftpmaster.internal/ubuntu noble/universe arm64 node-bootstrap-sass all 3.4.3-2 [187 kB] 301s Get:158 http://ftpmaster.internal/ubuntu noble/main arm64 javascript-common all 11+nmu1 [5936 B] 301s Get:159 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB] 301s Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB] 301s Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bslib all 0.6.1+dfsg-1 [5138 kB] 302s Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fontawesome all 0.5.2-1 [1300 kB] 302s Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tinytex all 0.49-1 [141 kB] 302s Get:164 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 302s Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-modernizr all 2.6.2+ds1-5 [48.3 kB] 302s Get:166 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB] 302s Get:167 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 302s Get:168 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc-data all 3.1.3-1 [92.4 kB] 302s Get:169 http://ftpmaster.internal/ubuntu noble/main arm64 liblua5.4-0 arm64 5.4.6-3 [158 kB] 302s Get:170 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc arm64 3.1.3+ds-2 [27.7 MB] 303s Get:171 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-later arm64 1.3.2+dfsg-1 [120 kB] 303s Get:172 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-promises arm64 1.2.1+dfsg-1 [282 kB] 303s Get:173 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-httpuv arm64 1.6.14+dfsg-1 [496 kB] 303s Get:174 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB] 303s Get:175 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sourcetools arm64 0.1.7-1-1 [47.2 kB] 303s Get:176 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB] 303s Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-commonmark arm64 1.9.1-1 [127 kB] 303s Get:178 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB] 303s Get:179 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-es5-shim all 4.6.7-2 [39.8 kB] 303s Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 303s Get:181 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 303s Get:182 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B] 303s Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 303s Get:184 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-d3 all 3.5.17-4 [132 kB] 303s Get:185 http://ftpmaster.internal/ubuntu noble/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 303s Get:186 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-shiny all 1.8.0+dfsg-1 [2762 kB] 303s Get:187 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rmarkdown all 2.25+dfsg-3 [1481 kB] 303s Get:188 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] 303s Get:189 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rstudioapi all 0.15.0-1 [277 kB] 303s Get:190 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB] 303s Get:191 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB] 303s Get:192 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB] 303s Get:193 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB] 303s Get:194 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 303s Get:195 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmltable all 2.4.2-1 [381 kB] 303s Get:196 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridis all 0.6.5-1 [2770 kB] 303s Get:197 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-formula all 1.2-5-1 [158 kB] 303s Get:198 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-chron arm64 2.3-61-2 [186 kB] 303s Get:199 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-png arm64 0.1-8-1 [39.9 kB] 303s Get:200 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jpeg arm64 0.1-10-1 [30.8 kB] 303s Get:201 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-deldir arm64 2.0-2-1 [270 kB] 303s Get:202 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 304s Get:203 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-interp arm64 1.1-6-1 [1433 kB] 304s Get:204 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-latticeextra all 0.6-30-1 [2198 kB] 304s Get:205 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-acepack arm64 1.4.2-1 [60.5 kB] 304s Get:206 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-hmisc arm64 5.1-1-1 [3486 kB] 306s Preconfiguring packages ... 306s Fetched 172 MB in 8s (21.9 MB/s) 306s Selecting previously unselected package zip. 306s (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 ... 74221 files and directories currently installed.) 306s Preparing to unpack .../000-zip_3.0-13_arm64.deb ... 306s Unpacking zip (3.0-13) ... 306s Selecting previously unselected package unzip. 306s Preparing to unpack .../001-unzip_6.0-28ubuntu3_arm64.deb ... 306s Unpacking unzip (6.0-28ubuntu3) ... 306s Selecting previously unselected package libpaper1:arm64. 306s Preparing to unpack .../002-libpaper1_1.1.29_arm64.deb ... 306s Unpacking libpaper1:arm64 (1.1.29) ... 306s Selecting previously unselected package libpaper-utils. 306s Preparing to unpack .../003-libpaper-utils_1.1.29_arm64.deb ... 306s Unpacking libpaper-utils (1.1.29) ... 306s Selecting previously unselected package xdg-utils. 306s Preparing to unpack .../004-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 306s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 306s Selecting previously unselected package libblas3:arm64. 306s Preparing to unpack .../005-libblas3_3.12.0-3_arm64.deb ... 306s Unpacking libblas3:arm64 (3.12.0-3) ... 306s Selecting previously unselected package fonts-dejavu-mono. 306s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 306s Unpacking fonts-dejavu-mono (2.37-8) ... 306s Selecting previously unselected package fonts-dejavu-core. 306s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 306s Unpacking fonts-dejavu-core (2.37-8) ... 306s Selecting previously unselected package fontconfig-config. 306s Preparing to unpack .../008-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 306s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 306s Selecting previously unselected package libfontconfig1:arm64. 306s Preparing to unpack .../009-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 306s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 306s Selecting previously unselected package libpixman-1-0:arm64. 306s Preparing to unpack .../010-libpixman-1-0_0.42.2-1_arm64.deb ... 306s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 306s Selecting previously unselected package libxcb-render0:arm64. 306s Preparing to unpack .../011-libxcb-render0_1.15-1_arm64.deb ... 306s Unpacking libxcb-render0:arm64 (1.15-1) ... 306s Selecting previously unselected package libxcb-shm0:arm64. 306s Preparing to unpack .../012-libxcb-shm0_1.15-1_arm64.deb ... 306s Unpacking libxcb-shm0:arm64 (1.15-1) ... 307s Selecting previously unselected package libxrender1:arm64. 307s Preparing to unpack .../013-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 307s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 307s Selecting previously unselected package libcairo2:arm64. 307s Preparing to unpack .../014-libcairo2_1.18.0-1_arm64.deb ... 307s Unpacking libcairo2:arm64 (1.18.0-1) ... 307s Selecting previously unselected package libgomp1:arm64. 307s Preparing to unpack .../015-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 307s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 307s Selecting previously unselected package libjpeg-turbo8:arm64. 307s Preparing to unpack .../016-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 307s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 307s Selecting previously unselected package libjpeg8:arm64. 307s Preparing to unpack .../017-libjpeg8_8c-2ubuntu11_arm64.deb ... 307s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 307s Selecting previously unselected package libgfortran5:arm64. 307s Preparing to unpack .../018-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 307s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 307s Selecting previously unselected package liblapack3:arm64. 307s Preparing to unpack .../019-liblapack3_3.12.0-3_arm64.deb ... 307s Unpacking liblapack3:arm64 (3.12.0-3) ... 307s Selecting previously unselected package fontconfig. 307s Preparing to unpack .../020-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 307s Unpacking fontconfig (2.15.0-1ubuntu1) ... 307s Selecting previously unselected package libgraphite2-3:arm64. 307s Preparing to unpack .../021-libgraphite2-3_1.3.14-2_arm64.deb ... 307s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 307s Selecting previously unselected package libharfbuzz0b:arm64. 307s Preparing to unpack .../022-libharfbuzz0b_8.3.0-2_arm64.deb ... 307s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 307s Selecting previously unselected package libthai-data. 307s Preparing to unpack .../023-libthai-data_0.1.29-2_all.deb ... 307s Unpacking libthai-data (0.1.29-2) ... 307s Selecting previously unselected package libdatrie1:arm64. 307s Preparing to unpack .../024-libdatrie1_0.2.13-3_arm64.deb ... 307s Unpacking libdatrie1:arm64 (0.2.13-3) ... 307s Selecting previously unselected package libthai0:arm64. 307s Preparing to unpack .../025-libthai0_0.1.29-2_arm64.deb ... 307s Unpacking libthai0:arm64 (0.1.29-2) ... 307s Selecting previously unselected package libpango-1.0-0:arm64. 307s Preparing to unpack .../026-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 307s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 307s Selecting previously unselected package libpangoft2-1.0-0:arm64. 307s Preparing to unpack .../027-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 307s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 307s Selecting previously unselected package libpangocairo-1.0-0:arm64. 307s Preparing to unpack .../028-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 307s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 307s Selecting previously unselected package libtcl8.6:arm64. 307s Preparing to unpack .../029-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 307s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 307s Selecting previously unselected package libdeflate0:arm64. 307s Preparing to unpack .../030-libdeflate0_1.19-1_arm64.deb ... 307s Unpacking libdeflate0:arm64 (1.19-1) ... 307s Selecting previously unselected package libjbig0:arm64. 307s Preparing to unpack .../031-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 307s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 307s Selecting previously unselected package liblerc4:arm64. 307s Preparing to unpack .../032-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 307s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 307s Selecting previously unselected package libsharpyuv0:arm64. 307s Preparing to unpack .../033-libsharpyuv0_1.3.2-0.4_arm64.deb ... 307s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 307s Selecting previously unselected package libwebp7:arm64. 307s Preparing to unpack .../034-libwebp7_1.3.2-0.4_arm64.deb ... 307s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 307s Selecting previously unselected package libtiff6:arm64. 307s Preparing to unpack .../035-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 307s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 307s Selecting previously unselected package libxft2:arm64. 307s Preparing to unpack .../036-libxft2_2.3.6-1_arm64.deb ... 307s Unpacking libxft2:arm64 (2.3.6-1) ... 308s Selecting previously unselected package x11-common. 308s Preparing to unpack .../037-x11-common_1%3a7.7+23ubuntu2_all.deb ... 308s Unpacking x11-common (1:7.7+23ubuntu2) ... 308s Selecting previously unselected package libxss1:arm64. 308s Preparing to unpack .../038-libxss1_1%3a1.2.3-1build2_arm64.deb ... 308s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 308s Selecting previously unselected package libtk8.6:arm64. 308s Preparing to unpack .../039-libtk8.6_8.6.13-2_arm64.deb ... 308s Unpacking libtk8.6:arm64 (8.6.13-2) ... 308s Selecting previously unselected package libice6:arm64. 308s Preparing to unpack .../040-libice6_2%3a1.0.10-1build2_arm64.deb ... 308s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 308s Selecting previously unselected package libsm6:arm64. 308s Preparing to unpack .../041-libsm6_2%3a1.2.3-1build2_arm64.deb ... 308s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 308s Selecting previously unselected package libxt6:arm64. 308s Preparing to unpack .../042-libxt6_1%3a1.2.1-1.1_arm64.deb ... 308s Unpacking libxt6:arm64 (1:1.2.1-1.1) ... 308s Selecting previously unselected package r-base-core. 308s Preparing to unpack .../043-r-base-core_4.3.2-1build1_arm64.deb ... 308s Unpacking r-base-core (4.3.2-1build1) ... 308s Selecting previously unselected package libtmglib3:arm64. 308s Preparing to unpack .../044-libtmglib3_3.12.0-3_arm64.deb ... 308s Unpacking libtmglib3:arm64 (3.12.0-3) ... 308s Selecting previously unselected package liblapacke:arm64. 308s Preparing to unpack .../045-liblapacke_3.12.0-3_arm64.deb ... 308s Unpacking liblapacke:arm64 (3.12.0-3) ... 308s Selecting previously unselected package emmax. 308s Preparing to unpack .../046-emmax_0~beta.20100307-5_arm64.deb ... 308s Unpacking emmax (0~beta.20100307-5) ... 308s Selecting previously unselected package plink. 308s Preparing to unpack .../047-plink_1.07+dfsg-4_arm64.deb ... 308s Unpacking plink (1.07+dfsg-4) ... 308s Selecting previously unselected package libgslcblas0:arm64. 308s Preparing to unpack .../048-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 308s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 308s Selecting previously unselected package libgsl27:arm64. 308s Preparing to unpack .../049-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 308s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 308s Selecting previously unselected package eigensoft. 308s Preparing to unpack .../050-eigensoft_8.0.0+dfsg-2_arm64.deb ... 308s Unpacking eigensoft (8.0.0+dfsg-2) ... 308s Selecting previously unselected package libreadonly-perl. 308s Preparing to unpack .../051-libreadonly-perl_2.050-3_all.deb ... 308s Unpacking libreadonly-perl (2.050-3) ... 308s Selecting previously unselected package libclass-method-modifiers-perl. 308s Preparing to unpack .../052-libclass-method-modifiers-perl_2.15-1_all.deb ... 308s Unpacking libclass-method-modifiers-perl (2.15-1) ... 308s Selecting previously unselected package libclass-xsaccessor-perl. 308s Preparing to unpack .../053-libclass-xsaccessor-perl_1.19-4build2_arm64.deb ... 308s Unpacking libclass-xsaccessor-perl (1.19-4build2) ... 309s Selecting previously unselected package libb-hooks-op-check-perl:arm64. 309s Preparing to unpack .../054-libb-hooks-op-check-perl_0.22-2build2_arm64.deb ... 309s Unpacking libb-hooks-op-check-perl:arm64 (0.22-2build2) ... 309s Selecting previously unselected package libdynaloader-functions-perl. 309s Preparing to unpack .../055-libdynaloader-functions-perl_0.003-3_all.deb ... 309s Unpacking libdynaloader-functions-perl (0.003-3) ... 309s Selecting previously unselected package libdevel-callchecker-perl:arm64. 309s Preparing to unpack .../056-libdevel-callchecker-perl_0.008-2build1_arm64.deb ... 309s Unpacking libdevel-callchecker-perl:arm64 (0.008-2build1) ... 309s Selecting previously unselected package libparams-classify-perl:arm64. 309s Preparing to unpack .../057-libparams-classify-perl_0.015-2build3_arm64.deb ... 309s Unpacking libparams-classify-perl:arm64 (0.015-2build3) ... 309s Selecting previously unselected package libmodule-runtime-perl. 309s Preparing to unpack .../058-libmodule-runtime-perl_0.016-2_all.deb ... 309s Unpacking libmodule-runtime-perl (0.016-2) ... 309s Selecting previously unselected package libimport-into-perl. 309s Preparing to unpack .../059-libimport-into-perl_1.002005-2_all.deb ... 309s Unpacking libimport-into-perl (1.002005-2) ... 309s Selecting previously unselected package librole-tiny-perl. 309s Preparing to unpack .../060-librole-tiny-perl_2.002004-1_all.deb ... 309s Unpacking librole-tiny-perl (2.002004-1) ... 309s Selecting previously unselected package libsub-quote-perl. 309s Preparing to unpack .../061-libsub-quote-perl_2.006008-1ubuntu1_all.deb ... 309s Unpacking libsub-quote-perl (2.006008-1ubuntu1) ... 309s Selecting previously unselected package libmoo-perl. 309s Preparing to unpack .../062-libmoo-perl_2.005005-1_all.deb ... 309s Unpacking libmoo-perl (2.005005-1) ... 309s Selecting previously unselected package libparallel-forkmanager-perl. 309s Preparing to unpack .../063-libparallel-forkmanager-perl_2.02-1_all.deb ... 309s Unpacking libparallel-forkmanager-perl (2.02-1) ... 309s Selecting previously unselected package libfile-slurp-perl. 309s Preparing to unpack .../064-libfile-slurp-perl_9999.32-2_all.deb ... 309s Unpacking libfile-slurp-perl (9999.32-2) ... 309s Selecting previously unselected package r-cran-getopt. 309s Preparing to unpack .../065-r-cran-getopt_1.20.4-1_all.deb ... 309s Unpacking r-cran-getopt (1.20.4-1) ... 309s Selecting previously unselected package r-cran-colorspace. 309s Preparing to unpack .../066-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ... 309s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 309s Selecting previously unselected package r-cran-fracdiff. 309s Preparing to unpack .../067-r-cran-fracdiff_1.5-3-1_arm64.deb ... 309s Unpacking r-cran-fracdiff (1.5-3-1) ... 309s Selecting previously unselected package r-cran-generics. 309s Preparing to unpack .../068-r-cran-generics_0.1.3-1_all.deb ... 309s Unpacking r-cran-generics (0.1.3-1) ... 309s Selecting previously unselected package r-cran-cli. 309s Preparing to unpack .../069-r-cran-cli_3.6.2-1_arm64.deb ... 309s Unpacking r-cran-cli (3.6.2-1) ... 309s Selecting previously unselected package r-cran-glue. 309s Preparing to unpack .../070-r-cran-glue_1.7.0-1_arm64.deb ... 309s Unpacking r-cran-glue (1.7.0-1) ... 309s Selecting previously unselected package r-cran-rlang. 309s Preparing to unpack .../071-r-cran-rlang_1.1.3-1_arm64.deb ... 309s Unpacking r-cran-rlang (1.1.3-1) ... 309s Selecting previously unselected package r-cran-lifecycle. 309s Preparing to unpack .../072-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 309s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 309s Selecting previously unselected package r-cran-gtable. 309s Preparing to unpack .../073-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 309s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 309s Selecting previously unselected package r-cran-isoband. 309s Preparing to unpack .../074-r-cran-isoband_0.2.7-1_arm64.deb ... 309s Unpacking r-cran-isoband (0.2.7-1) ... 309s Selecting previously unselected package r-cran-mass. 309s Preparing to unpack .../075-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 309s Unpacking r-cran-mass (7.3-60.0.1-1) ... 309s Selecting previously unselected package r-cran-lattice. 309s Preparing to unpack .../076-r-cran-lattice_0.22-5-1_arm64.deb ... 309s Unpacking r-cran-lattice (0.22-5-1) ... 309s Selecting previously unselected package r-cran-nlme. 309s Preparing to unpack .../077-r-cran-nlme_3.1.164-1_arm64.deb ... 309s Unpacking r-cran-nlme (3.1.164-1) ... 309s Selecting previously unselected package r-cran-matrix. 309s Preparing to unpack .../078-r-cran-matrix_1.6-5-1_arm64.deb ... 309s Unpacking r-cran-matrix (1.6-5-1) ... 309s Selecting previously unselected package r-cran-mgcv. 309s Preparing to unpack .../079-r-cran-mgcv_1.9-1-1_arm64.deb ... 309s Unpacking r-cran-mgcv (1.9-1-1) ... 310s Selecting previously unselected package r-cran-farver. 310s Preparing to unpack .../080-r-cran-farver_2.1.1-1_arm64.deb ... 310s Unpacking r-cran-farver (2.1.1-1) ... 310s Selecting previously unselected package r-cran-labeling. 310s Preparing to unpack .../081-r-cran-labeling_0.4.3-1_all.deb ... 310s Unpacking r-cran-labeling (0.4.3-1) ... 310s Selecting previously unselected package r-cran-munsell. 310s Preparing to unpack .../082-r-cran-munsell_0.5.0-2build1_all.deb ... 310s Unpacking r-cran-munsell (0.5.0-2build1) ... 310s Selecting previously unselected package r-cran-r6. 310s Preparing to unpack .../083-r-cran-r6_2.5.1-1_all.deb ... 310s Unpacking r-cran-r6 (2.5.1-1) ... 310s Selecting previously unselected package r-cran-rcolorbrewer. 310s Preparing to unpack .../084-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 310s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 310s Selecting previously unselected package r-cran-viridislite. 310s Preparing to unpack .../085-r-cran-viridislite_0.4.2-2_all.deb ... 310s Unpacking r-cran-viridislite (0.4.2-2) ... 310s Selecting previously unselected package r-cran-scales. 310s Preparing to unpack .../086-r-cran-scales_1.3.0-1_all.deb ... 310s Unpacking r-cran-scales (1.3.0-1) ... 310s Selecting previously unselected package r-cran-fansi. 310s Preparing to unpack .../087-r-cran-fansi_1.0.5-1_arm64.deb ... 310s Unpacking r-cran-fansi (1.0.5-1) ... 310s Selecting previously unselected package r-cran-magrittr. 310s Preparing to unpack .../088-r-cran-magrittr_2.0.3-1_arm64.deb ... 310s Unpacking r-cran-magrittr (2.0.3-1) ... 310s Selecting previously unselected package r-cran-utf8. 310s Preparing to unpack .../089-r-cran-utf8_1.2.4-1_arm64.deb ... 310s Unpacking r-cran-utf8 (1.2.4-1) ... 310s Selecting previously unselected package r-cran-vctrs. 310s Preparing to unpack .../090-r-cran-vctrs_0.6.5-1_arm64.deb ... 310s Unpacking r-cran-vctrs (0.6.5-1) ... 310s Selecting previously unselected package r-cran-pillar. 310s Preparing to unpack .../091-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 310s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 310s Selecting previously unselected package r-cran-pkgconfig. 310s Preparing to unpack .../092-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 310s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 310s Selecting previously unselected package r-cran-tibble. 310s Preparing to unpack .../093-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 310s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 310s Selecting previously unselected package r-cran-withr. 310s Preparing to unpack .../094-r-cran-withr_2.5.0-1_all.deb ... 310s Unpacking r-cran-withr (2.5.0-1) ... 310s Selecting previously unselected package r-cran-ggplot2. 310s Preparing to unpack .../095-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 310s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 310s Selecting previously unselected package r-cran-zoo. 310s Preparing to unpack .../096-r-cran-zoo_1.8-12-2_arm64.deb ... 310s Unpacking r-cran-zoo (1.8-12-2) ... 310s Selecting previously unselected package r-cran-lmtest. 310s Preparing to unpack .../097-r-cran-lmtest_0.9.40-1_arm64.deb ... 310s Unpacking r-cran-lmtest (0.9.40-1) ... 310s Selecting previously unselected package r-cran-nnet. 310s Preparing to unpack .../098-r-cran-nnet_7.3-19-2_arm64.deb ... 310s Unpacking r-cran-nnet (7.3-19-2) ... 310s Selecting previously unselected package r-cran-littler. 310s Preparing to unpack .../099-r-cran-littler_0.3.19-1_arm64.deb ... 310s Unpacking r-cran-littler (0.3.19-1) ... 310s Selecting previously unselected package littler. 311s Preparing to unpack .../100-littler_0.3.19-1_all.deb ... 311s Unpacking littler (0.3.19-1) ... 311s Selecting previously unselected package r-cran-pkgkitten. 311s Preparing to unpack .../101-r-cran-pkgkitten_0.2.3-1_all.deb ... 311s Unpacking r-cran-pkgkitten (0.2.3-1) ... 311s Selecting previously unselected package r-cran-rcpp. 311s Preparing to unpack .../102-r-cran-rcpp_1.0.12-1_arm64.deb ... 311s Unpacking r-cran-rcpp (1.0.12-1) ... 311s Selecting previously unselected package r-cran-timedate. 311s Preparing to unpack .../103-r-cran-timedate_4032.109-1_arm64.deb ... 311s Unpacking r-cran-timedate (4032.109-1) ... 311s Selecting previously unselected package r-cran-quadprog. 311s Preparing to unpack .../104-r-cran-quadprog_1.5-8-1build1_arm64.deb ... 311s Unpacking r-cran-quadprog (1.5-8-1build1) ... 311s Selecting previously unselected package r-cran-xts. 311s Preparing to unpack .../105-r-cran-xts_0.13.2-1_arm64.deb ... 311s Unpacking r-cran-xts (0.13.2-1) ... 311s Selecting previously unselected package r-cran-curl. 311s Preparing to unpack .../106-r-cran-curl_5.2.0+dfsg-1_arm64.deb ... 311s Unpacking r-cran-curl (5.2.0+dfsg-1) ... 311s Selecting previously unselected package r-cran-ttr. 311s Preparing to unpack .../107-r-cran-ttr_0.24.4-1_arm64.deb ... 311s Unpacking r-cran-ttr (0.24.4-1) ... 311s Selecting previously unselected package r-cran-jsonlite. 311s Preparing to unpack .../108-r-cran-jsonlite_1.8.8+dfsg-1_arm64.deb ... 311s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 311s Selecting previously unselected package r-cran-quantmod. 311s Preparing to unpack .../109-r-cran-quantmod_0.4.26-1_all.deb ... 311s Unpacking r-cran-quantmod (0.4.26-1) ... 311s Selecting previously unselected package r-cran-tseries. 311s Preparing to unpack .../110-r-cran-tseries_0.10-55-1_arm64.deb ... 311s Unpacking r-cran-tseries (0.10-55-1) ... 311s Selecting previously unselected package r-cran-urca. 311s Preparing to unpack .../111-r-cran-urca_1.3-3-1_arm64.deb ... 311s Unpacking r-cran-urca (1.3-3-1) ... 311s Selecting previously unselected package r-cran-rcpparmadillo. 311s Preparing to unpack .../112-r-cran-rcpparmadillo_0.12.8.0.0-1_arm64.deb ... 311s Unpacking r-cran-rcpparmadillo (0.12.8.0.0-1) ... 311s Selecting previously unselected package r-cran-forecast. 311s Preparing to unpack .../113-r-cran-forecast_8.21.1-1_arm64.deb ... 311s Unpacking r-cran-forecast (8.21.1-1) ... 311s Selecting previously unselected package r-bioc-biocgenerics. 311s Preparing to unpack .../114-r-bioc-biocgenerics_0.48.1-2_all.deb ... 311s Unpacking r-bioc-biocgenerics (0.48.1-2) ... 311s Selecting previously unselected package r-bioc-biobase. 311s Preparing to unpack .../115-r-bioc-biobase_2.62.0-1_arm64.deb ... 311s Unpacking r-bioc-biobase (2.62.0-1) ... 311s Selecting previously unselected package r-cran-survival. 311s Preparing to unpack .../116-r-cran-survival_3.5-8-1_arm64.deb ... 311s Unpacking r-cran-survival (3.5-8-1) ... 311s Selecting previously unselected package r-bioc-multtest. 311s Preparing to unpack .../117-r-bioc-multtest_2.58.0-1_arm64.deb ... 311s Unpacking r-bioc-multtest (2.58.0-1) ... 311s Selecting previously unselected package r-cran-optparse. 311s Preparing to unpack .../118-r-cran-optparse_1.7.4-1_all.deb ... 311s Unpacking r-cran-optparse (1.7.4-1) ... 311s Selecting previously unselected package r-cran-uroot. 311s Preparing to unpack .../119-r-cran-uroot_2.1-3-1_all.deb ... 311s Unpacking r-cran-uroot (2.1-3-1) ... 311s Selecting previously unselected package pique. 311s Preparing to unpack .../120-pique_1.0-7_all.deb ... 311s Unpacking pique (1.0-7) ... 311s Selecting previously unselected package pique-doc. 311s Preparing to unpack .../121-pique-doc_1.0-7_all.deb ... 311s Unpacking pique-doc (1.0-7) ... 311s Selecting previously unselected package r-cran-cluster. 312s Preparing to unpack .../122-r-cran-cluster_2.1.6-1_arm64.deb ... 312s Unpacking r-cran-cluster (2.1.6-1) ... 312s Selecting previously unselected package r-cran-rpart. 312s Preparing to unpack .../123-r-cran-rpart_4.1.23-1_arm64.deb ... 312s Unpacking r-cran-rpart (4.1.23-1) ... 312s Selecting previously unselected package r-cran-foreign. 312s Preparing to unpack .../124-r-cran-foreign_0.8.86-1_arm64.deb ... 312s Unpacking r-cran-foreign (0.8.86-1) ... 312s Selecting previously unselected package r-cran-gridextra. 312s Preparing to unpack .../125-r-cran-gridextra_2.3-3build1_all.deb ... 312s Unpacking r-cran-gridextra (2.3-3build1) ... 312s Selecting previously unselected package r-cran-data.table. 312s Preparing to unpack .../126-r-cran-data.table_1.14.10+dfsg-1_arm64.deb ... 312s Unpacking r-cran-data.table (1.14.10+dfsg-1) ... 312s Selecting previously unselected package r-cran-stringi. 312s Preparing to unpack .../127-r-cran-stringi_1.8.3-1_arm64.deb ... 312s Unpacking r-cran-stringi (1.8.3-1) ... 312s Selecting previously unselected package r-cran-stringr. 312s Preparing to unpack .../128-r-cran-stringr_1.5.1-1_all.deb ... 312s Unpacking r-cran-stringr (1.5.1-1) ... 312s Selecting previously unselected package r-cran-evaluate. 312s Preparing to unpack .../129-r-cran-evaluate_0.23-1_all.deb ... 312s Unpacking r-cran-evaluate (0.23-1) ... 312s Selecting previously unselected package r-cran-xfun. 312s Preparing to unpack .../130-r-cran-xfun_0.41+dfsg-1_arm64.deb ... 312s Unpacking r-cran-xfun (0.41+dfsg-1) ... 312s Selecting previously unselected package libjs-highlight.js. 312s Preparing to unpack .../131-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 312s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 312s Selecting previously unselected package libjs-jquery. 312s Preparing to unpack .../132-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 312s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 312s Selecting previously unselected package r-cran-highr. 312s Preparing to unpack .../133-r-cran-highr_0.10+dfsg-1_all.deb ... 312s Unpacking r-cran-highr (0.10+dfsg-1) ... 312s Selecting previously unselected package r-cran-yaml. 312s Preparing to unpack .../134-r-cran-yaml_2.3.8-1_arm64.deb ... 312s Unpacking r-cran-yaml (2.3.8-1) ... 312s Selecting previously unselected package fonts-mathjax. 312s Preparing to unpack .../135-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 312s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 312s Selecting previously unselected package libjs-mathjax. 313s Preparing to unpack .../136-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 313s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 313s Selecting previously unselected package fonts-glyphicons-halflings. 313s Preparing to unpack .../137-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 313s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 313s Selecting previously unselected package libjs-bootstrap. 313s Preparing to unpack .../138-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 313s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 313s Selecting previously unselected package libjs-jquery-datatables. 313s Preparing to unpack .../139-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 313s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 313s Selecting previously unselected package node-normalize.css. 313s Preparing to unpack .../140-node-normalize.css_8.0.1-5_all.deb ... 313s Unpacking node-normalize.css (8.0.1-5) ... 313s Selecting previously unselected package r-cran-knitr. 313s Preparing to unpack .../141-r-cran-knitr_1.45+dfsg-1_all.deb ... 313s Unpacking r-cran-knitr (1.45+dfsg-1) ... 313s Selecting previously unselected package r-cran-backports. 313s Preparing to unpack .../142-r-cran-backports_1.4.1-1_arm64.deb ... 313s Unpacking r-cran-backports (1.4.1-1) ... 313s Selecting previously unselected package r-cran-checkmate. 313s Preparing to unpack .../143-r-cran-checkmate_2.3.1-1_arm64.deb ... 313s Unpacking r-cran-checkmate (2.3.1-1) ... 313s Selecting previously unselected package r-cran-base64enc. 314s Preparing to unpack .../144-r-cran-base64enc_0.1-3-3_arm64.deb ... 314s Unpacking r-cran-base64enc (0.1-3-3) ... 314s Selecting previously unselected package r-cran-digest. 314s Preparing to unpack .../145-r-cran-digest_0.6.34-1_arm64.deb ... 314s Unpacking r-cran-digest (0.6.34-1) ... 314s Selecting previously unselected package r-cran-ellipsis. 314s Preparing to unpack .../146-r-cran-ellipsis_0.3.2-2_arm64.deb ... 314s Unpacking r-cran-ellipsis (0.3.2-2) ... 314s Selecting previously unselected package r-cran-fastmap. 314s Preparing to unpack .../147-r-cran-fastmap_1.1.1-1_arm64.deb ... 314s Unpacking r-cran-fastmap (1.1.1-1) ... 314s Selecting previously unselected package r-cran-htmltools. 314s Preparing to unpack .../148-r-cran-htmltools_0.5.7-1_arm64.deb ... 314s Unpacking r-cran-htmltools (0.5.7-1) ... 314s Selecting previously unselected package r-cran-cachem. 314s Preparing to unpack .../149-r-cran-cachem_1.0.8-1_arm64.deb ... 314s Unpacking r-cran-cachem (1.0.8-1) ... 314s Selecting previously unselected package r-cran-jquerylib. 314s Preparing to unpack .../150-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ... 314s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ... 314s Selecting previously unselected package r-cran-memoise. 314s Preparing to unpack .../151-r-cran-memoise_2.0.1-1_all.deb ... 314s Unpacking r-cran-memoise (2.0.1-1) ... 314s Selecting previously unselected package r-cran-mime. 314s Preparing to unpack .../152-r-cran-mime_0.12-1_arm64.deb ... 314s Unpacking r-cran-mime (0.12-1) ... 314s Selecting previously unselected package r-cran-fs. 314s Preparing to unpack .../153-r-cran-fs_1.6.3+dfsg-1_arm64.deb ... 314s Unpacking r-cran-fs (1.6.3+dfsg-1) ... 314s Selecting previously unselected package r-cran-rappdirs. 314s Preparing to unpack .../154-r-cran-rappdirs_0.3.3-1_arm64.deb ... 314s Unpacking r-cran-rappdirs (0.3.3-1) ... 314s Selecting previously unselected package r-cran-sass. 314s Preparing to unpack .../155-r-cran-sass_0.4.8+dfsg-1_arm64.deb ... 314s Unpacking r-cran-sass (0.4.8+dfsg-1) ... 314s Selecting previously unselected package node-bootstrap-sass. 314s Preparing to unpack .../156-node-bootstrap-sass_3.4.3-2_all.deb ... 314s Unpacking node-bootstrap-sass (3.4.3-2) ... 314s Selecting previously unselected package javascript-common. 314s Preparing to unpack .../157-javascript-common_11+nmu1_all.deb ... 314s Unpacking javascript-common (11+nmu1) ... 314s Selecting previously unselected package libjs-popper.js. 314s Preparing to unpack .../158-libjs-popper.js_1.16.1+ds-6_all.deb ... 314s Unpacking libjs-popper.js (1.16.1+ds-6) ... 314s Selecting previously unselected package libjs-bootstrap4. 314s Preparing to unpack .../159-libjs-bootstrap4_4.6.1+dfsg1-4_all.deb ... 314s Unpacking libjs-bootstrap4 (4.6.1+dfsg1-4) ... 314s Selecting previously unselected package r-cran-bslib. 314s Preparing to unpack .../160-r-cran-bslib_0.6.1+dfsg-1_all.deb ... 314s Unpacking r-cran-bslib (0.6.1+dfsg-1) ... 314s Selecting previously unselected package r-cran-fontawesome. 314s Preparing to unpack .../161-r-cran-fontawesome_0.5.2-1_all.deb ... 314s Unpacking r-cran-fontawesome (0.5.2-1) ... 314s Selecting previously unselected package r-cran-tinytex. 314s Preparing to unpack .../162-r-cran-tinytex_0.49-1_all.deb ... 314s Unpacking r-cran-tinytex (0.49-1) ... 314s Selecting previously unselected package libjs-jquery-ui. 314s Preparing to unpack .../163-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 314s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 314s Selecting previously unselected package libjs-modernizr. 314s Preparing to unpack .../164-libjs-modernizr_2.6.2+ds1-5_all.deb ... 314s Unpacking libjs-modernizr (2.6.2+ds1-5) ... 314s Selecting previously unselected package libjs-prettify. 315s Preparing to unpack .../165-libjs-prettify_2015.12.04+dfsg-1.1_all.deb ... 315s Unpacking libjs-prettify (2015.12.04+dfsg-1.1) ... 315s Selecting previously unselected package fonts-font-awesome. 315s Preparing to unpack .../166-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 315s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 315s Selecting previously unselected package pandoc-data. 315s Preparing to unpack .../167-pandoc-data_3.1.3-1_all.deb ... 315s Unpacking pandoc-data (3.1.3-1) ... 315s Selecting previously unselected package liblua5.4-0:arm64. 315s Preparing to unpack .../168-liblua5.4-0_5.4.6-3_arm64.deb ... 315s Unpacking liblua5.4-0:arm64 (5.4.6-3) ... 315s Selecting previously unselected package pandoc. 315s Preparing to unpack .../169-pandoc_3.1.3+ds-2_arm64.deb ... 315s Unpacking pandoc (3.1.3+ds-2) ... 316s Selecting previously unselected package r-cran-later. 316s Preparing to unpack .../170-r-cran-later_1.3.2+dfsg-1_arm64.deb ... 316s Unpacking r-cran-later (1.3.2+dfsg-1) ... 316s Selecting previously unselected package r-cran-promises. 316s Preparing to unpack .../171-r-cran-promises_1.2.1+dfsg-1_arm64.deb ... 316s Unpacking r-cran-promises (1.2.1+dfsg-1) ... 316s Selecting previously unselected package r-cran-httpuv. 316s Preparing to unpack .../172-r-cran-httpuv_1.6.14+dfsg-1_arm64.deb ... 316s Unpacking r-cran-httpuv (1.6.14+dfsg-1) ... 316s Selecting previously unselected package r-cran-xtable. 316s Preparing to unpack .../173-r-cran-xtable_1%3a1.8-4-2_all.deb ... 316s Unpacking r-cran-xtable (1:1.8-4-2) ... 316s Selecting previously unselected package r-cran-sourcetools. 316s Preparing to unpack .../174-r-cran-sourcetools_0.1.7-1-1_arm64.deb ... 316s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 316s Selecting previously unselected package r-cran-crayon. 316s Preparing to unpack .../175-r-cran-crayon_1.5.2-1_all.deb ... 316s Unpacking r-cran-crayon (1.5.2-1) ... 316s Selecting previously unselected package r-cran-commonmark. 316s Preparing to unpack .../176-r-cran-commonmark_1.9.1-1_arm64.deb ... 316s Unpacking r-cran-commonmark (1.9.1-1) ... 316s Selecting previously unselected package libjs-json. 316s Preparing to unpack .../177-libjs-json_0~20221030+~1.0.8-1_all.deb ... 316s Unpacking libjs-json (0~20221030+~1.0.8-1) ... 316s Selecting previously unselected package libjs-es5-shim. 316s Preparing to unpack .../178-libjs-es5-shim_4.6.7-2_all.deb ... 316s Unpacking libjs-es5-shim (4.6.7-2) ... 316s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 316s Preparing to unpack .../179-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 316s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 316s Selecting previously unselected package libjs-sifter.js. 316s Preparing to unpack .../180-libjs-sifter.js_0.6.0+dfsg-3_all.deb ... 316s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ... 316s Selecting previously unselected package libjs-microplugin.js. 316s Preparing to unpack .../181-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ... 316s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ... 316s Selecting previously unselected package libjs-jquery-selectize.js. 316s 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Unpacking r-cran-htmlwidgets (1.6.4+dfsg-1) ... 317s Selecting previously unselected package r-cran-rstudioapi. 317s Preparing to unpack .../188-r-cran-rstudioapi_0.15.0-1_all.deb ... 317s Unpacking r-cran-rstudioapi (0.15.0-1) ... 317s Selecting previously unselected package r-cran-tidyselect. 317s Preparing to unpack .../189-r-cran-tidyselect_1.2.0+dfsg-1_arm64.deb ... 317s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 317s Selecting previously unselected package r-cran-dplyr. 317s Preparing to unpack .../190-r-cran-dplyr_1.1.4-1_arm64.deb ... 317s Unpacking r-cran-dplyr (1.1.4-1) ... 317s Selecting previously unselected package r-cran-purrr. 317s Preparing to unpack .../191-r-cran-purrr_1.0.2-1_arm64.deb ... 317s Unpacking r-cran-purrr (1.0.2-1) ... 317s Selecting previously unselected package r-cran-cpp11. 317s Preparing to unpack .../192-r-cran-cpp11_0.4.7-1_all.deb ... 317s Unpacking r-cran-cpp11 (0.4.7-1) ... 317s Selecting previously unselected package r-cran-tidyr. 317s 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package r-cran-jpeg. 317s Preparing to unpack .../199-r-cran-jpeg_0.1-10-1_arm64.deb ... 317s Unpacking r-cran-jpeg (0.1-10-1) ... 317s Selecting previously unselected package r-cran-deldir. 317s Preparing to unpack .../200-r-cran-deldir_2.0-2-1_arm64.deb ... 317s Unpacking r-cran-deldir (2.0-2-1) ... 317s Selecting previously unselected package r-cran-rcppeigen. 317s Preparing to unpack .../201-r-cran-rcppeigen_0.3.3.9.4-1_arm64.deb ... 317s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 317s Selecting previously unselected package r-cran-interp. 317s Preparing to unpack .../202-r-cran-interp_1.1-6-1_arm64.deb ... 317s Unpacking r-cran-interp (1.1-6-1) ... 317s Selecting previously unselected package r-cran-latticeextra. 317s Preparing to unpack .../203-r-cran-latticeextra_0.6-30-1_all.deb ... 317s Unpacking r-cran-latticeextra (0.6-30-1) ... 317s Selecting previously unselected package r-cran-acepack. 317s Preparing to unpack .../204-r-cran-acepack_1.4.2-1_arm64.deb ... 317s Unpacking r-cran-acepack (1.4.2-1) ... 318s Selecting previously unselected package r-cran-hmisc. 318s Preparing to unpack .../205-r-cran-hmisc_5.1-1-1_arm64.deb ... 318s Unpacking r-cran-hmisc (5.1-1-1) ... 318s Setting up libjs-json (0~20221030+~1.0.8-1) ... 318s Setting up javascript-common (11+nmu1) ... 318s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 318s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 318s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 318s Setting up libpaper1:arm64 (1.1.29) ... 318s 318s Creating config file /etc/papersize with new version 318s Setting up libfile-slurp-perl (9999.32-2) ... 318s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 318s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 318s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 318s Setting up pique-doc (1.0-7) ... 318s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 318s Setting up libdynaloader-functions-perl (0.003-3) ... 318s Setting up libdatrie1:arm64 (0.2.13-3) ... 318s Setting up libgslcblas0:arm64 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libparams-classify-perl:arm64 (0.015-2build3) ... 321s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 321s Setting up libcairo2:arm64 (1.18.0-1) ... 321s Setting up libmodule-runtime-perl (0.016-2) ... 321s Setting up libxt6:arm64 (1:1.2.1-1.1) ... 321s Setting up emmax (0~beta.20100307-5) ... 321s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 321s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 321s Setting up libimport-into-perl (1.002005-2) ... 321s Setting up libmoo-perl (2.005005-1) ... 321s Setting up r-base-core (4.3.2-1build1) ... 321s 321s Creating config file /etc/R/Renviron with new version 321s Setting up r-cran-crayon (1.5.2-1) ... 321s Setting up libparallel-forkmanager-perl (2.02-1) ... 321s Setting up r-cran-labeling (0.4.3-1) ... 321s Setting up r-cran-sourcetools (0.1.7-1-1) ... 321s Setting up r-cran-lattice (0.22-5-1) ... 321s Setting up r-cran-nlme (3.1.164-1) ... 321s Setting up r-cran-farver (2.1.1-1) ... 321s Setting up r-cran-formula (1.2-5-1) 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Setting up r-cran-backports (1.4.1-1) ... 321s Setting up r-cran-mime (0.12-1) ... 321s Setting up r-cran-generics (0.1.3-1) ... 321s Setting up r-cran-base64enc (0.1-3-3) ... 321s Setting up r-cran-digest (0.6.34-1) ... 321s Setting up r-cran-yaml (2.3.8-1) ... 321s Setting up r-cran-evaluate (0.23-1) ... 321s Setting up r-cran-timedate (4032.109-1) ... 321s Setting up r-cran-highr (0.10+dfsg-1) ... 321s Setting up r-cran-fansi (1.0.5-1) ... 321s Setting up r-cran-mass (7.3-60.0.1-1) ... 321s Setting up r-cran-checkmate (2.3.1-1) ... 321s Setting up r-cran-acepack (1.4.2-1) ... 321s Setting up r-cran-data.table (1.14.10+dfsg-1) ... 321s Setting up r-cran-glue (1.7.0-1) ... 321s Setting up r-cran-foreign (0.8.86-1) ... 321s Setting up r-cran-fracdiff (1.5-3-1) ... 321s Setting up r-cran-xtable (1:1.8-4-2) ... 321s Setting up r-cran-cli (3.6.2-1) ... 321s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 321s Setting up r-cran-deldir (2.0-2-1) ... 321s Setting up r-cran-fastmap (1.1.1-1) ... 321s Setting up r-cran-png (0.1-8-1) ... 321s Setting up r-bioc-biobase (2.62.0-1) ... 321s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... 321s Setting up r-cran-rstudioapi (0.15.0-1) ... 321s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 321s Setting up r-cran-getopt (1.20.4-1) ... 321s Setting up r-cran-utf8 (1.2.4-1) ... 321s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 321s Setting up r-cran-stringi (1.8.3-1) ... 321s Setting up r-cran-cpp11 (0.4.7-1) ... 321s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 321s Setting up r-cran-isoband (0.2.7-1) ... 321s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 321s Setting up r-cran-zoo (1.8-12-2) ... 321s Setting up r-cran-later (1.3.2+dfsg-1) ... 321s Setting up r-cran-matrix (1.6-5-1) ... 321s Setting up r-cran-tinytex (0.49-1) ... 321s Setting up r-cran-knitr (1.45+dfsg-1) ... 321s Setting up r-cran-mgcv (1.9-1-1) ... 321s Setting up r-cran-cachem (1.0.8-1) ... 321s Setting up r-cran-lmtest (0.9.40-1) ... 321s Setting up r-cran-rcpparmadillo (0.12.8.0.0-1) ... 321s Setting up r-cran-optparse (1.7.4-1) ... 321s Setting up r-cran-vctrs (0.6.5-1) ... 321s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ... 321s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 321s Setting up r-cran-ellipsis (0.3.2-2) ... 321s Setting up r-cran-stringr (1.5.1-1) ... 321s Setting up r-cran-munsell (0.5.0-2build1) ... 321s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 321s Setting up r-cran-survival (3.5-8-1) ... 321s Setting up r-cran-xts (0.13.2-1) ... 321s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 321s Setting up r-cran-interp (1.1-6-1) ... 321s Setting up r-cran-gridextra (2.3-3build1) ... 321s Setting up r-cran-scales (1.3.0-1) ... 321s Setting up r-cran-memoise (2.0.1-1) ... 321s Setting up r-cran-promises (1.2.1+dfsg-1) ... 321s Setting up r-cran-purrr (1.0.2-1) ... 321s Setting up r-cran-htmltools (0.5.7-1) ... 321s Setting up r-cran-sass (0.4.8+dfsg-1) ... 321s Setting up r-cran-dplyr (1.1.4-1) ... 321s Setting up 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man-db (2.12.0-3) ... 322s Processing triggers for install-info (7.1-3) ... 322s Processing triggers for libc-bin (2.39-0ubuntu2) ... 334s (Reading database ... 94413 files and directories currently installed.) 334s Removing autopkgtest-satdep (0) ... 335s autopkgtest [21:46:33]: test run-unit-test: [----------------------- 335s wget --no-check-certificate http://ricediversity.org/data/sets/44kgwas/RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 335s --2024-03-07 21:46:33-- http://ricediversity.org/data/sets/44kgwas/RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 335s Resolving squid.internal (squid.internal)... 185.125.188.86, 185.125.188.85 335s Connecting to squid.internal (squid.internal)|185.125.188.86|:3128... connected. 336s Proxy request sent, awaiting response... 200 OK 336s Length: 7107854 (6.8M) [application/zip] 336s Saving to: ‘RiceDiversity.44K.MSU6.Genotypes_PLINK.zip’ 336s 336s 0K .......... .......... .......... .......... .......... 0% 288K 24s 336s 50K .......... .......... 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92% 31.0M 0s 337s 6400K .......... .......... .......... .......... .......... 92% 31.0M 0s 337s 6450K .......... .......... .......... .......... .......... 93% 35.7M 0s 337s 6500K .......... .......... .......... .......... .......... 94% 35.1M 0s 337s 6550K .......... .......... .......... .......... .......unzip RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 337s ... 95% 4.08M 0s 337s 6600K .......... .......... .......... .......... .......... 95% 86.5M 0s 337s 6650K .......... .......... .......... .......... .......... 96% 47.7M 0s 337s 6700K .......... .......... .......... .......... .......... 97% 76.3M 0s 337s 6750K .......... .......... .......... .......... .......... 97% 26.7M 0s 337s 6800K .......... .......... .......... .......... .......... 98% 53.4M 0s 337s 6850K .......... .......... .......... .......... .......... 99% 68.7M 0s 337s 6900K .......... .......... .......... .......... . 100% 231M=0.8s 337s 337s 2024-03-07 21:46:34 (8.72 MB/s) - ‘RiceDiversity.44K.MSU6.Genotypes_PLINK.zip’ saved [7107854/7107854] 337s 337s Archive: RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 337s creating: RiceDiversity_44K_Genotypes_PLINK/ 337s inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.fam 337s creating: __MACOSX/ 337s creating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/ 337s inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.fam 337s inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.map 337s inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.map 337s inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.ped 337s inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.ped 337s mv -i ./RiceDiversity_44K_Genotypes_PLINK/sativas* . 337s rmdir RiceDiversity_44K_Genotypes_PLINK 337s rm RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 337s pique-input -d -v -i sativas413 -o sativas_GWAS -p rice_phenotype.txt -k -c -e 5 337s Pre-process input data... 337s /usr/bin/p-link --missing-genotype 0 --recode12 --file sativas413 --out sativas413_recode12 337s 337s @----------------------------------------------------------@ 337s | PLINK! | v1.07 | 10/Aug/2009 | 337s |----------------------------------------------------------| 337s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 337s |----------------------------------------------------------| 337s | For documentation, citation & bug-report instructions: | 337s | http://pngu.mgh.harvard.edu/purcell/plink/ | 337s @----------------------------------------------------------@ 337s 337s Web-based version check ( --noweb to skip ) 337s Connecting to web... failed connection 337s 337s Problem connecting to web 337s 337s Writing this text to log file [ sativas413_recode12.log ] 337s Analysis started: Thu Mar 7 21:46:35 2024 337s 337s Options in effect: 337s --missing-genotype 0 337s --recode12 337s --file sativas413 337s --out sativas413_recode12 337s 337s 36901 (of 36901) markers to be included from [ sativas413.map ] 339s Warning, found 413 individuals with ambiguous sex codes 339s Writing list of these individuals to [ sativas413_recode12.nosex ] 339s 413 individuals read from [ sativas413.ped ] 339s 0 individuals with nonmissing phenotypes 339s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 339s Missing phenotype value is also -9 339s 0 cases, 0 controls and 413 missing 339s 0 males, 0 females, and 413 of unspecified sex 339s Before frequency and genotyping pruning, there are 36901 SNPs 339s 413 founders and 0 non-founders found 339s Total genotyping rate in remaining individuals is 0.956644 339s 0 SNPs failed missingness test ( GENO > 1 ) 339s 0 SNPs failed frequency test ( MAF < 0 ) 339s After frequency and genotyping pruning, there are 36901 SNPs 339s After filtering, 0 cases, 0 controls and 413 missing 339s After filtering, 0 males, 0 females, and 413 of unspecified sex 339s Writing recoded ped file to [ sativas413_recode12.ped ] 340s Writing new map file to [ sativas413_recode12.map ] 340s 340s Analysis finished: Thu Mar 7 21:46:38 2024 340s 340s Store phenotype data indexed by genotype... 340s cd sativas_GWAS 340s Filter accessions for phenotype from ../sativas413_recode12... 340s Checking concurrence of id's in .ped and .pheno input files... 340s 340s Total number of accession ids in ../sativas413_recode12.ped: 413 340s Number of accession id's in ../sativas413_recode12.ped not present in rice_phenotype.txt: 35 340s '398' '399' '400' '616' '619' '621' '622' '628' '635' '636' '637' '638' '639' '640' '641' '642' '643' '644' '645' '647' '651' '652' '648' '620' '623' '624' '625' '626' '627' '630' '632' '633' '634' '629' '618' 340s Total number of accession id's in rice_phenotype.txt: 378 340s Number of accession id's in rice_phenotype.txt not present in ../sativas413_recode12.ped: 0 340s 340s Quality control sativas_GWAS... 340s 340s Calculating MAF... 340s /usr/bin/p-link --missing-genotype 0 --freq --file sativas_GWAS --out sativas_GWAS 340s 340s @----------------------------------------------------------@ 340s | PLINK! | v1.07 | 10/Aug/2009 | 340s |----------------------------------------------------------| 340s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 340s |----------------------------------------------------------| 340s | For documentation, citation & bug-report instructions: | 340s | http://pngu.mgh.harvard.edu/purcell/plink/ | 340s @----------------------------------------------------------@ 340s 340s Web-based version check ( --noweb to skip ) 340s Connecting to web... failed connection 340s 340s Problem connecting to web 340s 340s Writing this text to log file [ sativas_GWAS.log ] 340s Analysis started: Thu Mar 7 21:46:38 2024 340s 340s Options in effect: 340s --missing-genotype 0 340s --freq 340s --file sativas_GWAS 340s --out sativas_GWAS 340s 340s 36901 (of 36901) markers to be included from [ sativas_GWAS.map ] 342s Warning, found 378 individuals with ambiguous sex codes 342s These individuals will be set to missing ( or use --allow-no-sex ) 342s Writing list of these individuals to [ sativas_GWAS.nosex ] 342s 378 individuals read from [ sativas_GWAS.ped ] 342s 0 individuals with nonmissing phenotypes 342s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 342s Missing phenotype value is also -9 342s 0 cases, 0 controls and 378 missing 342s 0 males, 0 females, and 378 of unspecified sex 342s Before frequency and genotyping pruning, there are 36901 SNPs 342s 378 founders and 0 non-founders found 342s Writing allele frequencies (founders-only) to [ sativas_GWAS.frq ] 342s 342s Analysis finished: Thu Mar 7 21:46:40 2024 342s 342s Create sativas_GWAS.covar file... 342s /usr/lib/eigensoft/smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log 349s Transpose sativas_GWAS... 349s /usr/bin/p-link --missing-genotype 0 --recode --transpose --file sativas_GWAS --out sativas_GWAS 349s 349s @----------------------------------------------------------@ 349s | PLINK! | v1.07 | 10/Aug/2009 | 349s |----------------------------------------------------------| 349s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 349s |----------------------------------------------------------| 349s | For documentation, citation & bug-report instructions: | 349s | http://pngu.mgh.harvard.edu/purcell/plink/ | 349s @----------------------------------------------------------@ 349s 349s Web-based version check ( --noweb to skip ) 349s Recent cached web-check found...Problem connecting to web 349s 349s Writing this text to log file [ sativas_GWAS.log ] 349s Analysis started: Thu Mar 7 21:46:47 2024 349s 349s Options in effect: 349s --missing-genotype 0 349s --recode 349s --transpose 349s --file sativas_GWAS 349s --out sativas_GWAS 349s 349s 36901 (of 36901) markers to be included from [ sativas_GWAS.map ] 351s Warning, found 378 individuals with ambiguous sex codes 351s Writing list of these individuals to [ sativas_GWAS.nosex ] 351s 378 individuals read from [ sativas_GWAS.ped ] 351s 0 individuals with nonmissing phenotypes 351s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 351s Missing phenotype value is also -9 351s 0 cases, 0 controls and 378 missing 351s 0 males, 0 females, and 378 of unspecified sex 351s Before frequency and genotyping pruning, there are 36901 SNPs 351s 378 founders and 0 non-founders found 351s Total genotyping rate in remaining individuals is 0.956642 351s 0 SNPs failed missingness test ( GENO > 1 ) 351s 0 SNPs failed frequency test ( MAF < 0 ) 351s After frequency and genotyping pruning, there are 36901 SNPs 351s After filtering, 0 cases, 0 controls and 378 missing 351s After filtering, 0 males, 0 females, and 378 of unspecified sex 351s Writing transposed ped file to [ sativas_GWAS.tped ] 352s Writing family information to [ sativas_GWAS.tfam ] 352s 352s Analysis finished: Thu Mar 7 21:46:50 2024 352s 352s Creating sativas_GWAS.hIBS.kin kinship file using IBS method... 352s /usr/bin/emmax-kin -v -h -s -d 10 sativas_GWAS 352s 352s Reading TFAM file sativas_GWAS.tfam .... 352s 352s Reading TPED file sativas_GWAS.tped .... 352s Reading 0 SNPs 352s Reading 1000 SNPs 352s Reading 2000 SNPs 352s Reading 3000 SNPs 352s Reading 4000 SNPs 352s Reading 5000 SNPs 353s Reading 6000 SNPs 353s Reading 7000 SNPs 353s Reading 8000 SNPs 353s Reading 9000 SNPs 353s Reading 10000 SNPs 353s Reading 11000 SNPs 354s Reading 12000 SNPs 354s Reading 13000 SNPs 354s Reading 14000 SNPs 354s Reading 15000 SNPs 354s Reading 16000 SNPs 354s Reading 17000 SNPs 354s Reading 18000 SNPs 355s Reading 19000 SNPs 355s Reading 20000 SNPs 355s Reading 21000 SNPs 355s Reading 22000 SNPs 355s Reading 23000 SNPs 355s Reading 24000 SNPs 355s Reading 25000 SNPs 356s Reading 26000 SNPs 356s Reading 27000 SNPs 356s Reading 28000 SNPs 356s Reading 29000 SNPs 356s Reading 30000 SNPs 357s Reading 31000 SNPs 357s Reading 32000 SNPs 357s Reading 33000 SNPs 357s Reading 34000 SNPs 357s Reading 35000 SNPs 357s Reading 36000 SNPs 357s Printing the kinship matrix to file 358s Creating phenotype files in sub-directory sativas_GWAS... 358s 358s cd .. 358s removing temp files... 358s pique-run -d -v -i sativas_GWAS -k IBS -c sativas_GWAS.covar -n 16 358s Warning can't run 16 threads on this system - default to max = 2 threads 358s cd sativas_GWAS 358s Starting Q_grain_Co, pid = 5740 358s cd Q_grain_Co 358s processing phenotype Q_grain_Co... 358s 358s nice emmax -d 10 -t ../sativas_GWAS -p Q_grain_Co.pheno -k ../sativas_GWAS.hIBS.kinf -o Q_grain_Co_sativas_GWAS -c ../sativas_GWAS.covar 358s cd A_Stem_thickness 358s processing phenotype A_Stem_thickness... 358s 358s nice emmax -d 10 -t ../sativas_GWAS -p A_Stem_thickness.pheno -k ../sativas_GWAS.hIBS.kinf -o A_Stem_thickness_sativas_GWAS -c ../sativas_GWAS.covar 358s nmiss = 90 , mphenoflag = 1 358s nmiss = 49 , mphenoflag = 1 358s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 358s k = 282, n-q = 282 358s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.474006 358s k = 323, n-q = 323 362s 362s number of SNP ids in Q_grain_Co_sativas_GWAS.ps for 'Q_grain_Co' phenotype: 36901 362s number of SNP ids in Q_grain_Co_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Co' phenotype: 0 362s 362s number of SNP ids in sativas_GWAS.tped: 36901 362s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Co_sativas_GWAS.ps: 0 362s 362s Error in file(filename, "r", encoding = encoding) : 362s cannot open the connection 362s Calls: source -> file 362s In addition: Warning message: 362s In file(filename, "r", encoding = encoding) : 362s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 362s Execution halted 362s cd .. 362s 362s number of SNP ids in A_Stem_thickness_sativas_GWAS.ps for 'A_Stem_thickness' phenotype: 36901 362s number of SNP ids in A_Stem_thickness_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Stem_thickness' phenotype: 0 362s 362s number of SNP ids in sativas_GWAS.tped: 36901 362s number of SNP ids in sativas_GWAS.tped not present in A_Stem_thickness_sativas_GWAS.ps: 0 362s 363s Error in file(filename, "r", encoding = encoding) : 363s cannot open the connection 363s Calls: source -> file 363s In addition: Warning message: 363s In file(filename, "r", encoding = encoding) : 363s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 363s Execution halted 363s cd .. 363s Starting A_Stem_thickness, pid = 5741 363s Finished A_Stem_thickness, pid = 5741, exit_code = 0 363s Finished Q_grain_Co, pid = 5740, exit_code = 0 363s Starting H_Root_dry_weight, pid = 5768 363s cd H_Root_dry_weight 363s processing phenotype H_Root_dry_weight... 363s 363s nice emmax -d 10 -t ../sativas_GWAS -p H_Root_dry_weight.pheno -k ../sativas_GWAS.hIBS.kinf -o H_Root_dry_weight_sativas_GWAS -c ../sativas_GWAS.covar 363s cd Q_FT 363s processing phenotype Q_FT... 363s 363s nice emmax -d 10 -t ../sativas_GWAS -p Q_FT.pheno -k ../sativas_GWAS.hIBS.kinf -o Q_FT_sativas_GWAS -c ../sativas_GWAS.covar 363s nmiss = 260 , mphenoflag = 1 363s nmiss = 85 , mphenoflag = 1 363s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 363s k = 112, n-q = 112 363s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.399886 363s k = 287, n-q = 287 365s 365s number of SNP ids in H_Root_dry_weight_sativas_GWAS.ps for 'H_Root_dry_weight' phenotype: 36901 365s number of SNP ids in H_Root_dry_weight_sativas_GWAS.ps not present in sativas_GWAS.tped for 'H_Root_dry_weight' phenotype: 0 365s 365s number of SNP ids in sativas_GWAS.tped: 36901 365s number of SNP ids in sativas_GWAS.tped not present in H_Root_dry_weight_sativas_GWAS.ps: 0 365s 365s Error in file(filename, "r", encoding = encoding) : 365s cannot open the connection 365s Calls: source -> file 365s In addition: Warning message: 365s In file(filename, "r", encoding = encoding) : 365s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 365s Execution halted 365s cd .. 365s Starting Q_FT, pid = 5769 365s Finished H_Root_dry_weight, pid = 5768, exit_code = 0 365s cd Amylose_Content 365s processing phenotype Amylose_Content... 365s 365s nice emmax -d 10 -t ../sativas_GWAS -p Amylose_Content.pheno -k ../sativas_GWAS.hIBS.kinf -o Amylose_Content_sativas_GWAS -c ../sativas_GWAS.covar 365s nmiss = 50 , mphenoflag = 1 365s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.447865 365s k = 322, n-q = 322 367s 367s number of SNP ids in Q_FT_sativas_GWAS.ps for 'Q_FT' phenotype: 36901 367s number of SNP ids in Q_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_FT' phenotype: 0 367s 367s number of SNP ids in sativas_GWAS.tped: 36901 367s number of SNP ids in sativas_GWAS.tped not present in Q_FT_sativas_GWAS.ps: 0 367s 367s Error in file(filename, "r", encoding = encoding) : 367s cannot open the connection 367s Calls: source -> file 367s In addition: Warning message: 367s In file(filename, "r", encoding = encoding) : 367s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 367s Execution halted 367s cd .. 368s Starting Amylose_Content, pid = 5784 368s Finished Q_FT, pid = 5769, exit_code = 0 368s cd F_grain_As 368s processing phenotype F_grain_As... 368s 368s nice emmax -d 10 -t ../sativas_GWAS -p F_grain_As.pheno -k ../sativas_GWAS.hIBS.kinf -o F_grain_As_sativas_GWAS -c ../sativas_GWAS.covar 368s nmiss = 73 , mphenoflag = 1 368s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 368s k = 299, n-q = 299 370s 370s number of SNP ids in Amylose_Content_sativas_GWAS.ps for 'Amylose_Content' phenotype: 36901 370s number of SNP ids in Amylose_Content_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Amylose_Content' phenotype: 0 370s 370s number of SNP ids in sativas_GWAS.tped: 36901 370s number of SNP ids in sativas_GWAS.tped not present in Amylose_Content_sativas_GWAS.ps: 0 370s 370s Error in file(filename, "r", encoding = encoding) : 370s cannot open the connection 370s Calls: source -> file 370s In addition: Warning message: 370s In file(filename, "r", encoding = encoding) : 370s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 370s Execution halted 370s cd .. 370s Starting F_grain_As, pid = 5798 370s Finished Amylose_Content, pid = 5784, exit_code = 0 370s cd H_R_S 370s processing phenotype H_R_S... 370s 370s nice emmax -d 10 -t ../sativas_GWAS -p H_R_S.pheno -k ../sativas_GWAS.hIBS.kinf -o H_R_S_sativas_GWAS -c ../sativas_GWAS.covar 370s nmiss = 260 , mphenoflag = 1 370s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 370s k = 112, n-q = 112 372s 372s number of SNP ids in H_R_S_sativas_GWAS.ps for 'H_R_S' phenotype: 36901 372s number of SNP ids in H_R_S_sativas_GWAS.ps not present in sativas_GWAS.tped for 'H_R_S' phenotype: 0 372s 372s number of SNP ids in sativas_GWAS.tped: 36901 372s number of SNP ids in sativas_GWAS.tped not present in H_R_S_sativas_GWAS.ps: 0 372s 372s Error in file(filename, "r", encoding = encoding) : 372s cannot open the connection 372s Calls: source -> file 372s In addition: Warning message: 372s In file(filename, "r", encoding = encoding) : 372s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 372s Execution halted 372s cd .. 372s Starting H_R_S, pid = 5812 372s Finished H_R_S, pid = 5812, exit_code = 0 372s cd Q_shoot_mass 372s processing phenotype Q_shoot_mass... 372s 372s nice emmax -d 10 -t ../sativas_GWAS -p Q_shoot_mass.pheno -k ../sativas_GWAS.hIBS.kinf -o Q_shoot_mass_sativas_GWAS -c ../sativas_GWAS.covar 372s 372s number of SNP ids in F_grain_As_sativas_GWAS.ps for 'F_grain_As' phenotype: 36901 372s number of SNP ids in F_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_As' phenotype: 0 372s 372s number of SNP ids in sativas_GWAS.tped: 36901 372s number of SNP ids in sativas_GWAS.tped not present in F_grain_As_sativas_GWAS.ps: 0 372s 372s nmiss = 87 , mphenoflag = 1 372s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.413538 372s k = 285, n-q = 285 372s Error in file(filename, "r", encoding = encoding) : 372s cannot open the connection 372s Calls: source -> file 372s In addition: Warning message: 372s In file(filename, "r", encoding = encoding) : 372s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 372s Execution halted 372s cd .. 373s Starting Q_shoot_mass, pid = 5826 373s Finished F_grain_As, pid = 5798, exit_code = 0 373s cd F_grain_yield 373s processing phenotype F_grain_yield... 373s 373s nice emmax -d 10 -t ../sativas_GWAS -p F_grain_yield.pheno -k ../sativas_GWAS.hIBS.kinf -o F_grain_yield_sativas_GWAS -c ../sativas_GWAS.covar 373s nmiss = 73 , mphenoflag = 1 373s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 373s k = 299, n-q = 299 376s 376s number of SNP ids in Q_shoot_mass_sativas_GWAS.ps for 'Q_shoot_mass' phenotype: 36901 376s number of SNP ids in Q_shoot_mass_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_shoot_mass' phenotype: 0 376s 376s number of SNP ids in sativas_GWAS.tped: 36901 376s number of SNP ids in sativas_GWAS.tped not present in Q_shoot_mass_sativas_GWAS.ps: 0 376s 376s Error in file(filename, "r", encoding = encoding) : 376s cannot open the connection 376s Calls: source -> file 376s In addition: Warning message: 376s In file(filename, "r", encoding = encoding) : 376s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 376s Execution halted 376s cd .. 377s Starting F_grain_yield, pid = 5840 377s Finished Q_shoot_mass, pid = 5826, exit_code = 0 377s cd HULLED_SEED_LENGTH 377s processing phenotype HULLED_SEED_LENGTH... 377s 377s nice emmax -d 10 -t ../sativas_GWAS -p HULLED_SEED_LENGTH.pheno -k ../sativas_GWAS.hIBS.kinf -o HULLED_SEED_LENGTH_sativas_GWAS -c ../sativas_GWAS.covar 377s 377s number of SNP ids in F_grain_yield_sativas_GWAS.ps for 'F_grain_yield' phenotype: 36901 377s number of SNP ids in F_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_yield' phenotype: 0 377s 377s number of SNP ids in sativas_GWAS.tped: 36901 377s number of SNP ids in sativas_GWAS.tped not present in F_grain_yield_sativas_GWAS.ps: 0 377s 377s nmiss = 34 , mphenoflag = 1 377s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.481982 377s k = 338, n-q = 338 378s Error in file(filename, "r", encoding = encoding) : 378s cannot open the connection 378s Calls: source -> file 378s In addition: Warning message: 378s In file(filename, "r", encoding = encoding) : 378s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 378s Execution halted 378s cd .. 378s Starting HULLED_SEED_LENGTH, pid = 5854 378s Finished F_grain_yield, pid = 5840, exit_code = 0 378s cd A_PH 378s processing phenotype A_PH... 378s 378s nice emmax -d 10 -t ../sativas_GWAS -p A_PH.pheno -k ../sativas_GWAS.hIBS.kinf -o A_PH_sativas_GWAS -c ../sativas_GWAS.covar 378s nmiss = 29 , mphenoflag = 1 378s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.570052 378s k = 343, n-q = 343 382s 382s number of SNP ids in HULLED_SEED_LENGTH_sativas_GWAS.ps for 'HULLED_SEED_LENGTH' phenotype: 36901 382s number of SNP ids in HULLED_SEED_LENGTH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'HULLED_SEED_LENGTH' phenotype: 0 382s 382s number of SNP ids in sativas_GWAS.tped: 36901 382s number of SNP ids in sativas_GWAS.tped not present in HULLED_SEED_LENGTH_sativas_GWAS.ps: 0 382s 383s Error in file(filename, "r", encoding = encoding) : 383s cannot open the connection 383s Calls: source -> file 383s In addition: Warning message: 383s In file(filename, "r", encoding = encoding) : 383s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 383s Execution halted 383s cd .. 383s Starting A_PH, pid = 5868 383s Finished HULLED_SEED_LENGTH, pid = 5854, exit_code = 0 383s cd A_Tiller_no. 383s processing phenotype A_Tiller_no.... 383s 383s nice emmax -d 10 -t ../sativas_GWAS -p A_Tiller_no..pheno -k ../sativas_GWAS.hIBS.kinf -o A_Tiller_no._sativas_GWAS -c ../sativas_GWAS.covar 383s nmiss = 46 , mphenoflag = 1 383s 383s number of SNP ids in A_PH_sativas_GWAS.ps for 'A_PH' phenotype: 36901 383s number of SNP ids in A_PH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_PH' phenotype: 0 383s 383s number of SNP ids in sativas_GWAS.tped: 36901 383s number of SNP ids in sativas_GWAS.tped not present in A_PH_sativas_GWAS.ps: 0 383s 383s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.524438 383s k = 326, n-q = 326 383s Error in file(filename, "r", encoding = encoding) : 383s cannot open the connection 383s Calls: source -> file 383s In addition: Warning message: 383s In file(filename, "r", encoding = encoding) : 383s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 383s Execution halted 383s cd .. 384s Starting A_Tiller_no., pid = 5882 384s Finished A_PH, pid = 5868, exit_code = 0 384s nmiss = 260 , mphenoflag = 1 384s cd H_Shoot_dry_weight 384s processing phenotype H_Shoot_dry_weight... 384s 384s nice emmax -d 10 -t ../sativas_GWAS -p H_Shoot_dry_weight.pheno -k ../sativas_GWAS.hIBS.kinf -o H_Shoot_dry_weight_sativas_GWAS -c ../sativas_GWAS.covar 384s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 384s k = 112, n-q = 112 386s 386s number of SNP ids in H_Shoot_dry_weight_sativas_GWAS.ps for 'H_Shoot_dry_weight' phenotype: 36901 386s number of SNP ids in H_Shoot_dry_weight_sativas_GWAS.ps not present in sativas_GWAS.tped for 'H_Shoot_dry_weight' phenotype: 0 386s 386s number of SNP ids in sativas_GWAS.tped: 36901 386s number of SNP ids in sativas_GWAS.tped not present in H_Shoot_dry_weight_sativas_GWAS.ps: 0 386s 386s Error in file(filename, "r", encoding = encoding) : 386s cannot open the connection 386s Calls: source -> file 386s In addition: Warning message: 386s In file(filename, "r", encoding = encoding) : 386s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 386s Execution halted 386s cd .. 386s Starting H_Shoot_dry_weight, pid = 5896 386s Finished H_Shoot_dry_weight, pid = 5896, exit_code = 0 386s cd A_Seed_length 386s processing phenotype A_Seed_length... 386s 386s nice emmax -d 10 -t ../sativas_GWAS -p A_Seed_length.pheno -k ../sativas_GWAS.hIBS.kinf -o A_Seed_length_sativas_GWAS -c ../sativas_GWAS.covar 386s nmiss = 20 , mphenoflag = 1 386s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.577637 386s k = 352, n-q = 352 388s 388s number of SNP ids in A_Tiller_no._sativas_GWAS.ps for 'A_Tiller_no.' phenotype: 36901 388s number of SNP ids in A_Tiller_no._sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Tiller_no.' phenotype: 0 388s 388s number of SNP ids in sativas_GWAS.tped: 36901 388s number of SNP ids in sativas_GWAS.tped not present in A_Tiller_no._sativas_GWAS.ps: 0 388s 388s Error in file(filename, "r", encoding = encoding) : 388s cannot open the connection 388s Calls: source -> file 388s In addition: Warning message: 388s In file(filename, "r", encoding = encoding) : 388s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 388s Execution halted 388s cd .. 388s Starting A_Seed_length, pid = 5910 388s Finished A_Tiller_no., pid = 5882, exit_code = 0 388s cd Daniel_shoot_As 388s processing phenotype Daniel_shoot_As... 388s 388s nice emmax -d 10 -t ../sativas_GWAS -p Daniel_shoot_As.pheno -k ../sativas_GWAS.hIBS.kinf -o Daniel_shoot_As_sativas_GWAS -c ../sativas_GWAS.covar 388s nmiss = 40 , mphenoflag = 1 388s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.552770 388s k = 332, n-q = 332 391s 391s number of SNP ids in A_Seed_length_sativas_GWAS.ps for 'A_Seed_length' phenotype: 36901 391s number of SNP ids in A_Seed_length_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Seed_length' phenotype: 0 391s 391s number of SNP ids in sativas_GWAS.tped: 36901 391s number of SNP ids in sativas_GWAS.tped not present in A_Seed_length_sativas_GWAS.ps: 0 391s 392s Error in file(filename, "r", encoding = encoding) : 392s cannot open the connection 392s Calls: source -> file 392s In addition: Warning message: 392s In file(filename, "r", encoding = encoding) : 392s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 392s Execution halted 392s cd .. 392s Starting Daniel_shoot_As, pid = 5924 392s Finished A_Seed_length, pid = 5910, exit_code = 0 392s cd F_FT 392s processing phenotype F_FT... 392s 392s nice emmax -d 10 -t ../sativas_GWAS -p F_FT.pheno -k ../sativas_GWAS.hIBS.kinf -o F_FT_sativas_GWAS -c ../sativas_GWAS.covar 392s nmiss = 73 , mphenoflag = 1 392s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 392s k = 299, n-q = 299 393s 393s number of SNP ids in Daniel_shoot_As_sativas_GWAS.ps for 'Daniel_shoot_As' phenotype: 36901 393s number of SNP ids in Daniel_shoot_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Daniel_shoot_As' phenotype: 0 393s 393s number of SNP ids in sativas_GWAS.tped: 36901 393s number of SNP ids in sativas_GWAS.tped not present in Daniel_shoot_As_sativas_GWAS.ps: 0 393s 393s Error in file(filename, "r", encoding = encoding) : 393s cannot open the connection 393s Calls: source -> file 393s In addition: Warning message: 393s In file(filename, "r", encoding = encoding) : 393s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 393s Execution halted 393s cd .. 393s Starting F_FT, pid = 5938 393s Finished Daniel_shoot_As, pid = 5924, exit_code = 0 393s cd F_shoot_As 393s processing phenotype F_shoot_As... 393s 393s nice emmax -d 10 -t ../sativas_GWAS -p F_shoot_As.pheno -k ../sativas_GWAS.hIBS.kinf -o F_shoot_As_sativas_GWAS -c ../sativas_GWAS.covar 393s nmiss = 73 , mphenoflag = 1 393s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.459771 393s k = 299, n-q = 299 396s 396s number of SNP ids in F_FT_sativas_GWAS.ps for 'F_FT' phenotype: 36901 396s number of SNP ids in F_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_FT' phenotype: 0 396s 396s number of SNP ids in sativas_GWAS.tped: 36901 396s number of SNP ids in sativas_GWAS.tped not present in F_FT_sativas_GWAS.ps: 0 396s 397s Error in file(filename, "r", encoding = encoding) : 397s cannot open the connection 397s Calls: source -> file 397s In addition: Warning message: 397s In file(filename, "r", encoding = encoding) : 397s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 397s Execution halted 397s cd .. 398s 398s number of SNP ids in F_shoot_As_sativas_GWAS.ps for 'F_shoot_As' phenotype: 36901 398s number of SNP ids in F_shoot_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_shoot_As' phenotype: 0 398s 398s number of SNP ids in sativas_GWAS.tped: 36901 398s number of SNP ids in sativas_GWAS.tped not present in F_shoot_As_sativas_GWAS.ps: 0 398s 398s Error in file(filename, "r", encoding = encoding) : 398s cannot open the connection 398s Calls: source -> file 398s In addition: Warning message: 398s In file(filename, "r", encoding = encoding) : 398s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 398s Execution halted 398s cd .. 398s Starting F_shoot_As, pid = 5952 398s Finished F_shoot_As, pid = 5952, exit_code = 0 398s Finished F_FT, pid = 5938, exit_code = 0 398s Starting A_Seed_weight, pid = 5978 398s cd A_Seed_weight 398s processing phenotype A_Seed_weight... 398s 398s nice emmax -d 10 -t ../sativas_GWAS -p A_Seed_weight.pheno -k ../sativas_GWAS.hIBS.kinf -o A_Seed_weight_sativas_GWAS -c ../sativas_GWAS.covar 398s cd A_FT 398s processing phenotype A_FT... 398s 398s nice emmax -d 10 -t ../sativas_GWAS -p A_FT.pheno -k ../sativas_GWAS.hIBS.kinf -o A_FT_sativas_GWAS -c ../sativas_GWAS.covar 398s nmiss = 21 , mphenoflag = 1 398s nmiss = 19 , mphenoflag = 1 398s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.575045 398s k = 351, n-q = 351 398s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.578644 398s k = 353, n-q = 353 404s 404s number of SNP ids in A_Seed_weight_sativas_GWAS.ps for 'A_Seed_weight' phenotype: 36901 404s number of SNP ids in A_Seed_weight_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Seed_weight' phenotype: 0 404s 404s number of SNP ids in sativas_GWAS.tped: 36901 404s number of SNP ids in sativas_GWAS.tped not present in A_Seed_weight_sativas_GWAS.ps: 0 404s 404s 404s number of SNP ids in A_FT_sativas_GWAS.ps for 'A_FT' phenotype: 36901 404s number of SNP ids in A_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_FT' phenotype: 0 404s 404s number of SNP ids in sativas_GWAS.tped: 36901 404s number of SNP ids in sativas_GWAS.tped not present in A_FT_sativas_GWAS.ps: 0 404s 404s Error in file(filename, "r", encoding = encoding) : 404s cannot open the connection 404s Calls: source -> file 404s In addition: Warning message: 404s In file(filename, "r", encoding = encoding) : 404s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 404s Execution halted 404s Error in file(filename, "r", encoding = encoding) : 404s cannot open the connection 404s Calls: source -> file 404s In addition: Warning message: 404s In file(filename, "r", encoding = encoding) : 404s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 404s Execution halted 404s cd .. 404s cd .. 405s Starting A_FT, pid = 5979 405s Finished A_FT, pid = 5979, exit_code = 0 405s Finished A_Seed_weight, pid = 5978, exit_code = 0 405s Starting H_Shoot_length_27, pid = 6006 405s cd H_Shoot_length_27 405s processing phenotype H_Shoot_length_27... 405s 405s nice emmax -d 10 -t ../sativas_GWAS -p H_Shoot_length_27.pheno -k ../sativas_GWAS.hIBS.kinf -o H_Shoot_length_27_sativas_GWAS -c ../sativas_GWAS.covar 405s cd Q_grain_Cu 405s processing phenotype Q_grain_Cu... 405s 405s nice emmax -d 10 -t ../sativas_GWAS -p Q_grain_Cu.pheno -k ../sativas_GWAS.hIBS.kinf -o Q_grain_Cu_sativas_GWAS -c ../sativas_GWAS.covar 405s nmiss = 260 , mphenoflag = 1 405s nmiss = 90 , mphenoflag = 1 405s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 405s k = 112, n-q = 112 405s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 405s k = 282, n-q = 282 407s 407s number of SNP ids in H_Shoot_length_27_sativas_GWAS.ps for 'H_Shoot_length_27' phenotype: 36901 407s number of SNP ids in H_Shoot_length_27_sativas_GWAS.ps not present in sativas_GWAS.tped for 'H_Shoot_length_27' phenotype: 0 407s 407s number of SNP ids in sativas_GWAS.tped: 36901 407s number of SNP ids in sativas_GWAS.tped not present in H_Shoot_length_27_sativas_GWAS.ps: 0 407s 407s Error in file(filename, "r", encoding = encoding) : 407s cannot open the connection 407s Calls: source -> file 407s In addition: Warning message: 407s In file(filename, "r", encoding = encoding) : 407s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 407s Execution halted 407s cd .. 407s Starting Q_grain_Cu, pid = 6007 407s Finished H_Shoot_length_27, pid = 6006, exit_code = 0 407s cd Q_PH 407s processing phenotype Q_PH... 407s 407s nice emmax -d 10 -t ../sativas_GWAS -p Q_PH.pheno -k ../sativas_GWAS.hIBS.kinf -o Q_PH_sativas_GWAS -c ../sativas_GWAS.covar 407s nmiss = 87 , mphenoflag = 1 407s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.413538 407s k = 285, n-q = 285 409s 409s number of SNP ids in Q_grain_Cu_sativas_GWAS.ps for 'Q_grain_Cu' phenotype: 36901 409s number of SNP ids in Q_grain_Cu_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Cu' phenotype: 0 409s 409s number of SNP ids in sativas_GWAS.tped: 36901 409s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Cu_sativas_GWAS.ps: 0 409s 409s Error in file(filename, "r", encoding = encoding) : 409s cannot open the connection 409s Calls: source -> file 409s In addition: Warning message: 409s In file(filename, "r", encoding = encoding) : 409s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 409s Execution halted 409s cd .. 410s Starting Q_PH, pid = 6022 410s Finished Q_grain_Cu, pid = 6007, exit_code = 0 410s cd Q_grain_As 410s processing phenotype Q_grain_As... 410s 410s nice emmax -d 10 -t ../sativas_GWAS -p Q_grain_As.pheno -k ../sativas_GWAS.hIBS.kinf -o Q_grain_As_sativas_GWAS -c ../sativas_GWAS.covar 410s nmiss = 90 , mphenoflag = 1 410s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 410s k = 282, n-q = 282 411s 411s number of SNP ids in Q_PH_sativas_GWAS.ps for 'Q_PH' phenotype: 36901 411s number of SNP ids in Q_PH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_PH' phenotype: 0 411s 411s number of SNP ids in sativas_GWAS.tped: 36901 411s number of SNP ids in sativas_GWAS.tped not present in Q_PH_sativas_GWAS.ps: 0 411s 411s Error in file(filename, "r", encoding = encoding) : 411s cannot open the connection 411s Calls: source -> file 411s In addition: Warning message: 411s In file(filename, "r", encoding = encoding) : 411s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 411s Execution halted 411s cd .. 412s Starting Q_grain_As, pid = 6036 412s Finished Q_PH, pid = 6022, exit_code = 0 412s cd F_As_TF 412s processing phenotype F_As_TF... 412s 412s nice emmax -d 10 -t ../sativas_GWAS -p F_As_TF.pheno -k ../sativas_GWAS.hIBS.kinf -o F_As_TF_sativas_GWAS -c ../sativas_GWAS.covar 412s nmiss = 75 , mphenoflag = 1 412s evals[0] = -0.000000, evals[1] = 0.000000, evals[n-1] = 2.455247 412s k = 297, n-q = 297 414s 414s number of SNP ids in Q_grain_As_sativas_GWAS.ps for 'Q_grain_As' phenotype: 36901 414s number of SNP ids in Q_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_As' phenotype: 0 414s 414s number of SNP ids in sativas_GWAS.tped: 36901 414s number of SNP ids in sativas_GWAS.tped not present in Q_grain_As_sativas_GWAS.ps: 0 414s 415s Error in file(filename, "r", encoding = encoding) : 415s cannot open the connection 415s Calls: source -> file 415s In addition: Warning message: 415s In file(filename, "r", encoding = encoding) : 415s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 415s Execution halted 415s cd .. 415s Starting F_As_TF, pid = 6050 415s Finished Q_grain_As, pid = 6036, exit_code = 0 415s cd A_grain_yield 415s processing phenotype A_grain_yield... 415s 415s nice emmax -d 10 -t ../sativas_GWAS -p A_grain_yield.pheno -k ../sativas_GWAS.hIBS.kinf -o A_grain_yield_sativas_GWAS -c ../sativas_GWAS.covar 415s nmiss = 49 , mphenoflag = 1 415s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.520537 415s k = 323, n-q = 323 417s 417s number of SNP ids in F_As_TF_sativas_GWAS.ps for 'F_As_TF' phenotype: 36901 417s number of SNP ids in F_As_TF_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_As_TF' phenotype: 0 417s 417s number of SNP ids in sativas_GWAS.tped: 36901 417s number of SNP ids in sativas_GWAS.tped not present in F_As_TF_sativas_GWAS.ps: 0 417s 417s Error in file(filename, "r", encoding = encoding) : 417s cannot open the connection 417s Calls: source -> file 417s In addition: Warning message: 417s In file(filename, "r", encoding = encoding) : 417s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 417s Execution halted 417s cd .. 417s Starting A_grain_yield, pid = 6064 417s Finished F_As_TF, pid = 6050, exit_code = 0 417s cd India_grain_As 417s processing phenotype India_grain_As... 417s 417s nice emmax -d 10 -t ../sativas_GWAS -p India_grain_As.pheno -k ../sativas_GWAS.hIBS.kinf -o India_grain_As_sativas_GWAS -c ../sativas_GWAS.covar 417s nmiss = 280 , mphenoflag = 1 417s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.487105 417s k = 92, n-q = 92 419s 419s number of SNP ids in India_grain_As_sativas_GWAS.ps for 'India_grain_As' phenotype: 36901 419s number of SNP ids in India_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'India_grain_As' phenotype: 0 419s 419s number of SNP ids in sativas_GWAS.tped: 36901 419s number of SNP ids in sativas_GWAS.tped not present in India_grain_As_sativas_GWAS.ps: 0 419s 419s Error in file(filename, "r", encoding = encoding) : 419s cannot open the connection 419s Calls: source -> file 419s In addition: Warning message: 419s In file(filename, "r", encoding = encoding) : 419s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 419s Execution halted 419s cd .. 419s Starting India_grain_As, pid = 6078 419s Finished India_grain_As, pid = 6078, exit_code = 0 419s cd F_grain_Zn 419s processing phenotype F_grain_Zn... 419s 419s nice emmax -d 10 -t ../sativas_GWAS -p F_grain_Zn.pheno -k ../sativas_GWAS.hIBS.kinf -o F_grain_Zn_sativas_GWAS -c ../sativas_GWAS.covar 419s nmiss = 73 , mphenoflag = 1 419s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 419s k = 299, n-q = 299 420s 420s number of SNP ids in A_grain_yield_sativas_GWAS.ps for 'A_grain_yield' phenotype: 36901 420s number of SNP ids in A_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_grain_yield' phenotype: 0 420s 420s number of SNP ids in sativas_GWAS.tped: 36901 420s number of SNP ids in sativas_GWAS.tped not present in A_grain_yield_sativas_GWAS.ps: 0 420s 420s Error in file(filename, "r", encoding = encoding) : 420s cannot open the connection 420s Calls: source -> file 420s In addition: Warning message: 420s In file(filename, "r", encoding = encoding) : 420s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 420s Execution halted 420s cd .. 420s Starting F_grain_Zn, pid = 6092 420s Finished A_grain_yield, pid = 6064, exit_code = 0 420s cd F_grain_Cu 420s processing phenotype F_grain_Cu... 420s 420s nice emmax -d 10 -t ../sativas_GWAS -p F_grain_Cu.pheno -k ../sativas_GWAS.hIBS.kinf -o F_grain_Cu_sativas_GWAS -c ../sativas_GWAS.covar 420s nmiss = 73 , mphenoflag = 1 420s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 420s k = 299, n-q = 299 423s 423s number of SNP ids in F_grain_Zn_sativas_GWAS.ps for 'F_grain_Zn' phenotype: 36901 423s number of SNP ids in F_grain_Zn_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Zn' phenotype: 0 423s 423s number of SNP ids in sativas_GWAS.tped: 36901 423s number of SNP ids in sativas_GWAS.tped not present in F_grain_Zn_sativas_GWAS.ps: 0 423s 424s Error in file(filename, "r", encoding = encoding) : 424s cannot open the connection 424s Calls: source -> file 424s In addition: Warning message: 424s In file(filename, "r", encoding = encoding) : 424s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 424s Execution halted 424s cd .. 424s Starting F_grain_Cu, pid = 6106 424s Finished F_grain_Zn, pid = 6092, exit_code = 0 424s cd Q_grain_Zn 424s processing phenotype Q_grain_Zn... 424s 424s nice emmax -d 10 -t ../sativas_GWAS -p Q_grain_Zn.pheno -k ../sativas_GWAS.hIBS.kinf -o Q_grain_Zn_sativas_GWAS -c ../sativas_GWAS.covar 424s nmiss = 90 , mphenoflag = 1 424s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 424s k = 282, n-q = 282 424s 424s number of SNP ids in F_grain_Cu_sativas_GWAS.ps for 'F_grain_Cu' phenotype: 36901 424s number of SNP ids in F_grain_Cu_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Cu' phenotype: 0 424s 424s number of SNP ids in sativas_GWAS.tped: 36901 424s number of SNP ids in sativas_GWAS.tped not present in F_grain_Cu_sativas_GWAS.ps: 0 424s 425s Error in file(filename, "r", encoding = encoding) : 425s cannot open the connection 425s Calls: source -> file 425s In addition: Warning message: 425s In file(filename, "r", encoding = encoding) : 425s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 425s Execution halted 425s cd .. 425s Starting Q_grain_Zn, pid = 6120 425s Finished F_grain_Cu, pid = 6106, exit_code = 0 425s cd H_Root_Length_27 425s processing phenotype H_Root_Length_27... 425s 425s nice emmax -d 10 -t ../sativas_GWAS -p H_Root_Length_27.pheno -k ../sativas_GWAS.hIBS.kinf -o H_Root_Length_27_sativas_GWAS -c ../sativas_GWAS.covar 425s nmiss = 260 , mphenoflag = 1 425s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 425s k = 112, n-q = 112 427s 427s number of SNP ids in H_Root_Length_27_sativas_GWAS.ps for 'H_Root_Length_27' phenotype: 36901 427s number of SNP ids in H_Root_Length_27_sativas_GWAS.ps not present in sativas_GWAS.tped for 'H_Root_Length_27' phenotype: 0 427s 427s number of SNP ids in sativas_GWAS.tped: 36901 427s number of SNP ids in sativas_GWAS.tped not present in H_Root_Length_27_sativas_GWAS.ps: 0 427s 427s Error in file(filename, "r", encoding = encoding) : 427s cannot open the connection 427s Calls: source -> file 427s In addition: Warning message: 427s In file(filename, "r", encoding = encoding) : 427s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 427s Execution halted 427s cd .. 428s 428s number of SNP ids in Q_grain_Zn_sativas_GWAS.ps for 'Q_grain_Zn' phenotype: 36901 428s number of SNP ids in Q_grain_Zn_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Zn' phenotype: 0 428s 428s number of SNP ids in sativas_GWAS.tped: 36901 428s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Zn_sativas_GWAS.ps: 0 428s 428s Error in file(filename, "r", encoding = encoding) : 428s cannot open the connection 428s Calls: source -> file 428s In addition: Warning message: 428s In file(filename, "r", encoding = encoding) : 428s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 428s Execution halted 428s cd .. 428s Starting H_Root_Length_27, pid = 6134 428s Finished H_Root_Length_27, pid = 6134, exit_code = 0 428s Finished Q_grain_Zn, pid = 6120, exit_code = 0 428s Starting Q_grain_Mo, pid = 6160 428s cd Q_grain_Mo 428s processing phenotype Q_grain_Mo... 428s 428s nice emmax -d 10 -t ../sativas_GWAS -p Q_grain_Mo.pheno -k ../sativas_GWAS.hIBS.kinf -o Q_grain_Mo_sativas_GWAS -c ../sativas_GWAS.covar 428s cd F_grain_Mo 428s processing phenotype F_grain_Mo... 428s 428s nice emmax -d 10 -t ../sativas_GWAS -p F_grain_Mo.pheno -k ../sativas_GWAS.hIBS.kinf -o F_grain_Mo_sativas_GWAS -c ../sativas_GWAS.covar 428s nmiss = 90 , mphenoflag = 1 428s nmiss = 73 , mphenoflag = 1 428s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 428s k = 282, n-q = 282 428s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 428s k = 299, n-q = 299 432s 432s number of SNP ids in Q_grain_Mo_sativas_GWAS.ps for 'Q_grain_Mo' phenotype: 36901 432s number of SNP ids in Q_grain_Mo_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Mo' phenotype: 0 432s 432s number of SNP ids in sativas_GWAS.tped: 36901 432s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Mo_sativas_GWAS.ps: 0 432s 432s Error in file(filename, "r", encoding = encoding) : 432s cannot open the connection 432s Calls: source -> file 432s In addition: Warning message: 432s In file(filename, "r", encoding = encoding) : 432s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 432s Execution halted 432s cd .. 432s Starting F_grain_Mo, pid = 6161 432s Finished Q_grain_Mo, pid = 6160, exit_code = 0 432s cd Q_grain_yield 432s processing phenotype Q_grain_yield... 432s 432s nice emmax -d 10 -t ../sativas_GWAS -p Q_grain_yield.pheno -k ../sativas_GWAS.hIBS.kinf -o Q_grain_yield_sativas_GWAS -c ../sativas_GWAS.covar 432s nmiss = 91 , mphenoflag = 1 432s 432s number of SNP ids in F_grain_Mo_sativas_GWAS.ps for 'F_grain_Mo' phenotype: 36901 432s number of SNP ids in F_grain_Mo_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Mo' phenotype: 0 432s 432s number of SNP ids in sativas_GWAS.tped: 36901 432s number of SNP ids in sativas_GWAS.tped not present in F_grain_Mo_sativas_GWAS.ps: 0 432s 432s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.399146 432s k = 281, n-q = 281 433s Error in file(filename, "r", encoding = encoding) : 433s cannot open the connection 433s Calls: source -> file 433s In addition: Warning message: 433s In file(filename, "r", encoding = encoding) : 433s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 433s Execution halted 433s cd .. 436s 436s number of SNP ids in Q_grain_yield_sativas_GWAS.ps for 'Q_grain_yield' phenotype: 36901 436s number of SNP ids in Q_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_yield' phenotype: 0 436s 436s number of SNP ids in sativas_GWAS.tped: 36901 436s number of SNP ids in sativas_GWAS.tped not present in Q_grain_yield_sativas_GWAS.ps: 0 436s 436s Error in file(filename, "r", encoding = encoding) : 436s cannot open the connection 436s Calls: source -> file 436s In addition: Warning message: 436s In file(filename, "r", encoding = encoding) : 436s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 436s Execution halted 436s cd .. 436s Starting Q_grain_yield, pid = 6176 436s Finished F_grain_Mo, pid = 6161, exit_code = 0 436s Finished Q_grain_yield, pid = 6176, exit_code = 0 436s Analysis complete 436s 437s autopkgtest [21:48:15]: test run-unit-test: -----------------------] 437s run-unit-test PASS 437s autopkgtest [21:48:15]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 438s autopkgtest [21:48:16]: @@@@@@@@@@@@@@@@@@@@ summary 438s run-unit-test PASS 442s Creating nova instance adt-noble-arm64-pique-20240307-214057-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240307.img (UUID 00fdfee3-5cf8-4806-8086-451645753def)...