0s autopkgtest [00:40:37]: starting date and time: 2024-03-22 00:40:37+0000 0s autopkgtest [00:40:37]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [00:40:37]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ot0lz3jd/out --timeout-copy=6000 -a i386 --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:r-base --apt-upgrade pique --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-10.secgroup --name adt-noble-i386-pique-20240322-004037-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 712s autopkgtest [00:52:27]: testbed dpkg architecture: amd64 712s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 712s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 712s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3765 kB] 712s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 712s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 712s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [703 kB] 712s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [467 kB] 712s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 712s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 712s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB] 712s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 712s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4237 kB] 712s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1271 kB] 712s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 712s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [93.7 kB] 712s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [26.8 kB] 712s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 712s autopkgtest [00:52:27]: testbed apt version: 2.7.12 712s autopkgtest [00:52:27]: test architecture: i386 712s autopkgtest [00:52:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 714s Fetched 11.3 MB in 2s (7433 kB/s) 714s Reading package lists... 716s Reading package lists... 717s Building dependency tree... 717s Reading state information... 717s Calculating upgrade... 717s The following packages will be upgraded: 717s cloud-init fonts-ubuntu-console python3-markupsafe 717s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 717s Need to get 629 kB of archives. 717s After this operation, 11.3 kB disk space will be freed. 717s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 717s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 python3-markupsafe amd64 2.1.5-1build1 [12.6 kB] 717s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 cloud-init all 24.1.2-0ubuntu1 [597 kB] 718s Preconfiguring packages ... 718s Fetched 629 kB in 0s (17.7 MB/s) 718s (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 ... 71865 files and directories currently installed.) 718s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 718s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 718s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_amd64.deb ... 718s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 718s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ... 718s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 719s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 719s Setting up cloud-init (24.1.2-0ubuntu1) ... 720s Setting up python3-markupsafe (2.1.5-1build1) ... 720s Processing triggers for man-db (2.12.0-3) ... 721s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 721s Reading package lists... 721s Building dependency tree... 721s Reading state information... 722s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 722s sh: Attempting to set up Debian/Ubuntu apt sources automatically 722s sh: Distribution appears to be Ubuntu 723s Reading package lists... 724s Building dependency tree... 724s Reading state information... 724s eatmydata is already the newest version (131-1). 724s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 724s Reading package lists... 724s Building dependency tree... 724s Reading state information... 724s dbus is already the newest version (1.14.10-4ubuntu1). 724s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 725s Reading package lists... 725s Building dependency tree... 725s Reading state information... 725s rng-tools-debian is already the newest version (2.4). 725s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 725s Reading package lists... 725s Building dependency tree... 725s Reading state information... 726s The following packages will be REMOVED: 726s cloud-init* python3-configobj* python3-debconf* 726s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 726s After this operation, 3256 kB disk space will be freed. 726s (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 ... 71864 files and directories currently installed.) 726s Removing cloud-init (24.1.2-0ubuntu1) ... 727s Removing python3-configobj (5.0.8-3) ... 727s Removing python3-debconf (1.5.86) ... 727s Processing triggers for man-db (2.12.0-3) ... 727s (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 ... 71475 files and directories currently installed.) 727s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 728s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 728s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 728s invoke-rc.d: policy-rc.d denied execution of try-restart. 728s Reading package lists... 728s Building dependency tree... 728s Reading state information... 728s linux-generic is already the newest version (6.8.0-11.11+1). 728s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 729s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 729s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 729s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 731s Reading package lists... 731s Reading package lists... 731s Building dependency tree... 731s Reading state information... 731s Calculating upgrade... 731s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 731s Reading package lists... 732s Building dependency tree... 732s Reading state information... 732s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 732s autopkgtest [00:52:49]: rebooting testbed after setup commands that affected boot 883s autopkgtest [00:55:20]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 884s autopkgtest [00:55:21]: @@@@@@@@@@@@@@@@@@@@ apt-source pique 885s Get:1 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (dsc) [2005 B] 885s Get:2 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (tar) [2017 kB] 885s Get:3 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (diff) [5236 B] 885s gpgv: Signature made Tue Dec 12 20:17:37 2023 UTC 885s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 885s gpgv: issuer "tille@debian.org" 885s gpgv: Can't check signature: No public key 885s dpkg-source: warning: cannot verify inline signature for ./pique_1.0-7.dsc: no acceptable signature found 885s autopkgtest [00:55:22]: testing package pique version 1.0-7 885s autopkgtest [00:55:22]: build not needed 885s autopkgtest [00:55:22]: test run-unit-test: preparing testbed 889s Note, using file '/tmp/autopkgtest.oYbRUi/1-autopkgtest-satdep.dsc' to get the build dependencies 890s Reading package lists... 890s Building dependency tree... 890s Reading state information... 890s Starting pkgProblemResolver with broken count: 0 890s Starting 2 pkgProblemResolver with broken count: 0 890s Done 890s The following NEW packages will be installed: 890s build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu 890s eigensoft emmax fontconfig fontconfig-config fonts-dejavu-core 890s fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings 890s fonts-mathjax g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 890s gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu javascript-common 890s libasan8 libatomic1 libb-hooks-op-check-perl libblas3 libc-dev-bin libc6-dev 890s libcairo2 libcc1-0 libclass-method-modifiers-perl libclass-xsaccessor-perl 890s libcrypt-dev libdatrie1 libdeflate0 libdevel-callchecker-perl 890s libdynaloader-functions-perl libfile-slurp-perl libfontconfig1 libgcc-13-dev 890s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 890s libhwasan0 libice6 libimport-into-perl libisl23 libitm1 libjbig0 890s libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3 890s libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables 890s libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax 890s libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify 890s libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 liblapacke 890s liblerc4 liblsan0 liblua5.4-0 libmodule-runtime-perl libmoo-perl libmpc3 890s libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 890s libpaper-utils libpaper1 libparallel-forkmanager-perl 890s libparams-classify-perl libpixman-1-0 libquadmath0 libreadonly-perl 890s librole-tiny-perl libsharpyuv0 libsm6 libstdc++-13-dev libsub-quote-perl 890s libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtmglib3 890s libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 890s libxss1 libxt6 linux-libc-dev littler node-bootstrap-sass node-html5shiv 890s node-normalize.css pandoc pandoc-data pique pique-doc plink r-base-core 890s r-bioc-biobase r-bioc-biocgenerics r-bioc-multtest r-cran-acepack 890s r-cran-backports r-cran-base64enc r-cran-bslib r-cran-cachem 890s r-cran-checkmate r-cran-chron r-cran-cli r-cran-cluster r-cran-colorspace 890s r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table 890s r-cran-deldir r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate 890s r-cran-fansi r-cran-farver r-cran-fastmap r-cran-fontawesome r-cran-forecast 890s r-cran-foreign r-cran-formula r-cran-fracdiff r-cran-fs r-cran-generics 890s r-cran-getopt r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable 890s r-cran-highr r-cran-hmisc r-cran-htmltable r-cran-htmltools 890s r-cran-htmlwidgets r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg 890s r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later 890s r-cran-lattice r-cran-latticeextra r-cran-lifecycle r-cran-littler 890s r-cran-lmtest r-cran-magrittr r-cran-mass r-cran-matrix r-cran-memoise 890s r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-nnet 890s r-cran-optparse r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-png 890s r-cran-promises r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 890s r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 890s r-cran-rcppeigen r-cran-rlang r-cran-rmarkdown r-cran-rpart 890s r-cran-rstudioapi r-cran-sass r-cran-scales r-cran-shiny r-cran-sourcetools 890s r-cran-stringi r-cran-stringr r-cran-survival r-cran-tibble r-cran-tidyr 890s r-cran-tidyselect r-cran-timedate r-cran-tinytex r-cran-tseries r-cran-ttr 890s r-cran-urca r-cran-uroot r-cran-utf8 r-cran-vctrs r-cran-viridis 890s r-cran-viridislite r-cran-withr r-cran-xfun r-cran-xtable r-cran-xts 890s r-cran-yaml r-cran-zoo rpcsvc-proto unzip x11-common xdg-utils zip 891s 0 upgraded, 239 newly installed, 0 to remove and 0 not upgraded. 891s Need to get 239 MB of archives. 891s After this operation, 766 MB of additional disk space will be used. 891s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB] 891s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 891s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 891s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB] 891s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] 891s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 891s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB] 891s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 891s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 891s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 891s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 891s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 891s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 891s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 891s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 891s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 891s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 891s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 891s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 891s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 891s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 891s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 891s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 891s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 891s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 891s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 891s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 891s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 891s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 891s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 891s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 891s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 891s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 891s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 891s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 891s Get:36 http://ftpmaster.internal/ubuntu noble/universe amd64 libgslcblas0 amd64 2.7.1+dfsg-6ubuntu1 [104 kB] 891s Get:37 http://ftpmaster.internal/ubuntu noble/universe amd64 libgsl27 amd64 2.7.1+dfsg-6ubuntu1 [987 kB] 891s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 891s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 891s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libtmglib3 amd64 3.12.0-3 [140 kB] 891s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 liblapacke amd64 3.12.0-3 [412 kB] 891s Get:42 http://ftpmaster.internal/ubuntu noble/universe amd64 eigensoft amd64 8.0.0+dfsg-2 [325 kB] 891s Get:43 http://ftpmaster.internal/ubuntu noble/universe amd64 emmax amd64 0~beta.20100307-5 [30.8 kB] 891s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 891s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 891s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB] 891s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB] 891s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB] 891s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 891s Get:50 http://ftpmaster.internal/ubuntu noble/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 891s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 891s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 javascript-common all 11+nmu1 [5936 B] 891s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libb-hooks-op-check-perl amd64 0.22-2build2 [9452 B] 891s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] 891s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] 891s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] 891s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 891s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB] 891s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libclass-method-modifiers-perl all 2.15-1 [16.1 kB] 891s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libclass-xsaccessor-perl amd64 1.19-4build2 [33.2 kB] 891s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] 891s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 891s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libdynaloader-functions-perl all 0.003-3 [12.1 kB] 891s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libdevel-callchecker-perl amd64 0.008-2build1 [13.9 kB] 891s Get:65 http://ftpmaster.internal/ubuntu noble/universe amd64 libfile-slurp-perl all 9999.32-2 [21.7 kB] 891s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 891s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB] 891s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 891s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] 891s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libparams-classify-perl amd64 0.015-2build3 [20.0 kB] 891s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libmodule-runtime-perl all 0.016-2 [16.4 kB] 891s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libimport-into-perl all 1.002005-2 [10.7 kB] 891s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] 891s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 891s Get:75 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 891s Get:76 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB] 891s Get:77 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB] 891s Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-d3 all 3.5.17-4 [132 kB] 891s Get:79 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB] 891s Get:80 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 891s Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 891s Get:82 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 891s Get:83 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 891s Get:84 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B] 891s Get:85 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 891s Get:86 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 891s Get:87 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB] 891s Get:88 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB] 891s Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] 891s Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 liblua5.4-0 amd64 5.4.6-3 [166 kB] 891s Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 librole-tiny-perl all 2.002004-1 [16.3 kB] 891s Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-quote-perl all 2.006008-1ubuntu1 [20.7 kB] 891s Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libmoo-perl all 2.005005-1 [47.4 kB] 891s Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] 891s Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] 891s Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB] 891s Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB] 891s Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB] 891s Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB] 891s Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B] 891s Get:101 http://ftpmaster.internal/ubuntu noble/universe amd64 libparallel-forkmanager-perl all 2.02-1 [27.7 kB] 891s Get:102 http://ftpmaster.internal/ubuntu noble/universe amd64 libreadonly-perl all 2.050-3 [19.9 kB] 891s Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB] 891s Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] 891s Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB] 891s Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] 891s Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB] 891s Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB] 891s Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] 891s Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] 891s Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB] 891s Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB] 891s Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB] 891s Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB] 891s Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 891s Get:116 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB] 891s Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-littler amd64 0.3.19-1 [94.1 kB] 891s Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 littler all 0.3.19-1 [2472 B] 891s Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB] 891s Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 891s Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB] 891s Get:122 http://ftpmaster.internal/ubuntu noble/universe amd64 pandoc-data all 3.1.3-1 [92.4 kB] 891s Get:123 http://ftpmaster.internal/ubuntu noble/universe amd64 pandoc amd64 3.1.3+ds-2 [26.9 MB] 892s Get:124 http://ftpmaster.internal/ubuntu noble/universe amd64 plink amd64 1.07+dfsg-4 [1089 kB] 892s Get:125 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-getopt all 1.20.4-1 [38.4 kB] 892s Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1541 kB] 892s Get:127 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fracdiff amd64 1.5-3-1 [108 kB] 892s Get:128 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 892s Get:129 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cli amd64 3.6.2-1 [1380 kB] 892s Get:130 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB] 892s Get:131 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rlang amd64 1.1.3-1 [1663 kB] 892s Get:132 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 892s Get:133 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 892s Get:134 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 892s Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mass amd64 7.3-60.0.1-1 [1119 kB] 892s Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB] 892s Get:137 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nlme amd64 3.1.164-1 [2260 kB] 892s Get:138 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB] 892s Get:139 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 892s Get:140 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-farver amd64 2.1.1-1 [1353 kB] 892s Get:141 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 892s Get:142 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-munsell all 0.5.0-2build1 [208 kB] 892s Get:143 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB] 892s Get:144 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 892s Get:145 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 892s Get:146 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 892s Get:147 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB] 892s Get:148 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 892s Get:149 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 892s Get:150 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 892s Get:151 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 892s Get:152 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 892s Get:153 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [415 kB] 892s Get:154 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-withr all 2.5.0-1 [225 kB] 892s Get:155 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 892s Get:156 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-zoo amd64 1.8-12-2 [984 kB] 892s Get:157 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lmtest amd64 0.9.40-1 [396 kB] 892s Get:158 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nnet amd64 7.3-19-2 [112 kB] 892s Get:159 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 892s Get:160 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcpp amd64 1.0.12-1 [1981 kB] 892s Get:161 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-timedate amd64 4032.109-1 [1229 kB] 892s Get:162 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-quadprog amd64 1.5-8-1build1 [30.9 kB] 892s Get:163 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xts amd64 0.13.2-1 [772 kB] 892s Get:164 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-curl amd64 5.2.0+dfsg-1 [188 kB] 892s Get:165 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ttr amd64 0.24.4-1 [511 kB] 892s Get:166 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [441 kB] 892s Get:167 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-quantmod all 0.4.26-1 [1027 kB] 892s Get:168 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tseries amd64 0.10-55-1 [369 kB] 892s Get:169 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-urca amd64 1.3-3-1 [1071 kB] 892s Get:170 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcpparmadillo amd64 0.12.8.0.0-1 [862 kB] 892s Get:171 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-forecast amd64 8.21.1-1 [1556 kB] 892s Get:172 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocgenerics all 0.48.1-2 [595 kB] 892s Get:173 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biobase amd64 2.62.0-1 [2136 kB] 892s Get:174 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-survival amd64 3.5-8-1 [6120 kB] 892s Get:175 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-multtest amd64 2.58.0-1 [836 kB] 892s Get:176 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-optparse all 1.7.4-1 [81.6 kB] 892s Get:177 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-uroot all 2.1-3-1 [1927 kB] 892s Get:178 http://ftpmaster.internal/ubuntu noble/universe amd64 pique all 1.0-7 [21.3 kB] 892s Get:179 http://ftpmaster.internal/ubuntu noble/universe amd64 pique-doc all 1.0-7 [1931 kB] 892s Get:180 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-acepack amd64 1.4.2-1 [61.3 kB] 892s Get:181 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-backports amd64 1.4.1-1 [101 kB] 892s Get:182 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-base64enc amd64 0.1-3-3 [27.6 kB] 892s Get:183 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fastmap amd64 1.1.1-1 [70.5 kB] 892s Get:184 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cachem amd64 1.0.8-1 [72.1 kB] 892s Get:185 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-digest amd64 0.6.34-1 [186 kB] 892s Get:186 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB] 892s Get:187 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-htmltools amd64 0.5.7-1 [369 kB] 892s Get:188 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB] 892s Get:189 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB] 892s Get:190 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mime amd64 0.12-1 [35.8 kB] 892s Get:191 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fs amd64 1.6.3+dfsg-1 [229 kB] 892s Get:192 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rappdirs amd64 0.3.3-1 [47.5 kB] 892s Get:193 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-sass amd64 0.4.8+dfsg-1 [996 kB] 892s Get:194 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bslib all 0.6.1+dfsg-1 [5138 kB] 892s Get:195 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-checkmate amd64 2.3.1-1 [713 kB] 892s Get:196 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-chron amd64 2.3-61-2 [186 kB] 892s Get:197 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cluster amd64 2.1.6-1 [554 kB] 892s Get:198 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-commonmark amd64 1.9.1-1 [131 kB] 892s Get:199 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB] 892s Get:200 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-crayon all 1.5.2-1 [164 kB] 892s Get:201 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-data.table amd64 1.14.10+dfsg-1 [1837 kB] 892s Get:202 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-deldir amd64 2.0-4-1 [270 kB] 892s Get:203 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [218 kB] 892s Get:204 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dplyr amd64 1.1.4-1 [1515 kB] 892s Get:205 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-evaluate all 0.23-1 [90.2 kB] 892s Get:206 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fontawesome all 0.5.2-1 [1300 kB] 892s Get:207 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-foreign amd64 0.8.86-1 [242 kB] 892s Get:208 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-formula all 1.2-5-1 [158 kB] 892s Get:209 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-gridextra all 2.3-3build1 [1024 kB] 892s Get:210 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xfun amd64 0.41+dfsg-1 [415 kB] 892s Get:211 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-highr all 0.10+dfsg-1 [38.3 kB] 892s Get:212 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rpart amd64 4.1.23-1 [661 kB] 892s Get:213 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringi amd64 1.8.3-1 [873 kB] 892s Get:214 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 892s Get:215 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-yaml amd64 2.3.8-1 [108 kB] 892s Get:216 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 892s Get:217 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-knitr all 1.45+dfsg-1 [917 kB] 892s Get:218 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tinytex all 0.49-1 [141 kB] 892s Get:219 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-modernizr all 2.6.2+ds1-5 [48.3 kB] 892s Get:220 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-later amd64 1.3.2+dfsg-1 [123 kB] 892s Get:221 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-promises amd64 1.2.1+dfsg-1 [284 kB] 892s Get:222 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-httpuv amd64 1.6.14+dfsg-1 [510 kB] 892s Get:223 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] 892s Get:224 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB] 892s Get:225 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 892s Get:226 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-shiny all 1.8.0+dfsg-1 [2762 kB] 892s Get:227 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rmarkdown all 2.25+dfsg-3 [1481 kB] 892s Get:228 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] 892s Get:229 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rstudioapi all 0.15.0-1 [277 kB] 892s Get:230 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-purrr amd64 1.0.2-1 [502 kB] 892s Get:231 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 892s Get:232 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-htmltable all 2.4.2-1 [381 kB] 892s Get:233 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-viridis all 0.6.5-1 [2770 kB] 892s Get:234 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-png amd64 0.1-8-1 [40.5 kB] 892s Get:235 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-jpeg amd64 0.1-10-1 [31.4 kB] 892s Get:236 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcppeigen amd64 0.3.3.9.4-1 [1189 kB] 892s Get:237 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-interp amd64 1.1-6-1 [1454 kB] 892s Get:238 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-latticeextra all 0.6-30-1 [2198 kB] 892s Get:239 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-hmisc amd64 5.1-1-1 [3491 kB] 893s Preconfiguring packages ... 893s Fetched 239 MB in 2s (123 MB/s) 893s Selecting previously unselected package libc-dev-bin. 893s (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 ... 71420 files and directories currently installed.) 893s Preparing to unpack .../000-libc-dev-bin_2.39-0ubuntu2_amd64.deb ... 893s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 893s Selecting previously unselected package linux-libc-dev:amd64. 893s Preparing to unpack .../001-linux-libc-dev_6.8.0-11.11_amd64.deb ... 893s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 893s Selecting previously unselected package libcrypt-dev:amd64. 893s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 894s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 894s Selecting previously unselected package libtirpc-dev:amd64. 894s Preparing to unpack .../003-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ... 894s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) ... 894s Selecting previously unselected package libnsl-dev:amd64. 894s Preparing to unpack .../004-libnsl-dev_1.3.0-3_amd64.deb ... 894s Unpacking libnsl-dev:amd64 (1.3.0-3) ... 894s Selecting previously unselected package rpcsvc-proto. 894s Preparing to unpack .../005-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 894s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 894s Selecting previously unselected package libc6-dev:amd64. 894s Preparing to unpack .../006-libc6-dev_2.39-0ubuntu2_amd64.deb ... 894s Unpacking libc6-dev:amd64 (2.39-0ubuntu2) ... 894s Selecting previously unselected package libisl23:amd64. 894s Preparing to unpack .../007-libisl23_0.26-3_amd64.deb ... 894s Unpacking libisl23:amd64 (0.26-3) ... 894s Selecting previously unselected package libmpc3:amd64. 894s Preparing to unpack .../008-libmpc3_1.3.1-1_amd64.deb ... 894s Unpacking libmpc3:amd64 (1.3.1-1) ... 894s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 894s Preparing to unpack .../009-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 894s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 894s Selecting previously unselected package cpp-13. 894s Preparing to unpack .../010-cpp-13_13.2.0-17ubuntu2_amd64.deb ... 894s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 894s Selecting previously unselected package cpp-x86-64-linux-gnu. 894s Preparing to unpack .../011-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 894s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 894s Selecting previously unselected package cpp. 894s Preparing to unpack .../012-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 894s Unpacking cpp (4:13.2.0-7ubuntu1) ... 894s Selecting previously unselected package libcc1-0:amd64. 894s Preparing to unpack .../013-libcc1-0_14-20240303-1ubuntu1_amd64.deb ... 894s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ... 894s Selecting previously unselected package libgomp1:amd64. 894s Preparing to unpack .../014-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 894s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 894s Selecting previously unselected package libitm1:amd64. 894s Preparing to unpack .../015-libitm1_14-20240303-1ubuntu1_amd64.deb ... 894s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 894s Selecting previously unselected package libatomic1:amd64. 894s Preparing to unpack .../016-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 894s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 894s Selecting previously unselected package libasan8:amd64. 894s Preparing to unpack .../017-libasan8_14-20240303-1ubuntu1_amd64.deb ... 894s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 894s Selecting previously unselected package liblsan0:amd64. 894s Preparing to unpack .../018-liblsan0_14-20240303-1ubuntu1_amd64.deb ... 894s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ... 894s Selecting previously unselected package libtsan2:amd64. 894s Preparing to unpack .../019-libtsan2_14-20240303-1ubuntu1_amd64.deb ... 894s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ... 894s Selecting previously unselected package libubsan1:amd64. 894s Preparing to unpack .../020-libubsan1_14-20240303-1ubuntu1_amd64.deb ... 894s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ... 894s Selecting previously unselected package libhwasan0:amd64. 894s Preparing to unpack .../021-libhwasan0_14-20240303-1ubuntu1_amd64.deb ... 894s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ... 894s Selecting previously unselected package libquadmath0:amd64. 895s Preparing to unpack .../022-libquadmath0_14-20240303-1ubuntu1_amd64.deb ... 895s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ... 895s Selecting previously unselected package libgcc-13-dev:amd64. 895s Preparing to unpack .../023-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 895s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 895s Selecting previously unselected package gcc-13-x86-64-linux-gnu. 895s Preparing to unpack .../024-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 895s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 895s Selecting previously unselected package gcc-13. 895s Preparing to unpack .../025-gcc-13_13.2.0-17ubuntu2_amd64.deb ... 895s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 895s Selecting previously unselected package gcc-x86-64-linux-gnu. 895s Preparing to unpack .../026-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 895s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 895s Selecting previously unselected package gcc. 895s Preparing to unpack .../027-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ... 895s Unpacking gcc (4:13.2.0-7ubuntu1) ... 895s Selecting previously unselected package libstdc++-13-dev:amd64. 895s Preparing to unpack .../028-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 895s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 895s Selecting previously unselected package g++-13-x86-64-linux-gnu. 895s Preparing to unpack .../029-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 895s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 896s Selecting previously unselected package g++-13. 896s Preparing to unpack .../030-g++-13_13.2.0-17ubuntu2_amd64.deb ... 896s Unpacking g++-13 (13.2.0-17ubuntu2) ... 896s Selecting previously unselected package g++-x86-64-linux-gnu. 896s Preparing to unpack .../031-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 896s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 896s Selecting previously unselected package g++. 896s Preparing to unpack .../032-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 896s Unpacking g++ (4:13.2.0-7ubuntu1) ... 896s Selecting previously unselected package build-essential. 896s Preparing to unpack .../033-build-essential_12.10ubuntu1_amd64.deb ... 896s Unpacking build-essential (12.10ubuntu1) ... 896s Selecting previously unselected package libblas3:amd64. 896s Preparing to unpack .../034-libblas3_3.12.0-3_amd64.deb ... 896s Unpacking libblas3:amd64 (3.12.0-3) ... 896s Selecting previously unselected package libgslcblas0:amd64. 896s Preparing to unpack .../035-libgslcblas0_2.7.1+dfsg-6ubuntu1_amd64.deb ... 896s Unpacking libgslcblas0:amd64 (2.7.1+dfsg-6ubuntu1) ... 896s Selecting previously unselected package libgsl27:amd64. 896s Preparing to unpack .../036-libgsl27_2.7.1+dfsg-6ubuntu1_amd64.deb ... 896s Unpacking libgsl27:amd64 (2.7.1+dfsg-6ubuntu1) ... 896s Selecting previously unselected package libgfortran5:amd64. 896s Preparing to unpack .../037-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 896s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 896s Selecting previously unselected package liblapack3:amd64. 896s Preparing to unpack .../038-liblapack3_3.12.0-3_amd64.deb ... 896s Unpacking liblapack3:amd64 (3.12.0-3) ... 896s Selecting previously unselected package libtmglib3:amd64. 896s Preparing to unpack .../039-libtmglib3_3.12.0-3_amd64.deb ... 896s Unpacking libtmglib3:amd64 (3.12.0-3) ... 896s Selecting previously unselected package liblapacke:amd64. 896s Preparing to unpack .../040-liblapacke_3.12.0-3_amd64.deb ... 896s Unpacking liblapacke:amd64 (3.12.0-3) ... 896s Selecting previously unselected package eigensoft. 896s Preparing to unpack .../041-eigensoft_8.0.0+dfsg-2_amd64.deb ... 896s Unpacking eigensoft (8.0.0+dfsg-2) ... 896s Selecting previously unselected package emmax. 896s Preparing to unpack .../042-emmax_0~beta.20100307-5_amd64.deb ... 896s Unpacking emmax (0~beta.20100307-5) ... 896s Selecting previously unselected package fonts-dejavu-mono. 896s Preparing to unpack .../043-fonts-dejavu-mono_2.37-8_all.deb ... 896s Unpacking fonts-dejavu-mono (2.37-8) ... 896s Selecting previously unselected package fonts-dejavu-core. 896s Preparing to unpack .../044-fonts-dejavu-core_2.37-8_all.deb ... 896s Unpacking fonts-dejavu-core (2.37-8) ... 896s Selecting previously unselected package fontconfig-config. 896s Preparing to unpack .../045-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ... 896s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 896s Selecting previously unselected package libfontconfig1:amd64. 896s Preparing to unpack .../046-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ... 896s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 896s Selecting previously unselected package fontconfig. 896s Preparing to unpack .../047-fontconfig_2.15.0-1ubuntu1_amd64.deb ... 896s Unpacking fontconfig (2.15.0-1ubuntu1) ... 896s Selecting previously unselected package fonts-font-awesome. 896s Preparing to unpack .../048-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 896s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 896s Selecting previously unselected package fonts-glyphicons-halflings. 896s Preparing to unpack .../049-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 896s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 897s Selecting previously unselected package fonts-mathjax. 897s Preparing to unpack .../050-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 897s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 897s Selecting previously unselected package javascript-common. 897s Preparing to unpack .../051-javascript-common_11+nmu1_all.deb ... 897s Unpacking javascript-common (11+nmu1) ... 897s Selecting previously unselected package libb-hooks-op-check-perl:amd64. 897s Preparing to unpack .../052-libb-hooks-op-check-perl_0.22-2build2_amd64.deb ... 897s Unpacking libb-hooks-op-check-perl:amd64 (0.22-2build2) ... 897s Selecting previously unselected package libpixman-1-0:amd64. 897s Preparing to unpack .../053-libpixman-1-0_0.42.2-1_amd64.deb ... 897s Unpacking libpixman-1-0:amd64 (0.42.2-1) ... 897s Selecting previously unselected package libxcb-render0:amd64. 897s Preparing to unpack .../054-libxcb-render0_1.15-1_amd64.deb ... 897s Unpacking libxcb-render0:amd64 (1.15-1) ... 897s Selecting previously unselected package libxcb-shm0:amd64. 897s Preparing to unpack .../055-libxcb-shm0_1.15-1_amd64.deb ... 897s Unpacking libxcb-shm0:amd64 (1.15-1) ... 897s Selecting previously unselected package libxrender1:amd64. 897s Preparing to unpack .../056-libxrender1_1%3a0.9.10-1.1_amd64.deb ... 897s Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... 897s Selecting previously unselected package libcairo2:amd64. 897s Preparing to unpack .../057-libcairo2_1.18.0-1_amd64.deb ... 897s Unpacking libcairo2:amd64 (1.18.0-1) ... 897s Selecting previously unselected package libclass-method-modifiers-perl. 897s Preparing to unpack .../058-libclass-method-modifiers-perl_2.15-1_all.deb ... 897s Unpacking libclass-method-modifiers-perl (2.15-1) ... 897s Selecting previously unselected package libclass-xsaccessor-perl. 897s Preparing to unpack .../059-libclass-xsaccessor-perl_1.19-4build2_amd64.deb ... 897s Unpacking libclass-xsaccessor-perl (1.19-4build2) ... 897s Selecting previously unselected package libdatrie1:amd64. 897s Preparing to unpack .../060-libdatrie1_0.2.13-3_amd64.deb ... 897s Unpacking libdatrie1:amd64 (0.2.13-3) ... 897s Selecting previously unselected package libdeflate0:amd64. 897s Preparing to unpack .../061-libdeflate0_1.19-1_amd64.deb ... 897s Unpacking libdeflate0:amd64 (1.19-1) ... 897s Selecting previously unselected package libdynaloader-functions-perl. 897s Preparing to unpack .../062-libdynaloader-functions-perl_0.003-3_all.deb ... 897s Unpacking libdynaloader-functions-perl (0.003-3) ... 897s Selecting previously unselected package libdevel-callchecker-perl:amd64. 897s Preparing to unpack .../063-libdevel-callchecker-perl_0.008-2build1_amd64.deb ... 897s Unpacking libdevel-callchecker-perl:amd64 (0.008-2build1) ... 897s Selecting previously unselected package libfile-slurp-perl. 897s Preparing to unpack .../064-libfile-slurp-perl_9999.32-2_all.deb ... 897s Unpacking libfile-slurp-perl (9999.32-2) ... 897s Selecting previously unselected package libgraphite2-3:amd64. 897s Preparing to unpack .../065-libgraphite2-3_1.3.14-2_amd64.deb ... 897s Unpacking libgraphite2-3:amd64 (1.3.14-2) ... 897s Selecting previously unselected package libharfbuzz0b:amd64. 897s Preparing to unpack .../066-libharfbuzz0b_8.3.0-2_amd64.deb ... 897s Unpacking libharfbuzz0b:amd64 (8.3.0-2) ... 897s Selecting previously unselected package x11-common. 897s Preparing to unpack .../067-x11-common_1%3a7.7+23ubuntu2_all.deb ... 897s Unpacking x11-common (1:7.7+23ubuntu2) ... 897s Selecting previously unselected package libice6:amd64. 897s Preparing to unpack .../068-libice6_2%3a1.0.10-1build2_amd64.deb ... 897s Unpacking libice6:amd64 (2:1.0.10-1build2) ... 897s Selecting previously unselected package libparams-classify-perl:amd64. 897s Preparing to unpack .../069-libparams-classify-perl_0.015-2build3_amd64.deb ... 897s Unpacking libparams-classify-perl:amd64 (0.015-2build3) ... 897s Selecting previously unselected package libmodule-runtime-perl. 897s Preparing to unpack .../070-libmodule-runtime-perl_0.016-2_all.deb ... 897s Unpacking libmodule-runtime-perl (0.016-2) ... 897s Selecting previously unselected package libimport-into-perl. 897s Preparing to unpack .../071-libimport-into-perl_1.002005-2_all.deb ... 897s Unpacking libimport-into-perl (1.002005-2) ... 897s Selecting previously unselected package libjpeg-turbo8:amd64. 897s Preparing to unpack .../072-libjpeg-turbo8_2.1.5-2ubuntu1_amd64.deb ... 897s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 897s Selecting previously unselected package libjpeg8:amd64. 897s Preparing to unpack .../073-libjpeg8_8c-2ubuntu11_amd64.deb ... 897s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 897s Selecting previously unselected package libjs-bootstrap. 897s Preparing to unpack .../074-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 897s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 897s Selecting previously unselected package libjs-popper.js. 897s Preparing to unpack .../075-libjs-popper.js_1.16.1+ds-6_all.deb ... 897s Unpacking libjs-popper.js (1.16.1+ds-6) ... 898s Selecting previously unselected package libjs-bootstrap4. 898s Preparing to unpack .../076-libjs-bootstrap4_4.6.1+dfsg1-4_all.deb ... 898s Unpacking libjs-bootstrap4 (4.6.1+dfsg1-4) ... 898s Selecting previously unselected package libjs-d3. 898s Preparing to unpack .../077-libjs-d3_3.5.17-4_all.deb ... 898s Unpacking libjs-d3 (3.5.17-4) ... 898s Selecting previously unselected package libjs-es5-shim. 898s Preparing to unpack .../078-libjs-es5-shim_4.6.7-2_all.deb ... 898s Unpacking libjs-es5-shim (4.6.7-2) ... 898s Selecting previously unselected package libjs-highlight.js. 898s Preparing to unpack .../079-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 898s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 898s Selecting previously unselected package libjs-jquery. 898s Preparing to unpack .../080-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 898s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 898s Selecting previously unselected package libjs-jquery-datatables. 898s Preparing to unpack .../081-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 898s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 898s Selecting previously unselected package libjs-sifter.js. 898s Preparing to unpack .../082-libjs-sifter.js_0.6.0+dfsg-3_all.deb ... 898s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ... 898s Selecting previously unselected package libjs-microplugin.js. 898s Preparing to unpack .../083-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ... 898s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ... 898s Selecting previously unselected package libjs-jquery-selectize.js. 898s Preparing to unpack .../084-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ... 898s Unpacking libjs-jquery-selectize.js 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package librole-tiny-perl. 898s Preparing to unpack .../090-librole-tiny-perl_2.002004-1_all.deb ... 898s Unpacking librole-tiny-perl (2.002004-1) ... 898s Selecting previously unselected package libsub-quote-perl. 898s Preparing to unpack .../091-libsub-quote-perl_2.006008-1ubuntu1_all.deb ... 898s Unpacking libsub-quote-perl (2.006008-1ubuntu1) ... 898s Selecting previously unselected package libmoo-perl. 898s Preparing to unpack .../092-libmoo-perl_2.005005-1_all.deb ... 898s Unpacking libmoo-perl (2.005005-1) ... 898s Selecting previously unselected package libthai-data. 898s Preparing to unpack .../093-libthai-data_0.1.29-2_all.deb ... 898s Unpacking libthai-data (0.1.29-2) ... 898s Selecting previously unselected package libthai0:amd64. 898s Preparing to unpack .../094-libthai0_0.1.29-2_amd64.deb ... 898s Unpacking libthai0:amd64 (0.1.29-2) ... 898s Selecting previously unselected package libpango-1.0-0:amd64. 898s Preparing to unpack .../095-libpango-1.0-0_1.51.0+ds-4_amd64.deb 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libparallel-forkmanager-perl (2.02-1) ... 898s Selecting previously unselected package libreadonly-perl. 898s Preparing to unpack .../101-libreadonly-perl_2.050-3_all.deb ... 898s Unpacking libreadonly-perl (2.050-3) ... 898s Selecting previously unselected package libsharpyuv0:amd64. 898s Preparing to unpack .../102-libsharpyuv0_1.3.2-0.4_amd64.deb ... 898s Unpacking libsharpyuv0:amd64 (1.3.2-0.4) ... 898s Selecting previously unselected package libsm6:amd64. 898s Preparing to unpack .../103-libsm6_2%3a1.2.3-1build2_amd64.deb ... 898s Unpacking libsm6:amd64 (2:1.2.3-1build2) ... 898s Selecting previously unselected package libtcl8.6:amd64. 898s Preparing to unpack .../104-libtcl8.6_8.6.13+dfsg-2_amd64.deb ... 898s Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ... 898s Selecting previously unselected package libjbig0:amd64. 898s Preparing to unpack .../105-libjbig0_2.1-6.1ubuntu1_amd64.deb ... 898s Unpacking libjbig0:amd64 (2.1-6.1ubuntu1) ... 898s Selecting previously unselected package libwebp7:amd64. 899s Preparing to unpack .../106-libwebp7_1.3.2-0.4_amd64.deb ... 899s Unpacking libwebp7:amd64 (1.3.2-0.4) ... 899s Selecting previously unselected package libtiff6:amd64. 899s Preparing to unpack .../107-libtiff6_4.5.1+git230720-3ubuntu1_amd64.deb ... 899s Unpacking libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 899s Selecting previously unselected package libxft2:amd64. 899s Preparing to unpack .../108-libxft2_2.3.6-1_amd64.deb ... 899s Unpacking libxft2:amd64 (2.3.6-1) ... 899s Selecting previously unselected package libxss1:amd64. 899s Preparing to unpack .../109-libxss1_1%3a1.2.3-1build2_amd64.deb ... 899s Unpacking libxss1:amd64 (1:1.2.3-1build2) ... 899s Selecting previously unselected package libtk8.6:amd64. 899s Preparing to unpack .../110-libtk8.6_8.6.13-2_amd64.deb ... 899s Unpacking libtk8.6:amd64 (8.6.13-2) ... 899s Selecting previously unselected package libxt6:amd64. 899s Preparing to unpack .../111-libxt6_1%3a1.2.1-1.1_amd64.deb ... 899s Unpacking libxt6:amd64 (1:1.2.1-1.1) ... 899s Selecting previously unselected package zip. 899s Preparing to unpack .../112-zip_3.0-13_amd64.deb ... 899s Unpacking zip (3.0-13) ... 899s Selecting previously unselected package unzip. 899s Preparing to unpack .../113-unzip_6.0-28ubuntu3_amd64.deb ... 899s Unpacking unzip (6.0-28ubuntu3) ... 899s Selecting previously unselected package xdg-utils. 899s Preparing to unpack .../114-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 899s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 899s Selecting previously unselected package r-base-core. 899s Preparing to unpack .../115-r-base-core_4.3.2-1build1_amd64.deb ... 899s Unpacking r-base-core (4.3.2-1build1) ... 899s Selecting previously unselected package r-cran-littler. 899s Preparing to unpack .../116-r-cran-littler_0.3.19-1_amd64.deb ... 899s Unpacking r-cran-littler (0.3.19-1) ... 899s Selecting previously unselected package littler. 899s Preparing to unpack .../117-littler_0.3.19-1_all.deb ... 899s Unpacking littler (0.3.19-1) ... 899s Selecting previously unselected package node-bootstrap-sass. 899s Preparing to unpack .../118-node-bootstrap-sass_3.4.3-2_all.deb ... 899s Unpacking node-bootstrap-sass (3.4.3-2) ... 899s Selecting previously unselected package node-html5shiv. 899s Preparing to unpack .../119-node-html5shiv_3.7.3+dfsg-5_all.deb ... 899s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 899s Selecting previously unselected package node-normalize.css. 899s Preparing to unpack .../120-node-normalize.css_8.0.1-5_all.deb ... 899s Unpacking node-normalize.css (8.0.1-5) ... 899s Selecting previously unselected package pandoc-data. 899s Preparing to unpack .../121-pandoc-data_3.1.3-1_all.deb ... 899s Unpacking pandoc-data (3.1.3-1) ... 899s Selecting previously unselected package pandoc. 899s Preparing to unpack .../122-pandoc_3.1.3+ds-2_amd64.deb ... 899s Unpacking pandoc (3.1.3+ds-2) ... 900s Selecting previously unselected package plink. 900s Preparing to unpack .../123-plink_1.07+dfsg-4_amd64.deb ... 900s Unpacking plink (1.07+dfsg-4) ... 900s Selecting previously unselected package r-cran-getopt. 900s Preparing to unpack .../124-r-cran-getopt_1.20.4-1_all.deb ... 900s Unpacking r-cran-getopt (1.20.4-1) ... 900s Selecting previously unselected package r-cran-colorspace. 900s Preparing to unpack .../125-r-cran-colorspace_2.1-0+dfsg-1_amd64.deb ... 900s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 900s Selecting previously unselected package r-cran-fracdiff. 900s Preparing to unpack .../126-r-cran-fracdiff_1.5-3-1_amd64.deb ... 900s Unpacking r-cran-fracdiff (1.5-3-1) ... 900s Selecting previously unselected package r-cran-generics. 900s Preparing to unpack .../127-r-cran-generics_0.1.3-1_all.deb ... 900s Unpacking r-cran-generics (0.1.3-1) ... 900s Selecting previously unselected package r-cran-cli. 900s Preparing to unpack .../128-r-cran-cli_3.6.2-1_amd64.deb ... 900s Unpacking r-cran-cli (3.6.2-1) ... 900s Selecting previously unselected package r-cran-glue. 900s Preparing to unpack .../129-r-cran-glue_1.7.0-1_amd64.deb ... 900s Unpacking r-cran-glue (1.7.0-1) ... 900s Selecting previously unselected package r-cran-rlang. 900s Preparing to unpack .../130-r-cran-rlang_1.1.3-1_amd64.deb ... 900s Unpacking r-cran-rlang (1.1.3-1) ... 900s Selecting previously unselected package r-cran-lifecycle. 900s Preparing to unpack .../131-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 900s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 901s Selecting previously unselected package r-cran-gtable. 901s Preparing to unpack .../132-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 901s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 901s Selecting previously unselected package r-cran-isoband. 901s Preparing to unpack .../133-r-cran-isoband_0.2.7-1_amd64.deb ... 901s Unpacking r-cran-isoband (0.2.7-1) ... 901s Selecting previously unselected package r-cran-mass. 901s Preparing to unpack .../134-r-cran-mass_7.3-60.0.1-1_amd64.deb ... 901s Unpacking r-cran-mass 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Selecting previously unselected package r-cran-fansi. 901s Preparing to unpack .../146-r-cran-fansi_1.0.5-1_amd64.deb ... 901s Unpacking r-cran-fansi (1.0.5-1) ... 901s Selecting previously unselected package r-cran-magrittr. 901s Preparing to unpack .../147-r-cran-magrittr_2.0.3-1_amd64.deb ... 901s Unpacking r-cran-magrittr (2.0.3-1) ... 901s Selecting previously unselected package r-cran-utf8. 901s Preparing to unpack .../148-r-cran-utf8_1.2.4-1_amd64.deb ... 901s Unpacking r-cran-utf8 (1.2.4-1) ... 901s Selecting previously unselected package r-cran-vctrs. 901s Preparing to unpack .../149-r-cran-vctrs_0.6.5-1_amd64.deb ... 901s Unpacking r-cran-vctrs (0.6.5-1) ... 901s Selecting previously unselected package r-cran-pillar. 901s Preparing to unpack .../150-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 901s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 901s Selecting previously unselected package r-cran-pkgconfig. 901s Preparing to unpack .../151-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 901s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 901s Selecting previously unselected package r-cran-tibble. 901s Preparing to unpack .../152-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ... 901s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 901s Selecting previously unselected package r-cran-withr. 901s Preparing to unpack .../153-r-cran-withr_2.5.0-1_all.deb ... 901s Unpacking r-cran-withr (2.5.0-1) ... 901s Selecting previously unselected package r-cran-ggplot2. 901s Preparing to unpack .../154-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 901s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 902s Selecting previously unselected package r-cran-zoo. 902s Preparing to unpack .../155-r-cran-zoo_1.8-12-2_amd64.deb ... 902s Unpacking r-cran-zoo (1.8-12-2) ... 902s Selecting previously unselected package r-cran-lmtest. 902s Preparing to unpack .../156-r-cran-lmtest_0.9.40-1_amd64.deb ... 902s Unpacking r-cran-lmtest (0.9.40-1) ... 902s Selecting previously unselected package r-cran-nnet. 902s Preparing to unpack .../157-r-cran-nnet_7.3-19-2_amd64.deb ... 902s Unpacking r-cran-nnet (7.3-19-2) ... 902s Selecting previously unselected package r-cran-pkgkitten. 902s Preparing to unpack .../158-r-cran-pkgkitten_0.2.3-1_all.deb ... 902s Unpacking r-cran-pkgkitten (0.2.3-1) ... 902s Selecting previously unselected package r-cran-rcpp. 902s Preparing to unpack .../159-r-cran-rcpp_1.0.12-1_amd64.deb ... 902s Unpacking r-cran-rcpp (1.0.12-1) ... 902s Selecting previously unselected package r-cran-timedate. 902s Preparing to unpack .../160-r-cran-timedate_4032.109-1_amd64.deb ... 902s Unpacking r-cran-timedate (4032.109-1) ... 902s Selecting previously unselected package r-cran-quadprog. 902s Preparing to unpack .../161-r-cran-quadprog_1.5-8-1build1_amd64.deb ... 902s Unpacking r-cran-quadprog (1.5-8-1build1) ... 902s Selecting previously unselected package r-cran-xts. 902s Preparing to unpack .../162-r-cran-xts_0.13.2-1_amd64.deb ... 902s Unpacking r-cran-xts (0.13.2-1) ... 902s Selecting previously unselected package r-cran-curl. 902s Preparing to unpack .../163-r-cran-curl_5.2.0+dfsg-1_amd64.deb ... 902s Unpacking r-cran-curl (5.2.0+dfsg-1) ... 902s Selecting previously unselected package r-cran-ttr. 902s Preparing to unpack .../164-r-cran-ttr_0.24.4-1_amd64.deb ... 902s Unpacking r-cran-ttr (0.24.4-1) ... 902s Selecting previously unselected package r-cran-jsonlite. 902s Preparing to unpack .../165-r-cran-jsonlite_1.8.8+dfsg-1_amd64.deb ... 902s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 902s Selecting previously unselected package r-cran-quantmod. 902s Preparing to unpack .../166-r-cran-quantmod_0.4.26-1_all.deb ... 902s Unpacking r-cran-quantmod (0.4.26-1) ... 902s Selecting previously unselected package r-cran-tseries. 902s Preparing to unpack .../167-r-cran-tseries_0.10-55-1_amd64.deb ... 902s Unpacking r-cran-tseries (0.10-55-1) ... 902s Selecting previously unselected package r-cran-urca. 902s Preparing to unpack .../168-r-cran-urca_1.3-3-1_amd64.deb ... 902s Unpacking r-cran-urca (1.3-3-1) ... 902s Selecting previously unselected package r-cran-rcpparmadillo. 902s Preparing to unpack .../169-r-cran-rcpparmadillo_0.12.8.0.0-1_amd64.deb ... 902s Unpacking r-cran-rcpparmadillo (0.12.8.0.0-1) ... 902s Selecting previously unselected package r-cran-forecast. 902s Preparing to unpack .../170-r-cran-forecast_8.21.1-1_amd64.deb ... 902s Unpacking r-cran-forecast (8.21.1-1) ... 902s Selecting previously unselected package r-bioc-biocgenerics. 902s Preparing to unpack .../171-r-bioc-biocgenerics_0.48.1-2_all.deb ... 902s Unpacking r-bioc-biocgenerics (0.48.1-2) ... 902s Selecting previously unselected package r-bioc-biobase. 902s Preparing to unpack .../172-r-bioc-biobase_2.62.0-1_amd64.deb ... 902s Unpacking r-bioc-biobase (2.62.0-1) ... 902s Selecting previously unselected package r-cran-survival. 902s Preparing to unpack .../173-r-cran-survival_3.5-8-1_amd64.deb ... 902s Unpacking r-cran-survival (3.5-8-1) ... 903s Selecting previously unselected package r-bioc-multtest. 903s Preparing to unpack .../174-r-bioc-multtest_2.58.0-1_amd64.deb ... 903s Unpacking r-bioc-multtest (2.58.0-1) ... 903s Selecting previously unselected package r-cran-optparse. 903s Preparing to unpack .../175-r-cran-optparse_1.7.4-1_all.deb ... 903s Unpacking r-cran-optparse (1.7.4-1) ... 903s Selecting previously unselected package r-cran-uroot. 903s Preparing to unpack .../176-r-cran-uroot_2.1-3-1_all.deb ... 903s Unpacking r-cran-uroot (2.1-3-1) ... 903s Selecting previously unselected package pique. 903s Preparing to unpack .../177-pique_1.0-7_all.deb ... 903s Unpacking pique (1.0-7) ... 903s Selecting previously unselected package pique-doc. 903s Preparing to unpack .../178-pique-doc_1.0-7_all.deb ... 903s Unpacking pique-doc (1.0-7) ... 903s Selecting previously unselected package r-cran-acepack. 903s Preparing to unpack .../179-r-cran-acepack_1.4.2-1_amd64.deb ... 903s Unpacking r-cran-acepack (1.4.2-1) ... 903s Selecting previously unselected package r-cran-backports. 903s Preparing to unpack .../180-r-cran-backports_1.4.1-1_amd64.deb ... 903s Unpacking r-cran-backports (1.4.1-1) ... 903s Selecting previously unselected package r-cran-base64enc. 903s Preparing to unpack .../181-r-cran-base64enc_0.1-3-3_amd64.deb ... 903s Unpacking r-cran-base64enc (0.1-3-3) ... 903s Selecting previously unselected package r-cran-fastmap. 903s Preparing to unpack .../182-r-cran-fastmap_1.1.1-1_amd64.deb ... 903s Unpacking r-cran-fastmap (1.1.1-1) ... 903s Selecting previously unselected package r-cran-cachem. 903s Preparing to unpack .../183-r-cran-cachem_1.0.8-1_amd64.deb ... 903s Unpacking r-cran-cachem (1.0.8-1) ... 903s Selecting previously unselected package r-cran-digest. 903s Preparing to unpack .../184-r-cran-digest_0.6.34-1_amd64.deb ... 903s Unpacking r-cran-digest (0.6.34-1) ... 903s Selecting previously unselected package r-cran-ellipsis. 903s Preparing to unpack .../185-r-cran-ellipsis_0.3.2-2_amd64.deb ... 903s Unpacking r-cran-ellipsis (0.3.2-2) ... 903s Selecting previously unselected package r-cran-htmltools. 903s Preparing to unpack .../186-r-cran-htmltools_0.5.7-1_amd64.deb ... 903s Unpacking r-cran-htmltools (0.5.7-1) ... 903s Selecting previously unselected package r-cran-jquerylib. 903s Preparing to unpack .../187-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ... 903s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ... 903s Selecting previously unselected package r-cran-memoise. 903s Preparing to unpack .../188-r-cran-memoise_2.0.1-1_all.deb ... 903s Unpacking r-cran-memoise (2.0.1-1) ... 903s Selecting previously unselected package r-cran-mime. 903s Preparing to unpack .../189-r-cran-mime_0.12-1_amd64.deb ... 903s Unpacking r-cran-mime (0.12-1) ... 903s Selecting previously unselected package r-cran-fs. 903s Preparing to unpack .../190-r-cran-fs_1.6.3+dfsg-1_amd64.deb ... 903s Unpacking r-cran-fs (1.6.3+dfsg-1) ... 903s Selecting previously unselected package r-cran-rappdirs. 903s Preparing to unpack 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unselected package r-cran-commonmark. 904s Preparing to unpack .../197-r-cran-commonmark_1.9.1-1_amd64.deb ... 904s Unpacking r-cran-commonmark (1.9.1-1) ... 904s Selecting previously unselected package r-cran-cpp11. 904s Preparing to unpack .../198-r-cran-cpp11_0.4.7-1_all.deb ... 904s Unpacking r-cran-cpp11 (0.4.7-1) ... 904s Selecting previously unselected package r-cran-crayon. 904s Preparing to unpack .../199-r-cran-crayon_1.5.2-1_all.deb ... 904s Unpacking r-cran-crayon (1.5.2-1) ... 904s Selecting previously unselected package r-cran-data.table. 904s Preparing to unpack .../200-r-cran-data.table_1.14.10+dfsg-1_amd64.deb ... 904s Unpacking r-cran-data.table (1.14.10+dfsg-1) ... 904s Selecting previously unselected package r-cran-deldir. 904s Preparing to unpack .../201-r-cran-deldir_2.0-4-1_amd64.deb ... 904s Unpacking r-cran-deldir (2.0-4-1) ... 904s Selecting previously unselected package r-cran-tidyselect. 904s Preparing to unpack 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previously unselected package r-cran-gridextra. 904s Preparing to unpack .../208-r-cran-gridextra_2.3-3build1_all.deb ... 904s Unpacking r-cran-gridextra (2.3-3build1) ... 904s Selecting previously unselected package r-cran-xfun. 904s Preparing to unpack .../209-r-cran-xfun_0.41+dfsg-1_amd64.deb ... 904s Unpacking r-cran-xfun (0.41+dfsg-1) ... 904s Selecting previously unselected package r-cran-highr. 904s Preparing to unpack .../210-r-cran-highr_0.10+dfsg-1_all.deb ... 904s Unpacking r-cran-highr (0.10+dfsg-1) ... 904s Selecting previously unselected package r-cran-rpart. 904s Preparing to unpack .../211-r-cran-rpart_4.1.23-1_amd64.deb ... 904s Unpacking r-cran-rpart (4.1.23-1) ... 904s Selecting previously unselected package r-cran-stringi. 904s Preparing to unpack .../212-r-cran-stringi_1.8.3-1_amd64.deb ... 904s Unpacking r-cran-stringi (1.8.3-1) ... 904s Selecting previously unselected package r-cran-stringr. 904s Preparing to unpack .../213-r-cran-stringr_1.5.1-1_all.deb ... 904s 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Setting up r-cran-formula (1.2-5-1) ... 910s Setting up r-cran-viridislite (0.4.2-2) ... 910s Setting up r-cran-cluster (2.1.6-1) ... 910s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 910s Setting up r-cran-nnet (7.3-19-2) ... 910s Setting up r-cran-commonmark (1.9.1-1) ... 910s Setting up r-cran-r6 (2.5.1-1) ... 910s Setting up r-cran-pkgkitten (0.2.3-1) ... 910s Setting up r-cran-jpeg (0.1-10-1) ... 910s Setting up r-cran-chron (2.3-61-2) ... 910s Setting up r-cran-magrittr (2.0.3-1) ... 910s Setting up r-cran-rappdirs (0.3.3-1) ... 910s Setting up r-cran-quadprog (1.5-8-1build1) ... 910s Setting up r-cran-littler (0.3.19-1) ... 910s Setting up r-cran-fs (1.6.3+dfsg-1) ... 910s Setting up r-cran-rcpp (1.0.12-1) ... 910s Setting up r-cran-curl (5.2.0+dfsg-1) ... 910s Setting up g++-13 (13.2.0-17ubuntu2) ... 910s Setting up r-bioc-biocgenerics (0.48.1-2) ... 910s Setting up r-cran-rlang (1.1.3-1) ... 910s Setting up littler (0.3.19-1) ... 910s Setting up r-cran-uroot (2.1-3-1) ... 910s Setting up r-cran-xfun (0.41+dfsg-1) ... 910s Setting up r-cran-urca (1.3-3-1) ... 910s Setting up r-cran-withr (2.5.0-1) ... 910s Setting up r-cran-backports (1.4.1-1) ... 910s Setting up r-cran-mime (0.12-1) ... 910s Setting up r-cran-generics (0.1.3-1) ... 910s Setting up r-cran-base64enc (0.1-3-3) ... 910s Setting up r-cran-digest (0.6.34-1) ... 910s Setting up r-cran-yaml (2.3.8-1) ... 910s Setting up r-cran-evaluate (0.23-1) ... 910s Setting up r-cran-timedate (4032.109-1) ... 910s Setting up r-cran-highr (0.10+dfsg-1) ... 910s Setting up r-cran-fansi (1.0.5-1) ... 910s Setting up r-cran-mass (7.3-60.0.1-1) ... 910s Setting up r-cran-checkmate (2.3.1-1) ... 910s Setting up r-cran-acepack (1.4.2-1) ... 910s Setting up r-cran-data.table (1.14.10+dfsg-1) ... 910s Setting up r-cran-glue (1.7.0-1) ... 910s Setting up r-cran-foreign (0.8.86-1) ... 910s Setting up r-cran-fracdiff (1.5-3-1) ... 910s Setting up r-cran-xtable (1:1.8-4-2) ... 910s Setting up r-cran-cli (3.6.2-1) ... 910s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 910s Setting up r-cran-deldir (2.0-4-1) ... 910s Setting up r-cran-fastmap (1.1.1-1) ... 910s Setting up r-cran-png (0.1-8-1) ... 910s Setting up r-bioc-biobase (2.62.0-1) ... 910s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... 910s Setting up r-cran-rstudioapi (0.15.0-1) ... 910s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 910s Setting up r-cran-getopt (1.20.4-1) ... 910s Setting up r-cran-utf8 (1.2.4-1) ... 910s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 910s Setting up r-cran-stringi (1.8.3-1) ... 910s Setting up r-cran-cpp11 (0.4.7-1) ... 910s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 910s Setting up r-cran-isoband (0.2.7-1) ... 910s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 910s Setting up r-cran-zoo (1.8-12-2) ... 910s Setting up r-cran-later (1.3.2+dfsg-1) ... 910s Setting up r-cran-matrix (1.6-5-1) ... 910s Setting up r-cran-tinytex (0.49-1) ... 910s Setting up r-cran-knitr (1.45+dfsg-1) ... 910s Setting up r-cran-mgcv (1.9-1-1) ... 910s Setting up g++ (4:13.2.0-7ubuntu1) ... 910s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 910s Setting up r-cran-cachem (1.0.8-1) ... 910s Setting up r-cran-lmtest (0.9.40-1) ... 910s Setting up build-essential (12.10ubuntu1) ... 910s Setting up r-cran-rcpparmadillo (0.12.8.0.0-1) ... 910s Setting up r-cran-optparse (1.7.4-1) ... 910s Setting up r-cran-vctrs (0.6.5-1) ... 910s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ... 910s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 910s Setting up r-cran-ellipsis (0.3.2-2) ... 910s Setting up r-cran-stringr (1.5.1-1) ... 910s Setting up r-cran-munsell (0.5.0-2build1) ... 910s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 910s Setting up r-cran-survival (3.5-8-1) ... 910s Setting up r-cran-xts (0.13.2-1) ... 910s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 910s Setting up r-cran-interp (1.1-6-1) ... 910s Setting up r-cran-gridextra (2.3-3build1) ... 910s Setting up r-cran-scales (1.3.0-1) ... 910s Setting up r-cran-memoise (2.0.1-1) ... 910s Setting up r-cran-promises (1.2.1+dfsg-1) ... 910s Setting up r-cran-purrr (1.0.2-1) ... 910s Setting up r-cran-htmltools (0.5.7-1) ... 910s Setting up r-cran-sass (0.4.8+dfsg-1) ... 910s Setting up r-cran-dplyr (1.1.4-1) ... 910s Setting up r-cran-ttr (0.24.4-1) ... 910s Setting up r-bioc-multtest (2.58.0-1) ... 910s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 910s Setting up r-cran-httpuv (1.6.14+dfsg-1) ... 910s Setting up r-cran-rpart (4.1.23-1) ... 910s Setting up r-cran-fontawesome (0.5.2-1) ... 910s Setting up r-cran-latticeextra (0.6-30-1) ... 910s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... 910s Setting up r-cran-viridis (0.6.5-1) ... 910s Setting up r-cran-bslib (0.6.1+dfsg-1) ... 910s Setting up r-cran-tidyr (1.3.1-1) ... 910s Setting up r-cran-quantmod (0.4.26-1) ... 910s Setting up r-cran-shiny (1.8.0+dfsg-1) ... 910s Setting up r-cran-tseries (0.10-55-1) ... 910s Setting up r-cran-rmarkdown (2.25+dfsg-3) ... 910s Setting up r-cran-forecast (8.21.1-1) ... 910s Setting up r-cran-htmlwidgets (1.6.4+dfsg-1) ... 910s Setting up pique (1.0-7) ... 910s Setting up r-cran-htmltable (2.4.2-1) ... 910s Setting up r-cran-hmisc (5.1-1-1) ... 910s Processing triggers for man-db (2.12.0-3) ... 911s Processing triggers for install-info (7.1-3) ... 911s Processing triggers for libc-bin (2.39-0ubuntu2) ... 918s Reading package lists... 918s Building dependency tree... 918s Reading state information... 918s Starting pkgProblemResolver with broken count: 0 918s Starting 2 pkgProblemResolver with broken count: 0 918s Done 918s The following NEW packages will be installed: 918s autopkgtest-satdep 919s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 919s Need to get 0 B/696 B of archives. 919s After this operation, 0 B of additional disk space will be used. 919s Get:1 /tmp/autopkgtest.oYbRUi/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 919s Selecting previously unselected package autopkgtest-satdep. 919s (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 ... 94632 files and directories currently installed.) 919s Preparing to unpack .../2-autopkgtest-satdep.deb ... 919s Unpacking autopkgtest-satdep (0) ... 919s Setting up autopkgtest-satdep (0) ... 921s (Reading database ... 94632 files and directories currently installed.) 921s Removing autopkgtest-satdep (0) ... 921s autopkgtest [00:55:58]: test run-unit-test: [----------------------- 921s wget --no-check-certificate http://ricediversity.org/data/sets/44kgwas/RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 921s --2024-03-22 00:55:58-- http://ricediversity.org/data/sets/44kgwas/RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 921s Resolving squid.internal (squid.internal)... 185.125.188.85, 185.125.188.86 921s Connecting to squid.internal (squid.internal)|185.125.188.85|:3128... connected. 921s Proxy request sent, awaiting response... 200 OK 921s Length: 7107854 (6.8M) [application/zip] 921s Saving to: ‘RiceDiversity.44K.MSU6.Genotypes_PLINK.zip’ 921s 921s 0K .......... .......... .......... .......... .......... 0% 306K 23s 921s 50K .......... .......... .......... .......... .......... 1% 612K 17s 921s 100K .......... .......... .......... .......... .......... 2% 17.4M 11s 921s 150K .......... .......... .......... .......... .......... 2% 18.1M 8s 922s 200K .......... .......... .......... .......... .......... 3% 644K 9s 922s 250K .......... .......... .......... .......... .......... 4% 21.4M 7s 922s 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77% 74.1M 0s 922s 5400K .......... .......... .......... .......... .......... 78% 86.4M 0s 922s 5450K .......... .......... .......... .......... .......... 79% 50.3M 0s 922s 5500K .......... .......... .......... .......... .......... 79% 149M 0s 922s 5550K .......... .......... .......... .......... .......... 80% 89.6M 0s 922s 5600K .......... .......... .......... .......... .......... 81% 51.0M 0s 922s 5650K .......... .......... .......... .......... .......... 82% 72.1M 0s 922s 5700K .......... .......... .......... .......... .......... 82% 212M 0s 922s 5750K .......... .......... .......... .......... .......... 83% 82.7M 0s 922s 5800K .......... .......... .......... .......... .......... 84% 96.6M 0s 922s 5850K .......... .......... .......... .......... .......... 84% 65.5M 0s 922s 5900K .......... .......... .......... .......... .......... 85% 29.3M 0s 922s 5950K .......... .......... .......... .......... .......... 86% 70.4M 0s 922s 6000K .......... .......... .......... .......... .......... 87% 64.2M 0s 922s 6050K .......... .......... .......... .......... .......... 87% 93.1T 0s 922s 6100K .......... .......... .......... .......... .......... 88% 96.9M 0s 922s 6150K .......... .......... .......... .......... .......... 89% 1.21M 0s 922s 6200K .......... .......... .......... .......... .......... 90% 48.6M 0s 922s 6250K .......... .......... .......... .......... .......... 90% 498M 0s 922s 6300K .......... .......... .......... .......... .......... 91% 57.1M 0s 922s 6350K .......... .......... .......... .......... .......... 92% 56.9M 0s 922s 6400K .......... .......... .......... .......... .......... 92% 72.0M 0s 922s 6450K .......... .......... .......... .......... .......... 93% 205M 0s 922s 6500K .......... .......... .......... .......... .......... 94% 92.3M 0s 922s 6550K .......... .......... .......... .......... .......... 95% 59.5M 0s 922s 6600K .......... .......... .......... .......... .......... 95% 57.3M 0s 922s 6650K .......... .......... .......... .......... .......... 96% 77.4M 0s 922s 6700K .......... .......... .......... .......... .......... 97% 93.1M 0s 922s 6750K .......... .......... .......... .......... .......... 97% 93.1T 0s 922s 6800K .......... .......... .......... .......... .......... 98% 50.0M 0s 922s 6850K .......... .......... .......... .......... .......... 99% 62.5M 0s 922s 6900K .......... .......... .......... .......... . 100% 59.2M=0.7s 922s 922s 2024-03-22 00:55:59 (9.10 MB/s) - ‘RiceDiversity.44K.MSU6.Genotypes_PLINK.zip’ saved [7107854/7107854] 922s 922s unzip RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 922s Archive: RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 922s creating: RiceDiversity_44K_Genotypes_PLINK/ 922s inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.fam 922s creating: __MACOSX/ 922s creating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/ 922s inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.fam 922s inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.map 922s inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.map 922s inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.ped 922s inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.ped 922s mv -i ./RiceDiversity_44K_Genotypes_PLINK/sativas* . 922s rmdir RiceDiversity_44K_Genotypes_PLINK 922s rm RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 922s pique-input -d -v -i sativas413 -o sativas_GWAS -p rice_phenotype.txt -k -c -e 5 922s Pre-process input data... 922s /usr/bin/p-link --missing-genotype 0 --recode12 --file sativas413 --out sativas413_recode12 922s 922s @----------------------------------------------------------@ 922s | PLINK! | v1.07 | 10/Aug/2009 | 922s |----------------------------------------------------------| 922s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 922s |----------------------------------------------------------| 922s | For documentation, citation & bug-report instructions: | 922s | http://pngu.mgh.harvard.edu/purcell/plink/ | 922s @----------------------------------------------------------@ 922s 922s Web-based version check ( --noweb to skip ) 1056s Connecting to web... failed connection 1056s 1056s Problem connecting to web 1056s 1056s Writing this text to log file [ sativas413_recode12.log ] 1056s Analysis started: Fri Mar 22 00:58:13 2024 1056s 1056s Options in effect: 1056s --missing-genotype 0 1056s --recode12 1056s --file sativas413 1056s --out sativas413_recode12 1056s 1056s 36901 (of 36901) markers to be included from [ sativas413.map ] 1057s Warning, found 413 individuals with ambiguous sex codes 1057s Writing list of these individuals to [ sativas413_recode12.nosex ] 1057s 413 individuals read from [ sativas413.ped ] 1057s 0 individuals with nonmissing phenotypes 1057s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 1057s Missing phenotype value is also -9 1057s 0 cases, 0 controls and 413 missing 1057s 0 males, 0 females, and 413 of unspecified sex 1057s Before frequency and genotyping pruning, there are 36901 SNPs 1057s 413 founders and 0 non-founders found 1058s Total genotyping rate in remaining individuals is 0.956644 1058s 0 SNPs failed missingness test ( GENO > 1 ) 1058s 0 SNPs failed frequency test ( MAF < 0 ) 1058s After frequency and genotyping pruning, there are 36901 SNPs 1058s After filtering, 0 cases, 0 controls and 413 missing 1058s After filtering, 0 males, 0 females, and 413 of unspecified sex 1058s Writing recoded ped file to [ sativas413_recode12.ped ] 1059s Writing new map file to [ sativas413_recode12.map ] 1059s 1059s Analysis finished: Fri Mar 22 00:58:16 2024 1059s 1059s Store phenotype data indexed by genotype... 1059s cd sativas_GWAS 1059s Filter accessions for phenotype from ../sativas413_recode12... 1059s Checking concurrence of id's in .ped and .pheno input files... 1059s 1059s Total number of accession ids in ../sativas413_recode12.ped: 413 1059s Number of accession id's in ../sativas413_recode12.ped not present in rice_phenotype.txt: 35 1059s '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' 1059s Total number of accession id's in rice_phenotype.txt: 378 1059s Number of accession id's in rice_phenotype.txt not present in ../sativas413_recode12.ped: 0 1059s 1059s Quality control sativas_GWAS... 1059s 1059s Calculating MAF... 1059s /usr/bin/p-link --missing-genotype 0 --freq --file sativas_GWAS --out sativas_GWAS 1059s 1059s @----------------------------------------------------------@ 1059s | PLINK! | v1.07 | 10/Aug/2009 | 1059s |----------------------------------------------------------| 1059s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 1059s |----------------------------------------------------------| 1059s | For documentation, citation & bug-report instructions: | 1059s | http://pngu.mgh.harvard.edu/purcell/plink/ | 1059s @----------------------------------------------------------@ 1059s 1059s Web-based version check ( --noweb to skip ) 1193s Connecting to web... failed connection 1193s 1193s Problem connecting to web 1193s 1193s Writing this text to log file [ sativas_GWAS.log ] 1193s Analysis started: Fri Mar 22 01:00:30 2024 1193s 1193s Options in effect: 1193s --missing-genotype 0 1193s --freq 1193s --file sativas_GWAS 1193s --out sativas_GWAS 1193s 1193s 36901 (of 36901) markers to be included from [ sativas_GWAS.map ] 1195s Warning, found 378 individuals with ambiguous sex codes 1195s These individuals will be set to missing ( or use --allow-no-sex ) 1195s Writing list of these individuals to [ sativas_GWAS.nosex ] 1195s 378 individuals read from [ sativas_GWAS.ped ] 1195s 0 individuals with nonmissing phenotypes 1195s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 1195s Missing phenotype value is also -9 1195s 0 cases, 0 controls and 378 missing 1195s 0 males, 0 females, and 378 of unspecified sex 1195s Before frequency and genotyping pruning, there are 36901 SNPs 1195s 378 founders and 0 non-founders found 1195s Writing allele frequencies (founders-only) to [ sativas_GWAS.frq ] 1195s 1195s Analysis finished: Fri Mar 22 01:00:32 2024 1195s 1195s Create sativas_GWAS.covar file... 1195s /usr/lib/eigensoft/smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log 1202s Transpose sativas_GWAS... 1202s /usr/bin/p-link --missing-genotype 0 --recode --transpose --file sativas_GWAS --out sativas_GWAS 1202s 1202s @----------------------------------------------------------@ 1202s | PLINK! | v1.07 | 10/Aug/2009 | 1202s |----------------------------------------------------------| 1202s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 1202s |----------------------------------------------------------| 1202s | For documentation, citation & bug-report instructions: | 1202s | http://pngu.mgh.harvard.edu/purcell/plink/ | 1202s @----------------------------------------------------------@ 1202s 1202s Web-based version check ( --noweb to skip ) 1202s Recent cached web-check found...Problem connecting to web 1202s 1202s Writing this text to log file [ sativas_GWAS.log ] 1202s Analysis started: Fri Mar 22 01:00:39 2024 1202s 1202s Options in effect: 1202s --missing-genotype 0 1202s --recode 1202s --transpose 1202s --file sativas_GWAS 1202s --out sativas_GWAS 1202s 1202s 36901 (of 36901) markers to be included from [ sativas_GWAS.map ] 1203s Warning, found 378 individuals with ambiguous sex codes 1203s Writing list of these individuals to [ sativas_GWAS.nosex ] 1203s 378 individuals read from [ sativas_GWAS.ped ] 1203s 0 individuals with nonmissing phenotypes 1203s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 1203s Missing phenotype value is also -9 1203s 0 cases, 0 controls and 378 missing 1203s 0 males, 0 females, and 378 of unspecified sex 1203s Before frequency and genotyping pruning, there are 36901 SNPs 1203s 378 founders and 0 non-founders found 1203s Total genotyping rate in remaining individuals is 0.956642 1203s 0 SNPs failed missingness test ( GENO > 1 ) 1203s 0 SNPs failed frequency test ( MAF < 0 ) 1203s After frequency and genotyping pruning, there are 36901 SNPs 1203s After filtering, 0 cases, 0 controls and 378 missing 1203s After filtering, 0 males, 0 females, and 378 of unspecified sex 1203s Writing transposed ped file to [ sativas_GWAS.tped ] 1205s Writing family information to [ sativas_GWAS.tfam ] 1205s 1205s Analysis finished: Fri Mar 22 01:00:42 2024 1205s 1205s Creating sativas_GWAS.hIBS.kin kinship file using IBS method... 1205s /usr/bin/emmax-kin -v -h -s -d 10 sativas_GWAS 1205s 1205s Reading TFAM file sativas_GWAS.tfam .... 1205s 1205s Reading TPED file sativas_GWAS.tped .... 1205s Reading 0 SNPs 1205s Reading 1000 SNPs 1205s Reading 2000 SNPs 1205s Reading 3000 SNPs 1205s Reading 4000 SNPs 1205s Reading 5000 SNPs 1205s Reading 6000 SNPs 1205s Reading 7000 SNPs 1205s Reading 8000 SNPs 1206s Reading 9000 SNPs 1206s Reading 10000 SNPs 1206s Reading 11000 SNPs 1206s Reading 12000 SNPs 1206s Reading 13000 SNPs 1206s Reading 14000 SNPs 1206s Reading 15000 SNPs 1206s Reading 16000 SNPs 1206s Reading 17000 SNPs 1207s Reading 18000 SNPs 1207s Reading 19000 SNPs 1207s Reading 20000 SNPs 1207s Reading 21000 SNPs 1207s Reading 22000 SNPs 1207s Reading 23000 SNPs 1207s Reading 24000 SNPs 1207s Reading 25000 SNPs 1208s Reading 26000 SNPs 1208s Reading 27000 SNPs 1208s Reading 28000 SNPs 1208s Reading 29000 SNPs 1208s Reading 30000 SNPs 1208s Reading 31000 SNPs 1208s Reading 32000 SNPs 1208s Reading 33000 SNPs 1208s Reading 34000 SNPs 1209s Reading 35000 SNPs 1209s Reading 36000 SNPs 1209s Printing the kinship matrix to file 1209s Creating phenotype files in sub-directory sativas_GWAS... 1209s 1209s cd .. 1209s removing temp files... 1209s pique-run -d -v -i sativas_GWAS -k IBS -c sativas_GWAS.covar -n 16 1209s Warning can't run 16 threads on this system - default to max = 2 threads 1209s cd sativas_GWAS 1209s Starting Q_shoot_mass, pid = 6163 1209s cd Q_shoot_mass 1209s processing phenotype Q_shoot_mass... 1209s 1209s 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 1209s cd F_grain_As 1209s processing phenotype F_grain_As... 1209s 1209s 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 1209s nmiss = 87 , mphenoflag = 1 1209s nmiss = 73 , mphenoflag = 1 1209s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.413538 1209s k = 285, n-q = 285 1209s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 1209s k = 299, n-q = 299 1213s 1213s number of SNP ids in Q_shoot_mass_sativas_GWAS.ps for 'Q_shoot_mass' phenotype: 36901 1213s number of SNP ids in Q_shoot_mass_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_shoot_mass' phenotype: 0 1213s 1213s number of SNP ids in sativas_GWAS.tped: 36901 1213s number of SNP ids in sativas_GWAS.tped not present in Q_shoot_mass_sativas_GWAS.ps: 0 1213s 1213s Error in file(filename, "r", encoding = encoding) : 1213s cannot open the connection 1213s Calls: source -> file 1213s In addition: Warning message: 1213s In file(filename, "r", encoding = encoding) : 1213s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1213s Execution halted 1213s cd .. 1213s 1213s number of SNP ids in F_grain_As_sativas_GWAS.ps for 'F_grain_As' phenotype: 36901 1213s number of SNP ids in F_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_As' phenotype: 0 1213s 1213s number of SNP ids in sativas_GWAS.tped: 36901 1213s number of SNP ids in sativas_GWAS.tped not present in F_grain_As_sativas_GWAS.ps: 0 1213s 1214s Error in file(filename, "r", encoding = encoding) : 1214s cannot open the connection 1214s Calls: source -> file 1214s In addition: Warning message: 1214s In file(filename, "r", encoding = encoding) : 1214s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1214s Execution halted 1214s cd .. 1214s Starting F_grain_As, pid = 6164 1214s Finished F_grain_As, pid = 6164, exit_code = 0 1214s Finished Q_shoot_mass, pid = 6163, exit_code = 0 1214s Starting H_Root_dry_weight, pid = 6191 1214s cd H_Root_dry_weight 1214s processing phenotype H_Root_dry_weight... 1214s 1214s 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 1214s cd F_grain_yield 1214s processing phenotype F_grain_yield... 1214s 1214s 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 1214s nmiss = 260 , mphenoflag = 1 1214s nmiss = 73 , mphenoflag = 1 1214s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 1214s k = 112, n-q = 112 1214s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 1214s k = 299, n-q = 299 1216s 1216s number of SNP ids in H_Root_dry_weight_sativas_GWAS.ps for 'H_Root_dry_weight' phenotype: 36901 1216s 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 1216s 1216s number of SNP ids in sativas_GWAS.tped: 36901 1216s number of SNP ids in sativas_GWAS.tped not present in H_Root_dry_weight_sativas_GWAS.ps: 0 1216s 1216s Error in file(filename, "r", encoding = encoding) : 1216s cannot open the connection 1216s Calls: source -> file 1216s In addition: Warning message: 1216s In file(filename, "r", encoding = encoding) : 1216s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1216s Execution halted 1216s cd .. 1216s Starting F_grain_yield, pid = 6192 1216s Finished H_Root_dry_weight, pid = 6191, exit_code = 0 1216s cd H_R_S 1216s processing phenotype H_R_S... 1216s 1216s 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 1216s nmiss = 260 , mphenoflag = 1 1216s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 1216s k = 112, n-q = 112 1218s 1218s number of SNP ids in H_R_S_sativas_GWAS.ps for 'H_R_S' phenotype: 36901 1218s number of SNP ids in H_R_S_sativas_GWAS.ps not present in sativas_GWAS.tped for 'H_R_S' phenotype: 0 1218s 1218s number of SNP ids in sativas_GWAS.tped: 36901 1218s number of SNP ids in sativas_GWAS.tped not present in H_R_S_sativas_GWAS.ps: 0 1218s 1218s Error in file(filename, "r", encoding = encoding) : 1218s cannot open the connection 1218s Calls: source -> file 1218s In addition: Warning message: 1218s In file(filename, "r", encoding = encoding) : 1218s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1218s Execution halted 1218s cd .. 1218s Starting H_R_S, pid = 6207 1218s Finished H_R_S, pid = 6207, exit_code = 0 1218s cd H_Root_Length_27 1218s processing phenotype H_Root_Length_27... 1218s 1218s 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 1218s nmiss = 260 , mphenoflag = 1 1218s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 1218s k = 112, n-q = 112 1219s 1219s number of SNP ids in F_grain_yield_sativas_GWAS.ps for 'F_grain_yield' phenotype: 36901 1219s number of SNP ids in F_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_yield' phenotype: 0 1219s 1219s number of SNP ids in sativas_GWAS.tped: 36901 1219s number of SNP ids in sativas_GWAS.tped not present in F_grain_yield_sativas_GWAS.ps: 0 1219s 1219s Error in file(filename, "r", encoding = encoding) : 1219s cannot open the connection 1219s Calls: source -> file 1219s In addition: Warning message: 1219s In file(filename, "r", encoding = encoding) : 1219s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1219s Execution halted 1219s cd .. 1219s Starting H_Root_Length_27, pid = 6221 1219s Finished F_grain_yield, pid = 6192, exit_code = 0 1219s cd A_Stem_thickness 1219s processing phenotype A_Stem_thickness... 1219s 1219s 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 1219s nmiss = 49 , mphenoflag = 1 1219s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.474006 1219s k = 323, n-q = 323 1220s 1220s number of SNP ids in H_Root_Length_27_sativas_GWAS.ps for 'H_Root_Length_27' phenotype: 36901 1220s 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 1220s 1220s number of SNP ids in sativas_GWAS.tped: 36901 1220s number of SNP ids in sativas_GWAS.tped not present in H_Root_Length_27_sativas_GWAS.ps: 0 1220s 1220s Error in file(filename, "r", encoding = encoding) : 1220s cannot open the connection 1220s Calls: source -> file 1220s In addition: Warning message: 1220s In file(filename, "r", encoding = encoding) : 1220s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1220s Execution halted 1220s cd .. 1220s Starting A_Stem_thickness, pid = 6235 1220s Finished H_Root_Length_27, pid = 6221, exit_code = 0 1220s cd Q_FT 1220s processing phenotype Q_FT... 1220s 1220s 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 1220s nmiss = 85 , mphenoflag = 1 1220s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.399886 1220s k = 287, n-q = 287 1224s 1224s number of SNP ids in A_Stem_thickness_sativas_GWAS.ps for 'A_Stem_thickness' phenotype: 36901 1224s number of SNP ids in A_Stem_thickness_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Stem_thickness' phenotype: 0 1224s 1224s number of SNP ids in sativas_GWAS.tped: 36901 1224s number of SNP ids in sativas_GWAS.tped not present in A_Stem_thickness_sativas_GWAS.ps: 0 1224s 1224s 1224s number of SNP ids in Q_FT_sativas_GWAS.ps for 'Q_FT' phenotype: 36901 1224s number of SNP ids in Q_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_FT' phenotype: 0 1224s 1224s number of SNP ids in sativas_GWAS.tped: 36901 1224s number of SNP ids in sativas_GWAS.tped not present in Q_FT_sativas_GWAS.ps: 0 1224s 1224s Error in file(filename, "r", encoding = encoding) : 1224s cannot open the connection 1224s Calls: source -> file 1224s In addition: Warning message: 1224s In file(filename, "r", encoding = encoding) : 1224s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1224s Execution halted 1224s cd .. 1225s Error in file(filename, "r", encoding = encoding) : 1225s cannot open the connection 1225s Calls: source -> file 1225s In addition: Warning message: 1225s In file(filename, "r", encoding = encoding) : 1225s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1225s Execution halted 1225s cd .. 1225s Starting Q_FT, pid = 6249 1225s Finished A_Stem_thickness, pid = 6235, exit_code = 0 1225s Finished Q_FT, pid = 6249, exit_code = 0 1225s Starting Q_grain_As, pid = 6275 1225s cd Q_grain_As 1225s processing phenotype Q_grain_As... 1225s 1225s 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 1225s cd Q_grain_Cu 1225s processing phenotype Q_grain_Cu... 1225s 1225s 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 1225s nmiss = 90 , mphenoflag = 1 1225s nmiss = 90 , mphenoflag = 1 1225s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 1225s k = 282, n-q = 282 1225s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 1225s k = 282, n-q = 282 1229s 1229s number of SNP ids in Q_grain_As_sativas_GWAS.ps for 'Q_grain_As' phenotype: 36901 1229s number of SNP ids in Q_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_As' phenotype: 0 1229s 1229s number of SNP ids in sativas_GWAS.tped: 36901 1229s number of SNP ids in sativas_GWAS.tped not present in Q_grain_As_sativas_GWAS.ps: 0 1229s 1229s 1229s number of SNP ids in Q_grain_Cu_sativas_GWAS.ps for 'Q_grain_Cu' phenotype: 36901 1229s number of SNP ids in Q_grain_Cu_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Cu' phenotype: 0 1229s 1229s number of SNP ids in sativas_GWAS.tped: 36901 1229s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Cu_sativas_GWAS.ps: 0 1229s 1229s Error in file(filename, "r", encoding = encoding) : 1229s cannot open the connection 1229s Calls: source -> file 1229s In addition: Warning message: 1229s In file(filename, "r", encoding = encoding) : 1229s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1229s Execution halted 1229s cd .. 1229s Error in file(filename, "r", encoding = encoding) : 1229s cannot open the connection 1229s Calls: source -> file 1229s In addition: Warning message: 1229s In file(filename, "r", encoding = encoding) : 1229s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1229s Execution halted 1229s cd .. 1230s Starting Q_grain_Cu, pid = 6276 1230s Finished Q_grain_Cu, pid = 6276, exit_code = 0 1230s Finished Q_grain_As, pid = 6275, exit_code = 0 1230s Starting F_grain_Zn, pid = 6317 1230s cd F_grain_Zn 1230s processing phenotype F_grain_Zn... 1230s 1230s 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 1230s cd F_shoot_As 1230s processing phenotype F_shoot_As... 1230s 1230s 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 1230s nmiss = 73 , mphenoflag = 1 1230s nmiss = 73 , mphenoflag = 1 1230s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.459771 1230s k = 299, n-q = 299 1230s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 1230s k = 299, n-q = 299 1235s 1235s number of SNP ids in F_grain_Zn_sativas_GWAS.ps for 'F_grain_Zn' phenotype: 36901 1235s number of SNP ids in F_grain_Zn_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Zn' phenotype: 0 1235s 1235s number of SNP ids in sativas_GWAS.tped: 36901 1235s number of SNP ids in sativas_GWAS.tped not present in F_grain_Zn_sativas_GWAS.ps: 0 1235s 1235s 1235s number of SNP ids in F_shoot_As_sativas_GWAS.ps for 'F_shoot_As' phenotype: 36901 1235s number of SNP ids in F_shoot_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_shoot_As' phenotype: 0 1235s 1235s number of SNP ids in sativas_GWAS.tped: 36901 1235s number of SNP ids in sativas_GWAS.tped not present in F_shoot_As_sativas_GWAS.ps: 0 1235s 1235s Error in file(filename, "r", encoding = encoding) : 1235s cannot open the connection 1235s Calls: source -> file 1235s In addition: Warning message: 1235s In file(filename, "r", encoding = encoding) : 1235s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1235s Execution halted 1235s cd .. 1235s Error in file(filename, "r", encoding = encoding) : 1235s cannot open the connection 1235s Calls: source -> file 1235s In addition: Warning message: 1235s In file(filename, "r", encoding = encoding) : 1235s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1235s Execution halted 1235s cd .. 1235s Starting F_shoot_As, pid = 6318 1235s Finished F_shoot_As, pid = 6318, exit_code = 0 1235s Finished F_grain_Zn, pid = 6317, exit_code = 0 1235s Starting Q_grain_Co, pid = 6345 1235s cd Q_grain_Co 1235s processing phenotype Q_grain_Co... 1235s 1235s 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 1235s cd A_Seed_weight 1235s processing phenotype A_Seed_weight... 1235s 1235s 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 1235s nmiss = 21 , mphenoflag = 1 1235s nmiss = 90 , mphenoflag = 1 1235s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 1235s k = 282, n-q = 282 1235s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.575045 1235s k = 351, n-q = 351 1239s 1239s number of SNP ids in Q_grain_Co_sativas_GWAS.ps for 'Q_grain_Co' phenotype: 36901 1239s number of SNP ids in Q_grain_Co_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Co' phenotype: 0 1239s 1239s number of SNP ids in sativas_GWAS.tped: 36901 1239s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Co_sativas_GWAS.ps: 0 1239s 1239s Error in file(filename, "r", encoding = encoding) : 1239s cannot open the connection 1239s Calls: source -> file 1239s In addition: Warning message: 1239s In file(filename, "r", encoding = encoding) : 1239s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1239s Execution halted 1239s cd .. 1240s Starting A_Seed_weight, pid = 6346 1240s Finished Q_grain_Co, pid = 6345, exit_code = 0 1240s cd F_FT 1240s processing phenotype F_FT... 1240s 1240s 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 1240s nmiss = 73 , mphenoflag = 1 1240s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 1240s k = 299, n-q = 299 1241s 1241s number of SNP ids in A_Seed_weight_sativas_GWAS.ps for 'A_Seed_weight' phenotype: 36901 1241s number of SNP ids in A_Seed_weight_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Seed_weight' phenotype: 0 1241s 1241s number of SNP ids in sativas_GWAS.tped: 36901 1241s number of SNP ids in sativas_GWAS.tped not present in A_Seed_weight_sativas_GWAS.ps: 0 1241s 1241s Error in file(filename, "r", encoding = encoding) : 1241s cannot open the connection 1241s Calls: source -> file 1241s In addition: Warning message: 1241s In file(filename, "r", encoding = encoding) : 1241s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1241s Execution halted 1241s cd .. 1241s Starting F_FT, pid = 6361 1241s Finished A_Seed_weight, pid = 6346, exit_code = 0 1241s cd F_grain_Cu 1241s processing phenotype F_grain_Cu... 1241s 1241s 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 1241s nmiss = 73 , mphenoflag = 1 1241s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 1241s k = 299, n-q = 299 1244s 1244s number of SNP ids in F_FT_sativas_GWAS.ps for 'F_FT' phenotype: 36901 1244s number of SNP ids in F_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_FT' phenotype: 0 1244s 1244s number of SNP ids in sativas_GWAS.tped: 36901 1244s number of SNP ids in sativas_GWAS.tped not present in F_FT_sativas_GWAS.ps: 0 1244s 1245s Error in file(filename, "r", encoding = encoding) : 1245s cannot open the connection 1245s Calls: source -> file 1245s In addition: Warning message: 1245s In file(filename, "r", encoding = encoding) : 1245s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1245s Execution halted 1245s cd .. 1245s Starting F_grain_Cu, pid = 6375 1245s Finished F_FT, pid = 6361, exit_code = 0 1245s cd A_FT 1245s processing phenotype A_FT... 1245s 1245s 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 1245s nmiss = 19 , mphenoflag = 1 1245s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.578644 1245s k = 353, n-q = 353 1245s 1245s number of SNP ids in F_grain_Cu_sativas_GWAS.ps for 'F_grain_Cu' phenotype: 36901 1245s number of SNP ids in F_grain_Cu_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Cu' phenotype: 0 1245s 1245s number of SNP ids in sativas_GWAS.tped: 36901 1245s number of SNP ids in sativas_GWAS.tped not present in F_grain_Cu_sativas_GWAS.ps: 0 1245s 1246s Error in file(filename, "r", encoding = encoding) : 1246s cannot open the connection 1246s Calls: source -> file 1246s In addition: Warning message: 1246s In file(filename, "r", encoding = encoding) : 1246s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1246s Execution halted 1246s cd .. 1246s Starting A_FT, pid = 6389 1246s Finished F_grain_Cu, pid = 6375, exit_code = 0 1246s cd A_grain_yield 1246s processing phenotype A_grain_yield... 1246s 1246s 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 1246s nmiss = 49 , mphenoflag = 1 1246s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.520537 1246s k = 323, n-q = 323 1251s 1251s number of SNP ids in A_FT_sativas_GWAS.ps for 'A_FT' phenotype: 36901 1251s number of SNP ids in A_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_FT' phenotype: 0 1251s 1251s number of SNP ids in sativas_GWAS.tped: 36901 1251s number of SNP ids in sativas_GWAS.tped not present in A_FT_sativas_GWAS.ps: 0 1251s 1251s Error in file(filename, "r", encoding = encoding) : 1251s cannot open the connection 1251s Calls: source -> file 1251s In addition: Warning message: 1251s In file(filename, "r", encoding = encoding) : 1251s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1251s Execution halted 1251s cd .. 1251s 1251s number of SNP ids in A_grain_yield_sativas_GWAS.ps for 'A_grain_yield' phenotype: 36901 1251s number of SNP ids in A_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_grain_yield' phenotype: 0 1251s 1251s number of SNP ids in sativas_GWAS.tped: 36901 1251s number of SNP ids in sativas_GWAS.tped not present in A_grain_yield_sativas_GWAS.ps: 0 1251s 1251s Starting A_grain_yield, pid = 6403 1251s Finished A_FT, pid = 6389, exit_code = 0 1251s cd Daniel_shoot_As 1251s processing phenotype Daniel_shoot_As... 1251s 1251s 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 1251s nmiss = 40 , mphenoflag = 1 1251s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.552770 1251s k = 332, n-q = 332 1251s Error in file(filename, "r", encoding = encoding) : 1251s cannot open the connection 1251s Calls: source -> file 1251s In addition: Warning message: 1251s In file(filename, "r", encoding = encoding) : 1251s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1251s Execution halted 1251s cd .. 1252s Starting Daniel_shoot_As, pid = 6423 1252s Finished A_grain_yield, pid = 6403, exit_code = 0 1252s cd H_Shoot_dry_weight 1252s processing phenotype H_Shoot_dry_weight... 1252s 1252s 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 1252s nmiss = 260 , mphenoflag = 1 1252s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 1252s k = 112, n-q = 112 1254s 1254s number of SNP ids in H_Shoot_dry_weight_sativas_GWAS.ps for 'H_Shoot_dry_weight' phenotype: 36901 1254s 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 1254s 1254s number of SNP ids in sativas_GWAS.tped: 36901 1254s number of SNP ids in sativas_GWAS.tped not present in H_Shoot_dry_weight_sativas_GWAS.ps: 0 1254s 1254s Error in file(filename, "r", encoding = encoding) : 1254s cannot open the connection 1254s Calls: source -> file 1254s In addition: Warning message: 1254s In file(filename, "r", encoding = encoding) : 1254s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1254s Execution halted 1254s cd .. 1254s Starting H_Shoot_dry_weight, pid = 6431 1254s Finished H_Shoot_dry_weight, pid = 6431, exit_code = 0 1254s cd F_grain_Mo 1254s processing phenotype F_grain_Mo... 1254s 1254s 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 1254s nmiss = 73 , mphenoflag = 1 1254s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 1254s k = 299, n-q = 299 1256s 1256s number of SNP ids in Daniel_shoot_As_sativas_GWAS.ps for 'Daniel_shoot_As' phenotype: 36901 1256s number of SNP ids in Daniel_shoot_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Daniel_shoot_As' phenotype: 0 1256s 1256s number of SNP ids in sativas_GWAS.tped: 36901 1256s number of SNP ids in sativas_GWAS.tped not present in Daniel_shoot_As_sativas_GWAS.ps: 0 1256s 1257s Error in file(filename, "r", encoding = encoding) : 1257s cannot open the connection 1257s Calls: source -> file 1257s In addition: Warning message: 1257s In file(filename, "r", encoding = encoding) : 1257s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1257s Execution halted 1257s cd .. 1257s Starting F_grain_Mo, pid = 6445 1257s Finished Daniel_shoot_As, pid = 6423, exit_code = 0 1257s cd Q_grain_Zn 1257s processing phenotype Q_grain_Zn... 1257s 1257s 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 1257s nmiss = 90 , mphenoflag = 1 1257s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 1257s k = 282, n-q = 282 1258s 1258s number of SNP ids in F_grain_Mo_sativas_GWAS.ps for 'F_grain_Mo' phenotype: 36901 1258s number of SNP ids in F_grain_Mo_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Mo' phenotype: 0 1258s 1258s number of SNP ids in sativas_GWAS.tped: 36901 1258s number of SNP ids in sativas_GWAS.tped not present in F_grain_Mo_sativas_GWAS.ps: 0 1258s 1259s Error in file(filename, "r", encoding = encoding) : 1259s cannot open the connection 1259s Calls: source -> file 1259s In addition: Warning message: 1259s In file(filename, "r", encoding = encoding) : 1259s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1259s Execution halted 1259s cd .. 1259s Starting Q_grain_Zn, pid = 6459 1259s Finished F_grain_Mo, pid = 6445, exit_code = 0 1259s cd A_Tiller_no. 1259s processing phenotype A_Tiller_no.... 1259s 1259s 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 1259s nmiss = 46 , mphenoflag = 1 1259s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.524438 1259s k = 326, n-q = 326 1261s 1261s number of SNP ids in Q_grain_Zn_sativas_GWAS.ps for 'Q_grain_Zn' phenotype: 36901 1261s number of SNP ids in Q_grain_Zn_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Zn' phenotype: 0 1261s 1261s number of SNP ids in sativas_GWAS.tped: 36901 1261s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Zn_sativas_GWAS.ps: 0 1261s 1261s Error in file(filename, "r", encoding = encoding) : 1261s cannot open the connection 1261s Calls: source -> file 1261s In addition: Warning message: 1261s In file(filename, "r", encoding = encoding) : 1261s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1261s Execution halted 1261s cd .. 1262s Starting A_Tiller_no., pid = 6473 1262s Finished Q_grain_Zn, pid = 6459, exit_code = 0 1262s cd F_As_TF 1262s processing phenotype F_As_TF... 1262s 1262s 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 1262s nmiss = 75 , mphenoflag = 1 1262s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.455247 1262s k = 297, n-q = 297 1264s 1264s number of SNP ids in A_Tiller_no._sativas_GWAS.ps for 'A_Tiller_no.' phenotype: 36901 1264s number of SNP ids in A_Tiller_no._sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Tiller_no.' phenotype: 0 1264s 1264s number of SNP ids in sativas_GWAS.tped: 36901 1264s number of SNP ids in sativas_GWAS.tped not present in A_Tiller_no._sativas_GWAS.ps: 0 1264s 1264s Error in file(filename, "r", encoding = encoding) : 1264s cannot open the connection 1264s Calls: source -> file 1264s In addition: Warning message: 1264s In file(filename, "r", encoding = encoding) : 1264s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1264s Execution halted 1264s cd .. 1265s Starting F_As_TF, pid = 6487 1265s Finished A_Tiller_no., pid = 6473, exit_code = 0 1265s cd H_Shoot_length_27 1265s processing phenotype H_Shoot_length_27... 1265s 1265s 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 1265s nmiss = 260 , mphenoflag = 1 1265s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 1265s k = 112, n-q = 112 1266s 1266s number of SNP ids in F_As_TF_sativas_GWAS.ps for 'F_As_TF' phenotype: 36901 1266s number of SNP ids in F_As_TF_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_As_TF' phenotype: 0 1266s 1266s number of SNP ids in sativas_GWAS.tped: 36901 1266s number of SNP ids in sativas_GWAS.tped not present in F_As_TF_sativas_GWAS.ps: 0 1266s 1267s 1267s number of SNP ids in H_Shoot_length_27_sativas_GWAS.ps for 'H_Shoot_length_27' phenotype: 36901 1267s 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 1267s 1267s number of SNP ids in sativas_GWAS.tped: 36901 1267s number of SNP ids in sativas_GWAS.tped not present in H_Shoot_length_27_sativas_GWAS.ps: 0 1267s 1267s Error in file(filename, "r", encoding = encoding) : 1267s cannot open the connection 1267s Calls: source -> file 1267s In addition: Warning message: 1267s In file(filename, "r", encoding = encoding) : 1267s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1267s Execution halted 1267s cd .. 1267s Error in file(filename, "r", encoding = encoding) : 1267s cannot open the connection 1267s Calls: source -> file 1267s In addition: Warning message: 1267s In file(filename, "r", encoding = encoding) : 1267s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1267s Execution halted 1267s cd .. 1267s Starting H_Shoot_length_27, pid = 6501 1267s Finished F_As_TF, pid = 6487, exit_code = 0 1267s Finished H_Shoot_length_27, pid = 6501, exit_code = 0 1267s Starting A_Seed_length, pid = 6527 1267s cd A_Seed_length 1267s processing phenotype A_Seed_length... 1267s 1267s 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 1267s cd Q_grain_Mo 1267s processing phenotype Q_grain_Mo... 1267s 1267s 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 1267s nmiss = 20 , mphenoflag = 1 1267s nmiss = 90 , mphenoflag = 1 1267s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 1267s k = 282, n-q = 282 1267s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.577637 1267s k = 352, n-q = 352 1271s 1271s number of SNP ids in Q_grain_Mo_sativas_GWAS.ps for 'Q_grain_Mo' phenotype: 36901 1271s number of SNP ids in Q_grain_Mo_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Mo' phenotype: 0 1271s 1271s number of SNP ids in sativas_GWAS.tped: 36901 1271s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Mo_sativas_GWAS.ps: 0 1271s 1271s Error in file(filename, "r", encoding = encoding) : 1271s cannot open the connection 1271s Calls: source -> file 1271s In addition: Warning message: 1271s In file(filename, "r", encoding = encoding) : 1271s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1271s Execution halted 1271s cd .. 1272s Starting Q_grain_Mo, pid = 6528 1272s Finished Q_grain_Mo, pid = 6528, exit_code = 0 1272s cd A_PH 1272s processing phenotype A_PH... 1272s 1272s 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 1272s nmiss = 29 , mphenoflag = 1 1272s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.570052 1272s k = 343, n-q = 343 1273s 1273s number of SNP ids in A_Seed_length_sativas_GWAS.ps for 'A_Seed_length' phenotype: 36901 1273s number of SNP ids in A_Seed_length_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Seed_length' phenotype: 0 1273s 1273s number of SNP ids in sativas_GWAS.tped: 36901 1273s number of SNP ids in sativas_GWAS.tped not present in A_Seed_length_sativas_GWAS.ps: 0 1273s 1273s Error in file(filename, "r", encoding = encoding) : 1273s cannot open the connection 1273s Calls: source -> file 1273s In addition: Warning message: 1273s In file(filename, "r", encoding = encoding) : 1273s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1273s Execution halted 1273s cd .. 1274s Starting A_PH, pid = 6543 1274s Finished A_Seed_length, pid = 6527, exit_code = 0 1274s cd HULLED_SEED_LENGTH 1274s processing phenotype HULLED_SEED_LENGTH... 1274s 1274s 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 1274s nmiss = 34 , mphenoflag = 1 1274s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.481982 1274s k = 338, n-q = 338 1278s 1278s number of SNP ids in A_PH_sativas_GWAS.ps for 'A_PH' phenotype: 36901 1278s number of SNP ids in A_PH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_PH' phenotype: 0 1278s 1278s number of SNP ids in sativas_GWAS.tped: 36901 1278s number of SNP ids in sativas_GWAS.tped not present in A_PH_sativas_GWAS.ps: 0 1278s 1278s Error in file(filename, "r", encoding = encoding) : 1278s cannot open the connection 1278s Calls: source -> file 1278s In addition: Warning message: 1278s In file(filename, "r", encoding = encoding) : 1278s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1278s Execution halted 1278s cd .. 1278s Starting HULLED_SEED_LENGTH, pid = 6557 1278s Finished A_PH, pid = 6543, exit_code = 0 1278s cd Q_PH 1278s processing phenotype Q_PH... 1278s 1278s 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 1278s nmiss = 87 , mphenoflag = 1 1278s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.413538 1278s k = 285, n-q = 285 1279s 1279s number of SNP ids in HULLED_SEED_LENGTH_sativas_GWAS.ps for 'HULLED_SEED_LENGTH' phenotype: 36901 1279s number of SNP ids in HULLED_SEED_LENGTH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'HULLED_SEED_LENGTH' phenotype: 0 1279s 1279s number of SNP ids in sativas_GWAS.tped: 36901 1279s number of SNP ids in sativas_GWAS.tped not present in HULLED_SEED_LENGTH_sativas_GWAS.ps: 0 1279s 1280s Error in file(filename, "r", encoding = encoding) : 1280s cannot open the connection 1280s Calls: source -> file 1280s In addition: Warning message: 1280s In file(filename, "r", encoding = encoding) : 1280s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1280s Execution halted 1280s cd .. 1280s Starting Q_PH, pid = 6571 1280s Finished HULLED_SEED_LENGTH, pid = 6557, exit_code = 0 1280s cd India_grain_As 1280s processing phenotype India_grain_As... 1280s 1280s 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 1280s nmiss = 280 , mphenoflag = 1 1280s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.487105 1280s k = 92, n-q = 92 1282s 1282s number of SNP ids in India_grain_As_sativas_GWAS.ps for 'India_grain_As' phenotype: 36901 1282s number of SNP ids in India_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'India_grain_As' phenotype: 0 1282s 1282s number of SNP ids in sativas_GWAS.tped: 36901 1282s number of SNP ids in sativas_GWAS.tped not present in India_grain_As_sativas_GWAS.ps: 0 1282s 1282s Error in file(filename, "r", encoding = encoding) : 1282s cannot open the connection 1282s Calls: source -> file 1282s In addition: Warning message: 1282s In file(filename, "r", encoding = encoding) : 1282s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1282s Execution halted 1282s cd .. 1282s Starting India_grain_As, pid = 6585 1282s Finished India_grain_As, pid = 6585, exit_code = 0 1282s cd Amylose_Content 1282s processing phenotype Amylose_Content... 1282s 1282s 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 1282s nmiss = 50 , mphenoflag = 1 1282s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.447865 1282s k = 322, n-q = 322 1282s 1282s number of SNP ids in Q_PH_sativas_GWAS.ps for 'Q_PH' phenotype: 36901 1282s number of SNP ids in Q_PH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_PH' phenotype: 0 1282s 1282s number of SNP ids in sativas_GWAS.tped: 36901 1282s number of SNP ids in sativas_GWAS.tped not present in Q_PH_sativas_GWAS.ps: 0 1282s 1283s Error in file(filename, "r", encoding = encoding) : 1283s cannot open the connection 1283s Calls: source -> file 1283s In addition: Warning message: 1283s In file(filename, "r", encoding = encoding) : 1283s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1283s Execution halted 1283s cd .. 1283s Starting Amylose_Content, pid = 6599 1283s Finished Q_PH, pid = 6571, exit_code = 0 1283s cd Q_grain_yield 1283s processing phenotype Q_grain_yield... 1283s 1283s 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 1283s nmiss = 91 , mphenoflag = 1 1283s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.399146 1283s k = 281, n-q = 281 1287s 1287s number of SNP ids in Amylose_Content_sativas_GWAS.ps for 'Amylose_Content' phenotype: 36901 1287s number of SNP ids in Amylose_Content_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Amylose_Content' phenotype: 0 1287s 1287s number of SNP ids in sativas_GWAS.tped: 36901 1287s number of SNP ids in sativas_GWAS.tped not present in Amylose_Content_sativas_GWAS.ps: 0 1287s 1287s 1287s number of SNP ids in Q_grain_yield_sativas_GWAS.ps for 'Q_grain_yield' phenotype: 36901 1287s number of SNP ids in Q_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_yield' phenotype: 0 1287s 1287s number of SNP ids in sativas_GWAS.tped: 36901 1287s number of SNP ids in sativas_GWAS.tped not present in Q_grain_yield_sativas_GWAS.ps: 0 1287s 1287s Error in file(filename, "r", encoding = encoding) : 1287s cannot open the connection 1287s Calls: source -> file 1287s In addition: Warning message: 1287s In file(filename, "r", encoding = encoding) : 1287s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1287s Execution halted 1287s cd .. 1287s Error in file(filename, "r", encoding = encoding) : 1287s cannot open the connection 1287s Calls: source -> file 1287s In addition: Warning message: 1287s In file(filename, "r", encoding = encoding) : 1287s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 1287s Execution halted 1288s cd .. 1288s Starting Q_grain_yield, pid = 6613 1288s Finished Amylose_Content, pid = 6599, exit_code = 0 1288s Finished Q_grain_yield, pid = 6613, exit_code = 0 1288s Analysis complete 1288s 1288s autopkgtest [01:02:05]: test run-unit-test: -----------------------] 1289s autopkgtest [01:02:06]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1289s run-unit-test PASS 1289s autopkgtest [01:02:06]: @@@@@@@@@@@@@@@@@@@@ summary 1289s run-unit-test PASS 1307s Creating nova instance adt-noble-i386-pique-20240322-004037-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240321.img (UUID 6f9effbc-61d8-4d0a-a7e9-883547f42ac1)...