0s autopkgtest [17:18:03]: starting date and time: 2024-03-16 17:18:03+0000 1s autopkgtest [17:18:04]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 1s autopkgtest [17:18:04]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.38q04igc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade pique --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-9.secgroup --name adt-noble-arm64-pique-20240316-171803-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 86s autopkgtest [17:19:29]: testbed dpkg architecture: arm64 86s autopkgtest [17:19:29]: testbed apt version: 2.7.12 86s autopkgtest [17:19:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 87s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 87s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 88s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 88s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 88s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 88s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 88s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 88s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 88s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 88s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 88s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 88s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 88s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 91s Fetched 9063 kB in 2s (3748 kB/s) 91s Reading package lists... 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 95s The following packages will be REMOVED: 95s libglib2.0-0 libssl3 95s The following NEW packages will be installed: 95s libglib2.0-0t64 libssl3t64 xdg-user-dirs 95s The following packages have been kept back: 95s curl 95s The following packages will be upgraded: 95s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 95s ubuntu-minimal ubuntu-standard 95s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 95s Need to get 4613 kB of archives. 95s After this operation, 211 kB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 95s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 96s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 96s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 96s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 96s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 96s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 96s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 96s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 96s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 96s Fetched 4613 kB in 1s (6404 kB/s) 96s (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 ... 74758 files and directories currently installed.) 96s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 96s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 96s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 96s udisks2 depends on libglib2.0-0 (>= 2.77.0). 96s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 96s python3-gi depends on libglib2.0-0 (>= 2.77.0). 96s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 96s netplan.io depends on libglib2.0-0 (>= 2.70.0). 96s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 96s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 96s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 96s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 96s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 96s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 96s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 96s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 96s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 96s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 96s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 96s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 96s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 96s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 96s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 96s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 96s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 96s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 96s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 96s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 96s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 96s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 96s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 96s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 96s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 96s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 96s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 96s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 96s fwupd depends on libglib2.0-0 (>= 2.79.0). 96s bolt depends on libglib2.0-0 (>= 2.56.0). 96s 97s (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 ... 74758 files and directories currently installed.) 97s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 97s Selecting previously unselected package libglib2.0-0t64:arm64. 97s (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 ... 74733 files and directories currently installed.) 97s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 97s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 97s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 97s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 97s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 97s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 97s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 97s wget depends on libssl3 (>= 3.0.0). 97s u-boot-tools depends on libssl3 (>= 3.0.0). 97s tnftp depends on libssl3 (>= 3.0.0). 97s tcpdump depends on libssl3 (>= 3.0.0). 97s systemd-resolved depends on libssl3 (>= 3.0.0). 97s systemd depends on libssl3 (>= 3.0.0). 97s sudo depends on libssl3 (>= 3.0.0). 97s sbsigntool depends on libssl3 (>= 3.0.0). 97s rsync depends on libssl3 (>= 3.0.0). 97s python3-cryptography depends on libssl3 (>= 3.0.0). 97s openssh-server depends on libssl3 (>= 3.0.10). 97s openssh-client depends on libssl3 (>= 3.0.10). 97s mtd-utils depends on libssl3 (>= 3.0.0). 97s mokutil depends on libssl3 (>= 3.0.0). 97s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 97s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 97s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 97s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 97s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 97s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 97s libnvme1 depends on libssl3 (>= 3.0.0). 97s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 97s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 97s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 97s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 97s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 97s kmod depends on libssl3 (>= 3.0.0). 97s dhcpcd-base depends on libssl3 (>= 3.0.0). 97s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 97s 97s (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 ... 74758 files and directories currently installed.) 97s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 97s Selecting previously unselected package libssl3t64:arm64. 97s (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 ... 74747 files and directories currently installed.) 97s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 97s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 97s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 97s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 97s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 97s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 97s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 97s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 97s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 97s Unpacking ubuntu-minimal (1.536) over (1.535) ... 97s Selecting previously unselected package xdg-user-dirs. 97s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 97s Unpacking xdg-user-dirs (0.18-1) ... 97s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 97s Unpacking ubuntu-standard (1.536) over (1.535) ... 97s Setting up ubuntu-minimal (1.536) ... 97s Setting up xdg-user-dirs (0.18-1) ... 97s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 97s Setting up libtirpc-common (1.3.4+ds-1.1) ... 97s Setting up ubuntu-standard (1.536) ... 97s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 97s No schema files found: doing nothing. 97s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 97s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 97s Setting up openssl (3.0.13-0ubuntu1) ... 97s Setting up readline-common (8.2-3.1) ... 97s Processing triggers for man-db (2.12.0-3) ... 98s Processing triggers for install-info (7.1-3) ... 98s Processing triggers for libc-bin (2.39-0ubuntu2) ... 98s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 100s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 100s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 100s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 100s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 102s Reading package lists... 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s Calculating upgrade... 103s The following packages have been kept back: 103s curl 103s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 107s autopkgtest [17:19:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 107s autopkgtest [17:19:50]: @@@@@@@@@@@@@@@@@@@@ apt-source pique 110s Get:1 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (dsc) [2005 B] 110s Get:2 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (tar) [2017 kB] 110s Get:3 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (diff) [5236 B] 110s gpgv: Signature made Tue Dec 12 20:17:37 2023 UTC 110s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 110s gpgv: issuer "tille@debian.org" 110s gpgv: Can't check signature: No public key 110s dpkg-source: warning: cannot verify inline signature for ./pique_1.0-7.dsc: no acceptable signature found 110s autopkgtest [17:19:53]: testing package pique version 1.0-7 110s autopkgtest [17:19:53]: build not needed 111s autopkgtest [17:19:54]: test run-unit-test: preparing testbed 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s Starting pkgProblemResolver with broken count: 0 115s Starting 2 pkgProblemResolver with broken count: 0 115s Done 115s The following additional packages will be installed: 115s curl eigensoft emmax fontconfig fontconfig-config fonts-dejavu-core 115s fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings 115s fonts-mathjax javascript-common libb-hooks-op-check-perl libblas3 libcairo2 115s libclass-method-modifiers-perl libclass-xsaccessor-perl libcurl4t64 115s libdatrie1 libdeflate0 libdevel-callchecker-perl 115s libdynaloader-functions-perl libfile-slurp-perl libfontconfig1 libgfortran5 115s libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libice6 115s libimport-into-perl libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 115s libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery 115s libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json 115s libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js 115s libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 115s liblapacke liblerc4 liblua5.4-0 libmodule-runtime-perl libmoo-perl 115s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 115s libpaper1 libparallel-forkmanager-perl libparams-classify-perl libpixman-1-0 115s libpng16-16t64 libpsl5t64 libreadline8t64 libreadonly-perl librole-tiny-perl 115s libsharpyuv0 libsm6 libsub-quote-perl libtcl8.6 libthai-data libthai0 115s libtiff6 libtirpc3t64 libtk8.6 libtmglib3 libwebp7 libxcb-render0 115s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler 115s node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data 115s pique pique-doc plink r-base-core r-bioc-biobase r-bioc-biocgenerics 115s r-bioc-multtest r-cran-acepack r-cran-backports r-cran-base64enc 115s r-cran-bslib r-cran-cachem r-cran-checkmate r-cran-chron r-cran-cli 115s r-cran-cluster r-cran-colorspace r-cran-commonmark r-cran-cpp11 115s r-cran-crayon r-cran-curl r-cran-data.table r-cran-deldir r-cran-digest 115s r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 115s r-cran-fastmap r-cran-fontawesome r-cran-forecast r-cran-foreign 115s r-cran-formula r-cran-fracdiff r-cran-fs r-cran-generics r-cran-getopt 115s r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-highr 115s r-cran-hmisc r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets 115s r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg r-cran-jquerylib 115s r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later r-cran-lattice 115s r-cran-latticeextra r-cran-lifecycle r-cran-littler r-cran-lmtest 115s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-memoise r-cran-mgcv 115s r-cran-mime r-cran-munsell r-cran-nlme r-cran-nnet r-cran-optparse 115s r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-png r-cran-promises 115s r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 r-cran-rappdirs 115s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen 115s r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass 115s r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr 115s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timedate 115s r-cran-tinytex r-cran-tseries r-cran-ttr r-cran-urca r-cran-uroot 115s r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr 115s r-cran-xfun r-cran-xtable r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common 115s xdg-utils zip 115s Suggested packages: 115s apache2 | lighttpd | httpd gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info 115s | gsl-ref-html libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix 115s libjs-mathjax-doc libscalar-number-perl libxstring-perl tcl8.6 tk8.6 nodejs 115s texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc 115s texlive-latex-extra context wkhtmltopdf librsvg2-bin groff ghc php python 115s ruby libjs-katex citation-style-language-styles elpa-ess r-doc-info 115s | r-doc-pdf r-mathlib r-base-html r-bioc-all r-cran-runit r-bioc-biocstyle 115s r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray 115s r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy 115s r-bioc-deseq2 r-bioc-annotate r-cran-snow r-cran-kernsmooth r-cran-kernlab 115s r-cran-mvtnorm r-cran-vcd r-cran-shinyjs r-cran-polyclip r-cran-covr 115s r-cran-markdown r-cran-sp r-cran-scatterplot3d r-cran-magick r-cran-sf 115s r-cran-testthat r-cran-httr r-cran-bit64 r-cran-dbi r-cran-formattable 115s r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-vdiffr 115s r-cran-roxygen2 r-cran-inline r-cran-bench r-cran-blob r-cran-brio 115s r-cran-callr r-cran-here r-cran-hms r-cran-pkgbuild r-cran-pkgload 115s r-cran-plm 115s Recommended packages: 115s gnuplot node-jquery libnamespace-clean-perl med-config r-recommended 115s r-base-dev r-doc-html r-cran-testthat r-cran-thematic r-cran-fastmatch 115s r-cran-devtools r-cran-tinytest r-cran-callr r-cran-covr r-cran-mockery 115s r-cran-processx r-cran-ps r-cran-rprojroot r-cran-whoami r-cran-xml2 115s r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr 115s r-cran-progress r-cran-spelling r-cran-webutils r-cran-bit64 r-cran-bit 115s r-cran-r.utils r-cran-nanotime r-cran-broom r-cran-dbi r-cran-dbplyr 115s r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite r-cran-unitizer r-cran-rsvg 115s r-cran-pkgload r-cran-hexbin r-cran-mapproj r-cran-maps r-cran-multcomp 115s r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-sf r-cran-svglite 115s r-cran-vdiffr r-cran-waldo r-cran-testit r-cran-cairo r-cran-markdown 115s r-cran-httr r-cran-r.rsp r-cran-codetools r-cran-formatr r-cran-gridsvg 115s r-cran-magick r-cran-reticulate r-cran-rgl r-cran-tikzdevice r-cran-webshot 115s node-highlight.js r-cran-lintr r-cran-tidyverse r-cran-lubridate 115s r-cran-future r-cran-usethis r-cran-dygraphs r-cran-rsconnect r-cran-downlit 115s r-cran-dichromat r-cran-hms r-cran-mockr r-cran-formattable r-cran-readr 115s r-cran-pkgdown r-cran-zeallot r-cran-remotes r-cran-renv r-cran-timeseries 115s r-cran-runit libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl 115s x11-utils x11-xserver-utils 115s The following packages will be REMOVED: 115s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 115s The following NEW packages will be installed: 115s autopkgtest-satdep eigensoft emmax fontconfig fontconfig-config 115s fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 115s fonts-glyphicons-halflings fonts-mathjax javascript-common 115s libb-hooks-op-check-perl libblas3 libcairo2 libclass-method-modifiers-perl 115s libclass-xsaccessor-perl libcurl4t64 libdatrie1 libdeflate0 115s libdevel-callchecker-perl libdynaloader-functions-perl libfile-slurp-perl 115s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 115s libharfbuzz0b libice6 libimport-into-perl libjbig0 libjpeg-turbo8 libjpeg8 115s libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js 115s libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js 115s libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js 115s libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js 115s libjs-twitter-bootstrap-datepicker liblapack3 liblapacke liblerc4 115s liblua5.4-0 libmodule-runtime-perl libmoo-perl libpango-1.0-0 115s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 115s libparallel-forkmanager-perl libparams-classify-perl libpixman-1-0 115s libpng16-16t64 libpsl5t64 libreadline8t64 libreadonly-perl librole-tiny-perl 115s libsharpyuv0 libsm6 libsub-quote-perl libtcl8.6 libthai-data libthai0 115s libtiff6 libtirpc3t64 libtk8.6 libtmglib3 libwebp7 libxcb-render0 115s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler 115s node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data 115s pique pique-doc plink r-base-core r-bioc-biobase r-bioc-biocgenerics 115s r-bioc-multtest r-cran-acepack r-cran-backports r-cran-base64enc 115s r-cran-bslib r-cran-cachem r-cran-checkmate r-cran-chron r-cran-cli 115s r-cran-cluster r-cran-colorspace r-cran-commonmark r-cran-cpp11 115s r-cran-crayon r-cran-curl r-cran-data.table r-cran-deldir r-cran-digest 115s r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 115s r-cran-fastmap r-cran-fontawesome r-cran-forecast r-cran-foreign 115s r-cran-formula r-cran-fracdiff r-cran-fs r-cran-generics r-cran-getopt 115s r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-highr 115s r-cran-hmisc r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets 115s r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg r-cran-jquerylib 115s r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later r-cran-lattice 115s r-cran-latticeextra r-cran-lifecycle r-cran-littler r-cran-lmtest 115s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-memoise r-cran-mgcv 115s r-cran-mime r-cran-munsell r-cran-nlme r-cran-nnet r-cran-optparse 115s r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-png r-cran-promises 115s r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 r-cran-rappdirs 115s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen 115s r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass 115s r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr 115s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timedate 115s r-cran-tinytex r-cran-tseries r-cran-ttr r-cran-urca r-cran-uroot 115s r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr 115s r-cran-xfun r-cran-xtable r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common 115s xdg-utils zip 116s The following packages will be upgraded: 116s curl 116s 1 upgraded, 212 newly installed, 5 to remove and 0 not upgraded. 116s Need to get 173 MB/173 MB of archives. 116s After this operation, 539 MB of additional disk space will be used. 116s Get:1 /tmp/autopkgtest.fRe5Yn/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 116s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 116s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 116s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 116s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 116s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 116s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 116s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 116s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 116s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 116s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 116s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 116s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libtmglib3 arm64 3.12.0-3 [112 kB] 116s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 liblapacke arm64 3.12.0-3 [427 kB] 116s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 eigensoft arm64 8.0.0+dfsg-2 [318 kB] 116s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 emmax arm64 0~beta.20100307-5 [29.9 kB] 116s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 116s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 116s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 116s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 116s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 116s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 116s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 116s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 116s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 javascript-common all 11+nmu1 [5936 B] 116s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libb-hooks-op-check-perl arm64 0.22-2build2 [9220 B] 116s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 116s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 116s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 116s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 116s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 117s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libclass-method-modifiers-perl all 2.15-1 [16.1 kB] 117s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libclass-xsaccessor-perl arm64 1.19-4build2 [33.1 kB] 117s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 117s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 117s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libdynaloader-functions-perl all 0.003-3 [12.1 kB] 117s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libdevel-callchecker-perl arm64 0.008-2build1 [13.7 kB] 117s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 libfile-slurp-perl all 9999.32-2 [21.7 kB] 117s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 117s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 117s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 117s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 117s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 117s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libparams-classify-perl arm64 0.015-2build3 [19.6 kB] 117s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libmodule-runtime-perl all 0.016-2 [16.4 kB] 117s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libimport-into-perl all 1.002005-2 [10.7 kB] 117s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 117s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 117s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 117s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB] 117s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB] 117s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-d3 all 3.5.17-4 [132 kB] 117s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-es5-shim all 4.6.7-2 [39.8 kB] 117s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 117s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 117s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 117s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 117s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B] 117s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 117s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 117s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB] 117s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB] 117s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 117s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 liblua5.4-0 arm64 5.4.6-3 [158 kB] 117s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 librole-tiny-perl all 2.002004-1 [16.3 kB] 117s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-quote-perl all 2.006008-1ubuntu1 [20.7 kB] 117s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libmoo-perl all 2.005005-1 [47.4 kB] 117s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 117s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 117s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 117s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 117s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 117s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 117s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 117s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 libparallel-forkmanager-perl all 2.02-1 [27.7 kB] 117s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 libreadonly-perl all 2.050-3 [19.9 kB] 117s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 117s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 117s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 117s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 117s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 117s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 117s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 117s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 117s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 117s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 117s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 117s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 117s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 117s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 118s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 118s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 118s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 node-bootstrap-sass all 3.4.3-2 [187 kB] 118s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 118s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 118s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc-data all 3.1.3-1 [92.4 kB] 118s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc arm64 3.1.3+ds-2 [27.7 MB] 119s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 plink arm64 1.07+dfsg-4 [1005 kB] 119s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-getopt all 1.20.4-1 [38.4 kB] 119s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB] 119s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fracdiff arm64 1.5-3-1 [108 kB] 119s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 119s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 120s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 120s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 120s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 120s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 120s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 120s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 120s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 120s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 120s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 120s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 120s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB] 120s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 120s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] 120s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 120s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 120s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 120s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 120s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 120s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 120s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 120s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 120s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 120s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 120s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 120s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 120s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 120s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-zoo arm64 1.8-12-2 [984 kB] 120s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lmtest arm64 0.9.40-1 [396 kB] 121s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nnet arm64 7.3-19-2 [111 kB] 121s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 121s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 121s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-timedate arm64 4032.109-1 [1229 kB] 121s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-quadprog arm64 1.5-8-1build1 [29.8 kB] 121s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xts arm64 0.13.2-1 [770 kB] 121s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-curl arm64 5.2.0+dfsg-1 [189 kB] 121s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ttr arm64 0.24.4-1 [509 kB] 121s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB] 121s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-quantmod all 0.4.26-1 [1027 kB] 121s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tseries arm64 0.10-55-1 [367 kB] 121s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-urca arm64 1.3-3-1 [1071 kB] 121s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpparmadillo arm64 0.12.8.0.0-1 [859 kB] 121s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-forecast arm64 8.21.1-1 [1547 kB] 121s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocgenerics all 0.48.1-2 [595 kB] 121s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biobase arm64 2.62.0-1 [2136 kB] 121s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 121s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-multtest arm64 2.58.0-1 [836 kB] 121s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-optparse all 1.7.4-1 [81.6 kB] 121s Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-uroot all 2.1-3-1 [1927 kB] 121s Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 pique all 1.0-7 [21.3 kB] 121s Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 pique-doc all 1.0-7 [1931 kB] 121s Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-acepack arm64 1.4.2-1 [60.5 kB] 121s Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-backports arm64 1.4.1-1 [101 kB] 121s Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-base64enc arm64 0.1-3-3 [27.4 kB] 121s Get:157 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fastmap arm64 1.1.1-1 [69.6 kB] 121s Get:158 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cachem arm64 1.0.8-1 [72.3 kB] 121s Get:159 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB] 121s Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 121s Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmltools arm64 0.5.7-1 [369 kB] 121s Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB] 122s Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB] 122s Get:164 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mime arm64 0.12-1 [35.8 kB] 122s Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fs arm64 1.6.3+dfsg-1 [227 kB] 122s Get:166 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rappdirs arm64 0.3.3-1 [47.5 kB] 122s Get:167 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sass arm64 0.4.8+dfsg-1 [952 kB] 122s Get:168 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bslib all 0.6.1+dfsg-1 [5138 kB] 122s Get:169 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-checkmate arm64 2.3.1-1 [711 kB] 122s Get:170 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-chron arm64 2.3-61-2 [186 kB] 122s Get:171 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cluster arm64 2.1.6-1 [552 kB] 122s Get:172 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-commonmark arm64 1.9.1-1 [127 kB] 122s Get:173 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB] 122s Get:174 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB] 122s Get:175 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-data.table arm64 1.14.10+dfsg-1 [1844 kB] 122s Get:176 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-deldir arm64 2.0-4-1 [270 kB] 122s Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB] 122s Get:178 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB] 122s Get:179 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB] 122s Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fontawesome all 0.5.2-1 [1300 kB] 122s Get:181 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreign arm64 0.8.86-1 [240 kB] 122s Get:182 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-formula all 1.2-5-1 [158 kB] 122s Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gridextra all 2.3-3build1 [1024 kB] 122s Get:184 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xfun arm64 0.41+dfsg-1 [415 kB] 122s Get:185 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-highr all 0.10+dfsg-1 [38.3 kB] 122s Get:186 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB] 122s Get:187 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB] 122s Get:188 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 122s Get:189 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-yaml arm64 2.3.8-1 [107 kB] 122s Get:190 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 122s Get:191 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-knitr all 1.45+dfsg-1 [917 kB] 122s Get:192 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tinytex all 0.49-1 [141 kB] 122s Get:193 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-modernizr all 2.6.2+ds1-5 [48.3 kB] 122s Get:194 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-later arm64 1.3.2+dfsg-1 [120 kB] 122s Get:195 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-promises arm64 1.2.1+dfsg-1 [282 kB] 122s Get:196 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-httpuv arm64 1.6.14+dfsg-1 [496 kB] 122s Get:197 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB] 122s Get:198 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sourcetools arm64 0.1.7-1-1 [47.2 kB] 122s Get:199 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 122s Get:200 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-shiny all 1.8.0+dfsg-1 [2762 kB] 123s Get:201 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rmarkdown all 2.25+dfsg-3 [1481 kB] 123s Get:202 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] 123s Get:203 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rstudioapi all 0.15.0-1 [277 kB] 123s Get:204 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB] 123s Get:205 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 123s Get:206 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmltable all 2.4.2-1 [381 kB] 123s Get:207 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridis all 0.6.5-1 [2770 kB] 123s Get:208 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-png arm64 0.1-8-1 [39.9 kB] 123s Get:209 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jpeg arm64 0.1-10-1 [30.8 kB] 123s Get:210 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 123s Get:211 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-interp arm64 1.1-6-1 [1433 kB] 123s Get:212 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-latticeextra all 0.6-30-1 [2198 kB] 123s Get:213 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-hmisc arm64 5.1-1-1 [3486 kB] 125s Preconfiguring packages ... 125s Fetched 173 MB in 8s (21.3 MB/s) 125s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 125s wget depends on libpsl5 (>= 0.16.0). 125s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 125s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 125s 125s (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 ... 74774 files and directories currently installed.) 125s Removing libpsl5:arm64 (0.21.2-1build1) ... 125s Selecting previously unselected package libpsl5t64:arm64. 125s (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 ... 74769 files and directories currently installed.) 125s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 125s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 125s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 125s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 125s (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 ... 74775 files and directories currently installed.) 125s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 125s Selecting previously unselected package libcurl4t64:arm64. 125s (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 ... 74770 files and directories currently installed.) 125s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 125s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 125s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 125s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 125s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 125s 125s (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 ... 74776 files and directories currently installed.) 125s Removing libpng16-16:arm64 (1.6.43-1) ... 125s Selecting previously unselected package libpng16-16t64:arm64. 125s (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 ... 74766 files and directories currently installed.) 125s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 125s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 125s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 125s parted depends on libreadline8 (>= 6.0). 125s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 125s gpgsm depends on libreadline8 (>= 6.0). 125s gpgconf depends on libreadline8 (>= 6.0). 125s gpg depends on libreadline8 (>= 6.0). 125s gawk depends on libreadline8 (>= 6.0). 125s fdisk depends on libreadline8 (>= 6.0). 125s 125s (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 ... 74777 files and directories currently installed.) 125s Removing libreadline8:arm64 (8.2-3) ... 125s Selecting previously unselected package libreadline8t64:arm64. 125s (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 ... 74765 files and directories currently installed.) 125s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 125s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 125s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 125s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 125s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 125s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 125s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 125s lsof depends on libtirpc3 (>= 1.0.2). 125s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 125s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 125s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 125s iproute2 depends on libtirpc3 (>= 1.0.2). 125s 125s (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 ... 74785 files and directories currently installed.) 125s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 126s Selecting previously unselected package libtirpc3t64:arm64. 126s (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 ... 74779 files and directories currently installed.) 126s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 126s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 126s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 126s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 126s Selecting previously unselected package libblas3:arm64. 126s Preparing to unpack .../001-libblas3_3.12.0-3_arm64.deb ... 126s Unpacking libblas3:arm64 (3.12.0-3) ... 126s Selecting previously unselected package libgslcblas0:arm64. 126s Preparing to unpack .../002-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 126s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 126s Selecting previously unselected package libgsl27:arm64. 126s Preparing to unpack .../003-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 126s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 126s Selecting previously unselected package libgfortran5:arm64. 126s Preparing to unpack .../004-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 126s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 126s Selecting previously unselected package liblapack3:arm64. 126s Preparing to unpack .../005-liblapack3_3.12.0-3_arm64.deb ... 126s Unpacking liblapack3:arm64 (3.12.0-3) ... 126s Selecting previously unselected package libtmglib3:arm64. 126s Preparing to unpack .../006-libtmglib3_3.12.0-3_arm64.deb ... 126s Unpacking libtmglib3:arm64 (3.12.0-3) ... 126s Selecting previously unselected package liblapacke:arm64. 126s Preparing to unpack .../007-liblapacke_3.12.0-3_arm64.deb ... 126s Unpacking liblapacke:arm64 (3.12.0-3) ... 126s Selecting previously unselected package eigensoft. 126s Preparing to unpack .../008-eigensoft_8.0.0+dfsg-2_arm64.deb ... 126s Unpacking eigensoft (8.0.0+dfsg-2) ... 126s Selecting previously unselected package emmax. 126s Preparing to unpack .../009-emmax_0~beta.20100307-5_arm64.deb ... 126s Unpacking emmax (0~beta.20100307-5) ... 126s Selecting previously unselected package fonts-dejavu-mono. 126s Preparing to unpack .../010-fonts-dejavu-mono_2.37-8_all.deb ... 126s Unpacking fonts-dejavu-mono (2.37-8) ... 126s Selecting previously unselected package fonts-dejavu-core. 126s Preparing to unpack .../011-fonts-dejavu-core_2.37-8_all.deb ... 126s Unpacking fonts-dejavu-core (2.37-8) ... 126s Selecting previously unselected package fontconfig-config. 126s Preparing to unpack .../012-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 127s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 128s Selecting previously unselected package libfontconfig1:arm64. 128s Preparing to unpack .../013-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 128s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 128s Selecting previously unselected package fontconfig. 128s Preparing to unpack .../014-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 128s Unpacking fontconfig (2.15.0-1ubuntu1) ... 128s Selecting previously unselected package fonts-font-awesome. 128s Preparing to unpack .../015-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 128s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 128s Selecting previously unselected package fonts-glyphicons-halflings. 128s Preparing to unpack .../016-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 128s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 128s Selecting previously unselected package fonts-mathjax. 128s Preparing to unpack .../017-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 128s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 128s Selecting previously unselected package javascript-common. 128s Preparing to unpack .../018-javascript-common_11+nmu1_all.deb ... 128s Unpacking javascript-common (11+nmu1) ... 128s Selecting previously unselected package libb-hooks-op-check-perl:arm64. 128s Preparing to unpack .../019-libb-hooks-op-check-perl_0.22-2build2_arm64.deb ... 128s Unpacking libb-hooks-op-check-perl:arm64 (0.22-2build2) ... 128s Selecting previously unselected package libpixman-1-0:arm64. 128s Preparing to unpack .../020-libpixman-1-0_0.42.2-1_arm64.deb ... 128s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 128s Selecting previously unselected package libxcb-render0:arm64. 128s Preparing to unpack .../021-libxcb-render0_1.15-1_arm64.deb ... 128s Unpacking libxcb-render0:arm64 (1.15-1) ... 128s Selecting previously unselected package libxcb-shm0:arm64. 128s Preparing to unpack .../022-libxcb-shm0_1.15-1_arm64.deb ... 128s Unpacking libxcb-shm0:arm64 (1.15-1) ... 128s Selecting previously unselected package libxrender1:arm64. 128s Preparing to unpack .../023-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 128s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 128s Selecting previously unselected package libcairo2:arm64. 128s Preparing to unpack .../024-libcairo2_1.18.0-1_arm64.deb ... 128s Unpacking libcairo2:arm64 (1.18.0-1) ... 128s Selecting previously unselected package libclass-method-modifiers-perl. 128s Preparing to unpack .../025-libclass-method-modifiers-perl_2.15-1_all.deb ... 128s Unpacking libclass-method-modifiers-perl (2.15-1) ... 128s Selecting previously unselected package libclass-xsaccessor-perl. 128s Preparing to unpack .../026-libclass-xsaccessor-perl_1.19-4build2_arm64.deb ... 128s Unpacking libclass-xsaccessor-perl (1.19-4build2) ... 128s Selecting previously unselected package libdatrie1:arm64. 128s Preparing to unpack .../027-libdatrie1_0.2.13-3_arm64.deb ... 128s Unpacking libdatrie1:arm64 (0.2.13-3) ... 128s Selecting previously unselected package libdeflate0:arm64. 128s Preparing to unpack .../028-libdeflate0_1.19-1_arm64.deb ... 128s Unpacking libdeflate0:arm64 (1.19-1) ... 128s Selecting previously unselected package libdynaloader-functions-perl. 128s Preparing to unpack .../029-libdynaloader-functions-perl_0.003-3_all.deb ... 128s Unpacking libdynaloader-functions-perl (0.003-3) ... 129s Selecting previously unselected package libdevel-callchecker-perl:arm64. 129s Preparing to unpack .../030-libdevel-callchecker-perl_0.008-2build1_arm64.deb ... 129s Unpacking libdevel-callchecker-perl:arm64 (0.008-2build1) ... 129s Selecting previously unselected package libfile-slurp-perl. 129s Preparing to unpack .../031-libfile-slurp-perl_9999.32-2_all.deb ... 129s Unpacking libfile-slurp-perl (9999.32-2) ... 129s Selecting previously unselected package libgomp1:arm64. 129s Preparing to unpack .../032-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 129s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 129s Selecting previously unselected package libgraphite2-3:arm64. 130s Preparing to unpack .../033-libgraphite2-3_1.3.14-2_arm64.deb ... 130s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 130s Selecting previously unselected package libharfbuzz0b:arm64. 130s Preparing to unpack .../034-libharfbuzz0b_8.3.0-2_arm64.deb ... 130s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 130s Selecting previously unselected package x11-common. 130s Preparing to unpack .../035-x11-common_1%3a7.7+23ubuntu2_all.deb ... 130s Unpacking x11-common (1:7.7+23ubuntu2) ... 130s Selecting previously unselected package libice6:arm64. 130s Preparing to unpack .../036-libice6_2%3a1.0.10-1build2_arm64.deb ... 130s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 130s Selecting previously unselected package libparams-classify-perl:arm64. 130s Preparing to unpack .../037-libparams-classify-perl_0.015-2build3_arm64.deb ... 130s Unpacking libparams-classify-perl:arm64 (0.015-2build3) ... 130s Selecting previously unselected package libmodule-runtime-perl. 130s Preparing to unpack .../038-libmodule-runtime-perl_0.016-2_all.deb ... 130s Unpacking libmodule-runtime-perl (0.016-2) ... 130s Selecting previously unselected package libimport-into-perl. 130s Preparing to unpack .../039-libimport-into-perl_1.002005-2_all.deb ... 130s Unpacking libimport-into-perl (1.002005-2) ... 130s Selecting previously unselected package libjpeg-turbo8:arm64. 130s Preparing to unpack .../040-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 130s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 130s Selecting previously unselected package libjpeg8:arm64. 130s Preparing to unpack .../041-libjpeg8_8c-2ubuntu11_arm64.deb ... 130s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 130s Selecting previously unselected package libjs-bootstrap. 130s Preparing to unpack .../042-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 130s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 130s Selecting previously unselected package libjs-popper.js. 130s Preparing to unpack .../043-libjs-popper.js_1.16.1+ds-6_all.deb ... 130s Unpacking libjs-popper.js (1.16.1+ds-6) ... 130s Selecting previously unselected package libjs-bootstrap4. 130s Preparing to unpack .../044-libjs-bootstrap4_4.6.1+dfsg1-4_all.deb ... 130s Unpacking libjs-bootstrap4 (4.6.1+dfsg1-4) ... 130s Selecting previously unselected package libjs-d3. 130s Preparing to unpack .../045-libjs-d3_3.5.17-4_all.deb ... 130s Unpacking libjs-d3 (3.5.17-4) ... 130s Selecting previously unselected package libjs-es5-shim. 130s Preparing to unpack .../046-libjs-es5-shim_4.6.7-2_all.deb ... 130s Unpacking libjs-es5-shim (4.6.7-2) ... 130s Selecting previously unselected package libjs-highlight.js. 130s Preparing to unpack .../047-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 130s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 131s Selecting previously unselected package libjs-jquery. 131s Preparing to unpack .../048-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 131s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 131s Selecting previously unselected package libjs-jquery-datatables. 131s Preparing to unpack .../049-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 131s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 131s Selecting previously unselected package libjs-sifter.js. 131s Preparing to unpack .../050-libjs-sifter.js_0.6.0+dfsg-3_all.deb ... 131s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ... 131s Selecting previously unselected package libjs-microplugin.js. 131s Preparing to unpack .../051-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ... 131s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ... 131s Selecting previously unselected package libjs-jquery-selectize.js. 131s Preparing to unpack .../052-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ... 131s Unpacking libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 131s Selecting previously unselected package libjs-jquery-ui. 131s Preparing to unpack .../053-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 131s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 131s Selecting previously unselected package libjs-json. 131s Preparing to unpack .../054-libjs-json_0~20221030+~1.0.8-1_all.deb ... 131s Unpacking libjs-json (0~20221030+~1.0.8-1) ... 131s Selecting previously unselected package libjs-prettify. 131s Preparing to unpack .../055-libjs-prettify_2015.12.04+dfsg-1.1_all.deb ... 131s Unpacking libjs-prettify (2015.12.04+dfsg-1.1) ... 131s Selecting previously unselected package liblerc4:arm64. 131s Preparing to unpack .../056-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 131s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 131s Selecting previously unselected package liblua5.4-0:arm64. 131s Preparing to unpack .../057-liblua5.4-0_5.4.6-3_arm64.deb ... 131s Unpacking liblua5.4-0:arm64 (5.4.6-3) ... 131s Selecting previously unselected package librole-tiny-perl. 131s Preparing to unpack .../058-librole-tiny-perl_2.002004-1_all.deb ... 131s Unpacking librole-tiny-perl (2.002004-1) ... 131s Selecting previously unselected package libsub-quote-perl. 131s Preparing to unpack .../059-libsub-quote-perl_2.006008-1ubuntu1_all.deb ... 131s Unpacking libsub-quote-perl (2.006008-1ubuntu1) ... 131s Selecting previously unselected package libmoo-perl. 131s Preparing to unpack .../060-libmoo-perl_2.005005-1_all.deb ... 131s Unpacking libmoo-perl (2.005005-1) ... 131s Selecting previously unselected package libthai-data. 131s Preparing to unpack .../061-libthai-data_0.1.29-2_all.deb ... 131s Unpacking libthai-data (0.1.29-2) ... 131s Selecting previously unselected package libthai0:arm64. 131s Preparing to unpack .../062-libthai0_0.1.29-2_arm64.deb ... 131s Unpacking libthai0:arm64 (0.1.29-2) ... 131s Selecting previously unselected package libpango-1.0-0:arm64. 131s Preparing to unpack .../063-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 131s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 131s Selecting previously unselected package libpangoft2-1.0-0:arm64. 131s Preparing to unpack .../064-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 131s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 131s Selecting previously unselected package libpangocairo-1.0-0:arm64. 131s Preparing to unpack .../065-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 131s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 131s Selecting previously unselected package libpaper1:arm64. 131s Preparing to unpack .../066-libpaper1_1.1.29_arm64.deb ... 131s Unpacking libpaper1:arm64 (1.1.29) ... 131s Selecting previously unselected package libpaper-utils. 131s Preparing to unpack .../067-libpaper-utils_1.1.29_arm64.deb ... 131s Unpacking libpaper-utils (1.1.29) ... 131s Selecting previously unselected package libparallel-forkmanager-perl. 131s Preparing to unpack .../068-libparallel-forkmanager-perl_2.02-1_all.deb ... 131s Unpacking libparallel-forkmanager-perl (2.02-1) ... 131s Selecting previously unselected package libreadonly-perl. 131s Preparing to unpack .../069-libreadonly-perl_2.050-3_all.deb ... 131s Unpacking libreadonly-perl (2.050-3) ... 131s Selecting previously unselected package libsharpyuv0:arm64. 131s Preparing to unpack .../070-libsharpyuv0_1.3.2-0.4_arm64.deb ... 131s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 131s Selecting previously unselected package libsm6:arm64. 132s Preparing to unpack .../071-libsm6_2%3a1.2.3-1build2_arm64.deb ... 132s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 132s Selecting previously unselected package libtcl8.6:arm64. 132s Preparing to unpack .../072-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 132s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 132s Selecting previously unselected package libjbig0:arm64. 132s Preparing to unpack .../073-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 132s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 132s Selecting previously unselected package libwebp7:arm64. 132s Preparing to unpack .../074-libwebp7_1.3.2-0.4_arm64.deb ... 132s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 132s Selecting previously unselected package libtiff6:arm64. 132s Preparing to unpack .../075-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 132s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 132s Selecting previously unselected package libxft2:arm64. 132s Preparing to unpack .../076-libxft2_2.3.6-1_arm64.deb ... 132s Unpacking libxft2:arm64 (2.3.6-1) ... 132s Selecting previously unselected package libxss1:arm64. 132s Preparing to unpack .../077-libxss1_1%3a1.2.3-1build2_arm64.deb ... 132s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 132s Selecting previously unselected package libtk8.6:arm64. 132s Preparing to unpack .../078-libtk8.6_8.6.13-2_arm64.deb ... 132s Unpacking libtk8.6:arm64 (8.6.13-2) ... 132s Selecting previously unselected package libxt6t64:arm64. 132s Preparing to unpack .../079-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 132s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 132s Selecting previously unselected package zip. 132s Preparing to unpack .../080-zip_3.0-13_arm64.deb ... 132s Unpacking zip (3.0-13) ... 132s Selecting previously unselected package unzip. 132s Preparing to unpack .../081-unzip_6.0-28ubuntu3_arm64.deb ... 132s Unpacking unzip (6.0-28ubuntu3) ... 132s Selecting previously unselected package xdg-utils. 132s Preparing to unpack .../082-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 132s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 132s Selecting previously unselected package r-base-core. 132s Preparing to unpack .../083-r-base-core_4.3.3-2build1_arm64.deb ... 132s Unpacking r-base-core (4.3.3-2build1) ... 132s Selecting previously unselected package r-cran-littler. 132s Preparing to unpack .../084-r-cran-littler_0.3.19-1_arm64.deb ... 132s Unpacking r-cran-littler (0.3.19-1) ... 133s Selecting previously unselected package littler. 133s Preparing to unpack .../085-littler_0.3.19-1_all.deb ... 133s Unpacking littler (0.3.19-1) ... 133s Selecting previously unselected package node-bootstrap-sass. 133s Preparing to unpack .../086-node-bootstrap-sass_3.4.3-2_all.deb ... 133s Unpacking node-bootstrap-sass (3.4.3-2) ... 133s Selecting previously unselected package node-html5shiv. 133s Preparing to unpack .../087-node-html5shiv_3.7.3+dfsg-5_all.deb ... 133s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 133s Selecting previously unselected package node-normalize.css. 133s Preparing to unpack .../088-node-normalize.css_8.0.1-5_all.deb ... 133s Unpacking node-normalize.css (8.0.1-5) ... 133s Selecting previously unselected package pandoc-data. 133s Preparing to unpack .../089-pandoc-data_3.1.3-1_all.deb ... 133s Unpacking pandoc-data (3.1.3-1) ... 133s Selecting previously unselected package pandoc. 133s Preparing to unpack .../090-pandoc_3.1.3+ds-2_arm64.deb ... 133s Unpacking pandoc (3.1.3+ds-2) ... 134s Selecting previously unselected package plink. 134s Preparing to unpack .../091-plink_1.07+dfsg-4_arm64.deb ... 134s Unpacking plink (1.07+dfsg-4) ... 134s Selecting previously unselected package r-cran-getopt. 134s Preparing to unpack .../092-r-cran-getopt_1.20.4-1_all.deb ... 134s Unpacking r-cran-getopt (1.20.4-1) ... 134s Selecting previously unselected package r-cran-colorspace. 134s Preparing to unpack .../093-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ... 134s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 134s Selecting previously unselected package r-cran-fracdiff. 134s Preparing to unpack .../094-r-cran-fracdiff_1.5-3-1_arm64.deb ... 134s Unpacking r-cran-fracdiff (1.5-3-1) ... 134s Selecting previously unselected package r-cran-generics. 134s Preparing to unpack .../095-r-cran-generics_0.1.3-1_all.deb ... 134s Unpacking r-cran-generics (0.1.3-1) ... 134s Selecting previously unselected package r-cran-cli. 134s Preparing to unpack .../096-r-cran-cli_3.6.2-1_arm64.deb ... 134s Unpacking r-cran-cli (3.6.2-1) ... 135s Selecting previously unselected package r-cran-glue. 135s Preparing to unpack .../097-r-cran-glue_1.7.0-1_arm64.deb ... 135s Unpacking r-cran-glue (1.7.0-1) ... 135s Selecting previously unselected package r-cran-rlang. 135s Preparing to unpack .../098-r-cran-rlang_1.1.3-1_arm64.deb ... 135s Unpacking r-cran-rlang (1.1.3-1) ... 135s Selecting previously unselected package r-cran-lifecycle. 135s Preparing to unpack .../099-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 135s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 135s Selecting previously unselected package r-cran-gtable. 135s Preparing to unpack .../100-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 135s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 135s Selecting previously unselected package r-cran-isoband. 135s Preparing to unpack .../101-r-cran-isoband_0.2.7-1_arm64.deb ... 135s Unpacking r-cran-isoband (0.2.7-1) ... 135s Selecting previously unselected package r-cran-mass. 135s Preparing to unpack .../102-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 135s Unpacking r-cran-mass (7.3-60.0.1-1) ... 135s Selecting previously unselected package r-cran-lattice. 135s Preparing to unpack .../103-r-cran-lattice_0.22-5-1_arm64.deb ... 135s Unpacking r-cran-lattice (0.22-5-1) ... 135s Selecting previously unselected package r-cran-nlme. 135s Preparing to unpack .../104-r-cran-nlme_3.1.164-1_arm64.deb ... 135s Unpacking r-cran-nlme (3.1.164-1) ... 135s Selecting previously unselected package r-cran-matrix. 135s Preparing to unpack .../105-r-cran-matrix_1.6-5-1_arm64.deb ... 135s Unpacking r-cran-matrix (1.6-5-1) ... 135s Selecting previously unselected package r-cran-mgcv. 135s Preparing to unpack .../106-r-cran-mgcv_1.9-1-1_arm64.deb ... 135s Unpacking r-cran-mgcv (1.9-1-1) ... 135s Selecting previously unselected package r-cran-farver. 135s Preparing to unpack .../107-r-cran-farver_2.1.1-1_arm64.deb ... 135s Unpacking r-cran-farver (2.1.1-1) ... 135s Selecting previously unselected package r-cran-labeling. 135s Preparing to unpack .../108-r-cran-labeling_0.4.3-1_all.deb ... 135s Unpacking r-cran-labeling (0.4.3-1) ... 135s Selecting previously unselected package r-cran-munsell. 135s Preparing to unpack .../109-r-cran-munsell_0.5.0-2build1_all.deb ... 135s Unpacking r-cran-munsell (0.5.0-2build1) ... 135s Selecting previously unselected package r-cran-r6. 135s Preparing to unpack .../110-r-cran-r6_2.5.1-1_all.deb ... 135s Unpacking r-cran-r6 (2.5.1-1) ... 135s Selecting previously unselected package r-cran-rcolorbrewer. 135s Preparing to unpack .../111-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 135s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 135s Selecting previously unselected package r-cran-viridislite. 135s Preparing to unpack .../112-r-cran-viridislite_0.4.2-2_all.deb ... 135s Unpacking r-cran-viridislite (0.4.2-2) ... 135s Selecting previously unselected package r-cran-scales. 135s Preparing to unpack .../113-r-cran-scales_1.3.0-1_all.deb ... 135s Unpacking r-cran-scales (1.3.0-1) ... 135s Selecting previously unselected package r-cran-fansi. 135s Preparing to unpack .../114-r-cran-fansi_1.0.5-1_arm64.deb ... 135s Unpacking r-cran-fansi (1.0.5-1) ... 135s Selecting previously unselected package r-cran-magrittr. 135s Preparing to unpack .../115-r-cran-magrittr_2.0.3-1_arm64.deb ... 135s Unpacking r-cran-magrittr (2.0.3-1) ... 135s Selecting previously unselected package r-cran-utf8. 135s Preparing to unpack .../116-r-cran-utf8_1.2.4-1_arm64.deb ... 135s Unpacking r-cran-utf8 (1.2.4-1) ... 135s Selecting previously unselected package r-cran-vctrs. 135s Preparing to unpack .../117-r-cran-vctrs_0.6.5-1_arm64.deb ... 135s Unpacking r-cran-vctrs (0.6.5-1) ... 136s Selecting previously unselected package r-cran-pillar. 136s Preparing to unpack .../118-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 136s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 136s Selecting previously unselected package r-cran-pkgconfig. 136s Preparing to unpack .../119-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 136s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 136s Selecting previously unselected package r-cran-tibble. 136s Preparing to unpack .../120-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 136s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 136s Selecting previously unselected package r-cran-withr. 136s Preparing to unpack .../121-r-cran-withr_2.5.0-1_all.deb ... 136s Unpacking r-cran-withr (2.5.0-1) ... 136s Selecting previously unselected package r-cran-ggplot2. 136s Preparing to unpack .../122-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 136s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 136s Selecting previously unselected package r-cran-zoo. 136s Preparing to unpack .../123-r-cran-zoo_1.8-12-2_arm64.deb ... 136s Unpacking r-cran-zoo (1.8-12-2) ... 136s Selecting previously unselected package r-cran-lmtest. 136s Preparing to unpack .../124-r-cran-lmtest_0.9.40-1_arm64.deb ... 136s Unpacking r-cran-lmtest (0.9.40-1) ... 136s Selecting previously unselected package r-cran-nnet. 136s Preparing to unpack .../125-r-cran-nnet_7.3-19-2_arm64.deb ... 136s Unpacking r-cran-nnet (7.3-19-2) ... 136s Selecting previously unselected package r-cran-pkgkitten. 136s Preparing to unpack .../126-r-cran-pkgkitten_0.2.3-1_all.deb ... 136s Unpacking r-cran-pkgkitten (0.2.3-1) ... 136s Selecting previously unselected package r-cran-rcpp. 136s Preparing to unpack .../127-r-cran-rcpp_1.0.12-1_arm64.deb ... 136s Unpacking r-cran-rcpp (1.0.12-1) ... 136s Selecting previously unselected package r-cran-timedate. 136s Preparing to unpack .../128-r-cran-timedate_4032.109-1_arm64.deb ... 136s Unpacking r-cran-timedate (4032.109-1) ... 136s Selecting previously unselected package r-cran-quadprog. 136s Preparing to unpack .../129-r-cran-quadprog_1.5-8-1build1_arm64.deb ... 136s Unpacking r-cran-quadprog (1.5-8-1build1) ... 136s Selecting previously unselected package r-cran-xts. 136s Preparing to unpack .../130-r-cran-xts_0.13.2-1_arm64.deb ... 136s Unpacking r-cran-xts (0.13.2-1) ... 136s Selecting previously unselected package r-cran-curl. 136s Preparing to unpack .../131-r-cran-curl_5.2.0+dfsg-1_arm64.deb ... 136s Unpacking r-cran-curl (5.2.0+dfsg-1) ... 136s Selecting previously unselected package r-cran-ttr. 136s Preparing to unpack .../132-r-cran-ttr_0.24.4-1_arm64.deb ... 136s Unpacking r-cran-ttr (0.24.4-1) ... 136s Selecting previously unselected package r-cran-jsonlite. 136s Preparing to unpack .../133-r-cran-jsonlite_1.8.8+dfsg-1_arm64.deb ... 136s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 136s Selecting previously unselected package r-cran-quantmod. 136s Preparing to unpack .../134-r-cran-quantmod_0.4.26-1_all.deb ... 136s Unpacking r-cran-quantmod (0.4.26-1) ... 136s Selecting previously unselected package r-cran-tseries. 136s Preparing to unpack .../135-r-cran-tseries_0.10-55-1_arm64.deb ... 136s Unpacking r-cran-tseries (0.10-55-1) ... 136s Selecting previously unselected package r-cran-urca. 136s Preparing to unpack .../136-r-cran-urca_1.3-3-1_arm64.deb ... 136s Unpacking r-cran-urca (1.3-3-1) ... 136s Selecting previously unselected package r-cran-rcpparmadillo. 137s Preparing to unpack .../137-r-cran-rcpparmadillo_0.12.8.0.0-1_arm64.deb ... 137s Unpacking r-cran-rcpparmadillo (0.12.8.0.0-1) ... 137s Selecting previously unselected package r-cran-forecast. 137s Preparing to unpack .../138-r-cran-forecast_8.21.1-1_arm64.deb ... 137s Unpacking r-cran-forecast (8.21.1-1) ... 137s Selecting previously unselected package r-bioc-biocgenerics. 137s Preparing to unpack .../139-r-bioc-biocgenerics_0.48.1-2_all.deb ... 137s Unpacking r-bioc-biocgenerics (0.48.1-2) ... 137s Selecting previously unselected package r-bioc-biobase. 137s Preparing to unpack .../140-r-bioc-biobase_2.62.0-1_arm64.deb ... 137s Unpacking r-bioc-biobase (2.62.0-1) ... 137s Selecting previously unselected package r-cran-survival. 137s Preparing to unpack .../141-r-cran-survival_3.5-8-1_arm64.deb ... 137s Unpacking r-cran-survival (3.5-8-1) ... 137s Selecting previously unselected package r-bioc-multtest. 137s Preparing to unpack .../142-r-bioc-multtest_2.58.0-1_arm64.deb ... 137s Unpacking r-bioc-multtest (2.58.0-1) ... 137s Selecting previously unselected package r-cran-optparse. 137s Preparing to unpack .../143-r-cran-optparse_1.7.4-1_all.deb ... 137s Unpacking r-cran-optparse (1.7.4-1) ... 137s Selecting previously unselected package r-cran-uroot. 137s Preparing to unpack .../144-r-cran-uroot_2.1-3-1_all.deb ... 137s Unpacking r-cran-uroot (2.1-3-1) ... 137s Selecting previously unselected package pique. 137s Preparing to unpack .../145-pique_1.0-7_all.deb ... 137s Unpacking pique (1.0-7) ... 137s Selecting previously unselected package pique-doc. 137s Preparing to unpack .../146-pique-doc_1.0-7_all.deb ... 137s Unpacking pique-doc (1.0-7) ... 137s Selecting previously unselected package r-cran-acepack. 137s Preparing to unpack .../147-r-cran-acepack_1.4.2-1_arm64.deb ... 137s Unpacking r-cran-acepack (1.4.2-1) ... 137s Selecting previously unselected package r-cran-backports. 137s Preparing to unpack .../148-r-cran-backports_1.4.1-1_arm64.deb ... 137s Unpacking r-cran-backports (1.4.1-1) ... 137s Selecting previously unselected package r-cran-base64enc. 137s Preparing to unpack .../149-r-cran-base64enc_0.1-3-3_arm64.deb ... 137s Unpacking r-cran-base64enc (0.1-3-3) ... 137s Selecting previously unselected package r-cran-fastmap. 137s Preparing to unpack .../150-r-cran-fastmap_1.1.1-1_arm64.deb ... 137s Unpacking r-cran-fastmap (1.1.1-1) ... 137s Selecting previously unselected package r-cran-cachem. 137s Preparing to unpack .../151-r-cran-cachem_1.0.8-1_arm64.deb ... 137s Unpacking r-cran-cachem (1.0.8-1) ... 137s Selecting previously unselected package r-cran-digest. 137s Preparing to unpack .../152-r-cran-digest_0.6.34-1_arm64.deb ... 137s Unpacking r-cran-digest (0.6.34-1) ... 137s Selecting previously unselected package r-cran-ellipsis. 137s Preparing to unpack .../153-r-cran-ellipsis_0.3.2-2_arm64.deb ... 137s Unpacking r-cran-ellipsis (0.3.2-2) ... 137s Selecting previously unselected package r-cran-htmltools. 137s Preparing to unpack .../154-r-cran-htmltools_0.5.7-1_arm64.deb ... 137s Unpacking r-cran-htmltools (0.5.7-1) ... 137s Selecting previously unselected package r-cran-jquerylib. 137s Preparing to unpack .../155-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ... 137s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ... 137s Selecting previously unselected package r-cran-memoise. 137s Preparing to unpack .../156-r-cran-memoise_2.0.1-1_all.deb ... 137s Unpacking r-cran-memoise (2.0.1-1) ... 137s Selecting previously unselected package r-cran-mime. 138s Preparing to unpack .../157-r-cran-mime_0.12-1_arm64.deb ... 138s Unpacking r-cran-mime (0.12-1) ... 138s Selecting previously unselected package r-cran-fs. 138s Preparing to unpack .../158-r-cran-fs_1.6.3+dfsg-1_arm64.deb ... 138s Unpacking r-cran-fs (1.6.3+dfsg-1) ... 138s Selecting previously unselected package r-cran-rappdirs. 138s Preparing to unpack .../159-r-cran-rappdirs_0.3.3-1_arm64.deb ... 138s Unpacking r-cran-rappdirs (0.3.3-1) ... 138s Selecting previously unselected package r-cran-sass. 138s Preparing to unpack .../160-r-cran-sass_0.4.8+dfsg-1_arm64.deb ... 138s Unpacking r-cran-sass (0.4.8+dfsg-1) ... 138s Selecting previously unselected package r-cran-bslib. 138s Preparing to unpack .../161-r-cran-bslib_0.6.1+dfsg-1_all.deb ... 138s Unpacking r-cran-bslib (0.6.1+dfsg-1) ... 138s Selecting previously unselected package r-cran-checkmate. 138s Preparing to unpack .../162-r-cran-checkmate_2.3.1-1_arm64.deb ... 138s Unpacking r-cran-checkmate (2.3.1-1) ... 138s Selecting previously unselected package r-cran-chron. 138s Preparing to unpack .../163-r-cran-chron_2.3-61-2_arm64.deb ... 138s Unpacking r-cran-chron (2.3-61-2) ... 138s Selecting previously unselected package r-cran-cluster. 138s Preparing to unpack .../164-r-cran-cluster_2.1.6-1_arm64.deb ... 138s Unpacking r-cran-cluster (2.1.6-1) ... 138s Selecting previously unselected package r-cran-commonmark. 138s Preparing to unpack .../165-r-cran-commonmark_1.9.1-1_arm64.deb ... 138s Unpacking r-cran-commonmark (1.9.1-1) ... 138s Selecting previously unselected package r-cran-cpp11. 139s Preparing to unpack .../166-r-cran-cpp11_0.4.7-1_all.deb ... 139s Unpacking r-cran-cpp11 (0.4.7-1) ... 139s Selecting previously unselected package r-cran-crayon. 139s Preparing to unpack .../167-r-cran-crayon_1.5.2-1_all.deb ... 139s Unpacking r-cran-crayon (1.5.2-1) ... 139s Selecting previously unselected package r-cran-data.table. 139s Preparing to unpack .../168-r-cran-data.table_1.14.10+dfsg-1_arm64.deb ... 139s Unpacking r-cran-data.table (1.14.10+dfsg-1) ... 139s Selecting previously unselected package r-cran-deldir. 139s Preparing to unpack .../169-r-cran-deldir_2.0-4-1_arm64.deb ... 139s Unpacking r-cran-deldir (2.0-4-1) ... 139s Selecting previously unselected package r-cran-tidyselect. 139s Preparing to unpack .../170-r-cran-tidyselect_1.2.0+dfsg-1_arm64.deb ... 139s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 139s Selecting previously unselected package r-cran-dplyr. 139s Preparing to unpack .../171-r-cran-dplyr_1.1.4-1_arm64.deb ... 139s Unpacking r-cran-dplyr (1.1.4-1) ... 139s Selecting previously unselected package r-cran-evaluate. 139s Preparing to unpack .../172-r-cran-evaluate_0.23-1_all.deb ... 139s Unpacking r-cran-evaluate (0.23-1) ... 139s Selecting previously unselected package r-cran-fontawesome. 139s Preparing to unpack .../173-r-cran-fontawesome_0.5.2-1_all.deb ... 139s Unpacking r-cran-fontawesome (0.5.2-1) ... 139s Selecting previously unselected package r-cran-foreign. 139s Preparing to unpack .../174-r-cran-foreign_0.8.86-1_arm64.deb ... 139s Unpacking r-cran-foreign (0.8.86-1) ... 139s Selecting previously unselected package r-cran-formula. 139s Preparing to unpack .../175-r-cran-formula_1.2-5-1_all.deb ... 139s Unpacking r-cran-formula (1.2-5-1) ... 139s Selecting previously unselected package r-cran-gridextra. 139s Preparing to unpack .../176-r-cran-gridextra_2.3-3build1_all.deb ... 139s Unpacking r-cran-gridextra (2.3-3build1) ... 139s Selecting previously unselected package r-cran-xfun. 139s Preparing to unpack .../177-r-cran-xfun_0.41+dfsg-1_arm64.deb ... 139s Unpacking r-cran-xfun (0.41+dfsg-1) ... 139s Selecting previously unselected package r-cran-highr. 139s Preparing to unpack .../178-r-cran-highr_0.10+dfsg-1_all.deb ... 139s Unpacking r-cran-highr (0.10+dfsg-1) ... 139s Selecting previously unselected package r-cran-rpart. 139s Preparing to unpack .../179-r-cran-rpart_4.1.23-1_arm64.deb ... 139s Unpacking r-cran-rpart (4.1.23-1) ... 139s Selecting previously unselected package r-cran-stringi. 139s Preparing to unpack .../180-r-cran-stringi_1.8.3-1_arm64.deb ... 139s Unpacking r-cran-stringi (1.8.3-1) ... 139s Selecting previously unselected package r-cran-stringr. 139s Preparing to unpack .../181-r-cran-stringr_1.5.1-1_all.deb ... 139s Unpacking r-cran-stringr (1.5.1-1) ... 139s Selecting previously unselected package r-cran-yaml. 139s Preparing to unpack .../182-r-cran-yaml_2.3.8-1_arm64.deb ... 139s Unpacking r-cran-yaml (2.3.8-1) ... 139s Selecting previously unselected package libjs-mathjax. 139s Preparing to unpack .../183-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 139s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 140s Selecting previously unselected package r-cran-knitr. 140s Preparing to unpack .../184-r-cran-knitr_1.45+dfsg-1_all.deb ... 140s Unpacking r-cran-knitr (1.45+dfsg-1) ... 140s Selecting previously unselected package r-cran-tinytex. 140s Preparing to unpack .../185-r-cran-tinytex_0.49-1_all.deb ... 140s Unpacking r-cran-tinytex (0.49-1) ... 140s Selecting previously unselected package libjs-modernizr. 140s Preparing to unpack .../186-libjs-modernizr_2.6.2+ds1-5_all.deb ... 140s Unpacking libjs-modernizr (2.6.2+ds1-5) ... 140s Selecting previously unselected package r-cran-later. 140s Preparing to unpack .../187-r-cran-later_1.3.2+dfsg-1_arm64.deb ... 140s Unpacking r-cran-later (1.3.2+dfsg-1) ... 140s Selecting previously unselected package r-cran-promises. 140s Preparing to unpack .../188-r-cran-promises_1.2.1+dfsg-1_arm64.deb ... 140s Unpacking r-cran-promises (1.2.1+dfsg-1) ... 140s Selecting previously unselected package r-cran-httpuv. 140s Preparing to unpack .../189-r-cran-httpuv_1.6.14+dfsg-1_arm64.deb ... 140s Unpacking r-cran-httpuv (1.6.14+dfsg-1) ... 140s Selecting previously unselected package r-cran-xtable. 140s Preparing to unpack .../190-r-cran-xtable_1%3a1.8-4-2_all.deb ... 140s Unpacking r-cran-xtable (1:1.8-4-2) ... 140s Selecting previously unselected package r-cran-sourcetools. 140s Preparing to unpack .../191-r-cran-sourcetools_0.1.7-1-1_arm64.deb ... 140s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 140s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 140s Preparing to unpack .../192-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 140s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 141s Selecting previously unselected package r-cran-shiny. 141s Preparing to unpack .../193-r-cran-shiny_1.8.0+dfsg-1_all.deb ... 141s Unpacking r-cran-shiny (1.8.0+dfsg-1) ... 141s Selecting previously unselected package r-cran-rmarkdown. 141s Preparing to unpack .../194-r-cran-rmarkdown_2.25+dfsg-3_all.deb ... 141s Unpacking r-cran-rmarkdown (2.25+dfsg-3) ... 141s Selecting previously unselected package r-cran-htmlwidgets. 141s Preparing to unpack .../195-r-cran-htmlwidgets_1.6.4+dfsg-1_all.deb ... 141s Unpacking r-cran-htmlwidgets (1.6.4+dfsg-1) ... 141s Selecting previously unselected package r-cran-rstudioapi. 141s Preparing to unpack .../196-r-cran-rstudioapi_0.15.0-1_all.deb ... 141s Unpacking r-cran-rstudioapi (0.15.0-1) ... 141s Selecting previously unselected package r-cran-purrr. 141s Preparing to unpack .../197-r-cran-purrr_1.0.2-1_arm64.deb ... 141s Unpacking r-cran-purrr (1.0.2-1) ... 141s Selecting previously unselected package r-cran-tidyr. 141s Preparing to unpack .../198-r-cran-tidyr_1.3.1-1_arm64.deb ... 141s Unpacking r-cran-tidyr (1.3.1-1) ... 141s Selecting previously unselected package r-cran-htmltable. 141s Preparing to unpack .../199-r-cran-htmltable_2.4.2-1_all.deb ... 141s Unpacking r-cran-htmltable (2.4.2-1) ... 141s Selecting previously unselected package r-cran-viridis. 141s Preparing to unpack .../200-r-cran-viridis_0.6.5-1_all.deb ... 141s Unpacking r-cran-viridis (0.6.5-1) ... 141s Selecting previously unselected package r-cran-png. 141s Preparing to unpack .../201-r-cran-png_0.1-8-1_arm64.deb ... 141s Unpacking r-cran-png (0.1-8-1) ... 141s Selecting previously unselected package r-cran-jpeg. 141s Preparing to unpack .../202-r-cran-jpeg_0.1-10-1_arm64.deb ... 141s Unpacking r-cran-jpeg (0.1-10-1) ... 141s Selecting previously unselected package r-cran-rcppeigen. 141s Preparing to unpack .../203-r-cran-rcppeigen_0.3.3.9.4-1_arm64.deb ... 141s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 141s Selecting previously unselected package r-cran-interp. 141s Preparing to unpack .../204-r-cran-interp_1.1-6-1_arm64.deb ... 141s Unpacking r-cran-interp (1.1-6-1) ... 141s Selecting previously unselected package r-cran-latticeextra. 141s Preparing to unpack .../205-r-cran-latticeextra_0.6-30-1_all.deb ... 141s Unpacking r-cran-latticeextra (0.6-30-1) ... 141s Selecting previously unselected package r-cran-hmisc. 142s Preparing to unpack .../206-r-cran-hmisc_5.1-1-1_arm64.deb ... 142s Unpacking r-cran-hmisc (5.1-1-1) ... 142s Selecting previously unselected package autopkgtest-satdep. 142s Preparing to unpack .../207-1-autopkgtest-satdep.deb ... 142s Unpacking autopkgtest-satdep (0) ... 142s Setting up libjs-json (0~20221030+~1.0.8-1) ... 142s Setting up javascript-common (11+nmu1) ... 142s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 142s Setting up 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triggers for libc-bin (2.39-0ubuntu2) ... 158s (Reading database ... 94983 files and directories currently installed.) 158s Removing autopkgtest-satdep (0) ... 159s autopkgtest [17:20:42]: test run-unit-test: [----------------------- 159s wget --no-check-certificate http://ricediversity.org/data/sets/44kgwas/RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 159s --2024-03-16 17:20:42-- http://ricediversity.org/data/sets/44kgwas/RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 159s Resolving squid.internal (squid.internal)... 185.125.188.86, 185.125.188.85 159s Connecting to squid.internal (squid.internal)|185.125.188.86|:3128... connected. 160s Proxy request sent, awaiting response... 200 OK 160s Length: 7107854 (6.8M) [application/zip] 160s Saving to: ‘RiceDiversity.44K.MSU6.Genotypes_PLINK.zip’ 160s 160s 0K .......... .......... .......... .......... .......... 0% 290K 24s 160s 50K .......... .......... .......... .......... .......... 1% 634K 17s 160s 100K .......... .......... .......... 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51.0M 1s 160s 3300K .......... .......... .......... .......... .......... 48% 29.8M 1s 160s 3350K .......... .......... .......... .......... .......... 48% 40.2M 1s 160s 3400K .......... .......... .......... .......... .......... 49% 15.7M 1s 161s 3450K .......... .......... .......... .......... .......... 50% 2.27M 1s 161s 3500K .......... .......... .......... .......... .......... 51% 36.9M 1s 161s 3550K .......... .......... .......... .......... .......... 51% 43.6M 1s 161s 3600K .......... .......... .......... .......... .......... 52% 34.2M 1s 161s 3650K .......... .......... .......... .......... .......... 53% 47.0M 1s 161s 3700K .......... .......... .......... .......... .......... 54% 14.4M 1s 161s 3750K .......... .......... .......... .......... .......... 54% 45.2M 1s 161s 3800K .......... .......... .......... .......... .......... 55% 25.2M 1s 161s 3850K .......... .......... .......... .......... .......... 56% 79.9M 1s 161s 3900K .......... .......... .......... .......... .......... 56% 37.9M 1s 161s 3950K .......... .......... .......... .......... .......... 57% 34.3M 1s 161s 4000K .......... .......... .......... .......... .......... 58% 40.4M 0s 161s 4050K .......... .......... .......... .......... .......... 59% 40.8M 0s 161s 4100K .......... .......... .......... .......... .......... 59% 53.7M 0s 161s 4150K .......... .......... .......... .......... .......... 60% 38.9M 0s 161s 4200K .......... .......... .......... .......... .......... 61% 35.4M 0s 161s 4250K .......... .......... .......... .......... .......... 61% 63.8M 0s 161s 4300K .......... .......... .......... .......... .......... 62% 35.3M 0s 161s 4350K .......... .......... .......... .......... .......... 63% 75.2M 0s 161s 4400K .......... .......... .......... .......... .......... 64% 34.6M 0s 161s 4450K .......... .......... .......... .......... .......... 64% 51.7M 0s 161s 4500K .......... .......... .......... .......... .......... 65% 56.0M 0s 161s 4550K .......... .......... .......... .......... .......... 66% 71.4M 0s 161s 4600K .......... .......... .......... .......... .......... 66% 35.9M 0s 161s 4650K .......... .......... .......... .......... .......... 67% 42.8M 0s 161s 4700K .......... .......... .......... .......... .......... 68% 59.9M 0s 161s 4750K .......... .......... .......... .......... .......... 69% 54.6M 0s 161s 4800K .......... .......... .......... .......... .......... 69% 59.2M 0s 161s 4850K .......... .......... .......... .......... .......... 70% 44.5M 0s 161s 4900K .......... .......... .......... .......... .......... 71% 66.7M 0s 161s 4950K .......... .......... .......... .......... .......... 72% 62.6M 0s 161s 5000K .......... .......... .......... .......... .......... 72% 63.9M 0s 161s 5050K .......... .......... .......... .......... .......... 73% 35.9M 0s 161s 5100K .......... .......... .......... .......... .......... 74% 48.3M 0s 161s 5150K .......... .......... .......... .......... .......... 74% 76.4M 0s 161s 5200K .......... .......... .......... .......... .......... 75% 109M 0s 161s 5250K .......... .......... .......... .......... .......... 76% 51.3M 0s 161s 5300K .......... .......... .......... .......... .......... 77% 42.1M 0s 161s 5350K .......... .......... .......... .......... .......... 77% 78.5M 0s 161s 5400K .......... .......... .......... .......... .......... 78% 57.2M 0s 161s 5450K .......... .......... .......... .......... .......... 79% 65.0M 0s 161s 5500K .......... .......... .......... .......... .......... 79% 64.0M 0s 161s 5550K .......... .......... .......... .......... .......... 80% 76.1M 0s 161s 5600K .......... .......... .......... .......... .......... 81% 88.8M 0s 161s 5650K .......... .......... .......... .......... .......... 82% 100M 0s 161s 5700K .......... .......... .......... .......... .......... 82% 60.5M 0s 161s 5750K .......... .......... .......... .......... .......... 83% 59.9M 0s 161s 5800K .......... .......... .......... .......... .......... 84% 51.1M 0s 161s 5850K .......... .......... .......... .......... .......... 84% 63.5M 0s 161s 5900K .......... .......... .......... .......... .......... 85% 247M 0s 161s 5950K .......... .......... .......... .......... .......... 86% 201M 0s 161s 6000K .......... .......... .......... .......... .......... 87% 41.7M 0s 161s 6050K .......... .......... .......... .......... .......... 87% 3.93M 0s 161s 6100K .......... .......... .......... .......... .......... 88% 25.2M 0s 161s 6150K .......... .......... .......... .......... .......... 89% 37.9M 0s 161s 6200K .......... .......... .......... .......... .......... 90% 2.64M 0s 161s 6250K .......... .......... .......... .......... .......... 90% 68.3M 0s 161s 6300K .......... .......... .......... .......... .......... 91% 76.4M 0s 161s 6350K .......... .......... .......... .......... .......... 92% 41.9M 0s 161s 6400K .......... .......... .......... .......... .......... 92% 69.2M 0s 161s 6450K .......... .......... .......... .......... .......... 93% 141M 0s 161s 6500K .......... .......... .......... .......... .......... 94% 128M 0s 161s 6550K .......... .......... .......... .......... .......... 95% 70.4M 0s 161s 6600K .......... .......... .......... .......... .......... 95% 47.1M 0s 161s 6650K .......... .......... .......... .......... .......... 96% 111M 0s 161s 6700K .......... .......... .......... .......... .......... 97% 680M 0s 161s 6750K .......... .......... .......... .......... .......... 97% 71.4M 0s 161s 6800K .......... .......... .......... .......... .......... 98% 36.8M 0s 161s 6850K .......... .......... .......... .......... .......... 99% 75.7M 0s 161s 6900K .......... .......... .......... .......... . 100% 76.9T=0.8s 161s 161s 2024-03-16 17:20:44 (8.85 MB/s) - ‘RiceDiversity.44K.MSU6.Genotypes_PLINK.zip’ saved [7107854/7107854] 161s 161s unzip RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 161s Archive: RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 161s creating: RiceDiversity_44K_Genotypes_PLINK/ 161s inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.fam 161s creating: __MACOSX/ 161s creating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/ 161s inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.fam 161s inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.map 161s inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.map 161s inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.ped 161s inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.ped 161s mv -i ./RiceDiversity_44K_Genotypes_PLINK/sativas* . 161s rmdir RiceDiversity_44K_Genotypes_PLINK 161s rm RiceDiversity.44K.MSU6.Genotypes_PLINK.zip 161s pique-input -d -v -i sativas413 -o sativas_GWAS -p rice_phenotype.txt -k -c -e 5 161s Pre-process input data... 161s /usr/bin/p-link --missing-genotype 0 --recode12 --file sativas413 --out sativas413_recode12 161s 161s @----------------------------------------------------------@ 161s | PLINK! | v1.07 | 10/Aug/2009 | 161s |----------------------------------------------------------| 161s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 161s |----------------------------------------------------------| 161s | For documentation, citation & bug-report instructions: | 161s | http://pngu.mgh.harvard.edu/purcell/plink/ | 161s @----------------------------------------------------------@ 161s 161s Web-based version check ( --noweb to skip ) 161s Connecting to web... failed connection 161s 161s Problem connecting to web 161s 161s Writing this text to log file [ sativas413_recode12.log ] 161s Analysis started: Sat Mar 16 17:20:44 2024 161s 161s Options in effect: 161s --missing-genotype 0 161s --recode12 161s --file sativas413 161s --out sativas413_recode12 161s 161s 36901 (of 36901) markers to be included from [ sativas413.map ] 163s Warning, found 413 individuals with ambiguous sex codes 163s Writing list of these individuals to [ sativas413_recode12.nosex ] 163s 413 individuals read from [ sativas413.ped ] 163s 0 individuals with nonmissing phenotypes 163s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 163s Missing phenotype value is also -9 163s 0 cases, 0 controls and 413 missing 163s 0 males, 0 females, and 413 of unspecified sex 163s Before frequency and genotyping pruning, there are 36901 SNPs 163s 413 founders and 0 non-founders found 163s Total genotyping rate in remaining individuals is 0.956644 163s 0 SNPs failed missingness test ( GENO > 1 ) 163s 0 SNPs failed frequency test ( MAF < 0 ) 163s After frequency and genotyping pruning, there are 36901 SNPs 163s After filtering, 0 cases, 0 controls and 413 missing 163s After filtering, 0 males, 0 females, and 413 of unspecified sex 163s Writing recoded ped file to [ sativas413_recode12.ped ] 164s Writing new map file to [ sativas413_recode12.map ] 164s 164s Analysis finished: Sat Mar 16 17:20:47 2024 164s 164s Store phenotype data indexed by genotype... 164s cd sativas_GWAS 164s Filter accessions for phenotype from ../sativas413_recode12... 164s Checking concurrence of id's in .ped and .pheno input files... 164s 164s Total number of accession ids in ../sativas413_recode12.ped: 413 164s Number of accession id's in ../sativas413_recode12.ped not present in rice_phenotype.txt: 35 164s '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' 164s Total number of accession id's in rice_phenotype.txt: 378 164s Number of accession id's in rice_phenotype.txt not present in ../sativas413_recode12.ped: 0 164s 164s Quality control sativas_GWAS... 164s 164s Calculating MAF... 164s /usr/bin/p-link --missing-genotype 0 --freq --file sativas_GWAS --out sativas_GWAS 164s 164s @----------------------------------------------------------@ 164s | PLINK! | v1.07 | 10/Aug/2009 | 164s |----------------------------------------------------------| 164s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 164s |----------------------------------------------------------| 164s | For documentation, citation & bug-report instructions: | 164s | http://pngu.mgh.harvard.edu/purcell/plink/ | 164s @----------------------------------------------------------@ 164s 164s Web-based version check ( --noweb to skip ) 164s Connecting to web... failed connection 164s 164s Problem connecting to web 164s 164s Writing this text to log file [ sativas_GWAS.log ] 164s Analysis started: Sat Mar 16 17:20:47 2024 164s 164s Options in effect: 164s --missing-genotype 0 164s --freq 164s --file sativas_GWAS 164s --out sativas_GWAS 164s 164s 36901 (of 36901) markers to be included from [ sativas_GWAS.map ] 166s Warning, found 378 individuals with ambiguous sex codes 166s These individuals will be set to missing ( or use --allow-no-sex ) 166s Writing list of these individuals to [ sativas_GWAS.nosex ] 166s 378 individuals read from [ sativas_GWAS.ped ] 166s 0 individuals with nonmissing phenotypes 166s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 166s Missing phenotype value is also -9 166s 0 cases, 0 controls and 378 missing 166s 0 males, 0 females, and 378 of unspecified sex 166s Before frequency and genotyping pruning, there are 36901 SNPs 166s 378 founders and 0 non-founders found 166s Writing allele frequencies (founders-only) to [ sativas_GWAS.frq ] 166s 166s Analysis finished: Sat Mar 16 17:20:49 2024 166s 166s Create sativas_GWAS.covar file... 166s /usr/lib/eigensoft/smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log 173s Transpose sativas_GWAS... 173s /usr/bin/p-link --missing-genotype 0 --recode --transpose --file sativas_GWAS --out sativas_GWAS 174s 174s @----------------------------------------------------------@ 174s | PLINK! | v1.07 | 10/Aug/2009 | 174s |----------------------------------------------------------| 174s | (C) 2009 Shaun Purcell, GNU General Public License, v2 | 174s |----------------------------------------------------------| 174s | For documentation, citation & bug-report instructions: | 174s | http://pngu.mgh.harvard.edu/purcell/plink/ | 174s @----------------------------------------------------------@ 174s 174s Web-based version check ( --noweb to skip ) 174s Recent cached web-check found...Problem connecting to web 174s 174s Writing this text to log file [ sativas_GWAS.log ] 174s Analysis started: Sat Mar 16 17:20:57 2024 174s 174s Options in effect: 174s --missing-genotype 0 174s --recode 174s --transpose 174s --file sativas_GWAS 174s --out sativas_GWAS 174s 174s 36901 (of 36901) markers to be included from [ sativas_GWAS.map ] 175s Warning, found 378 individuals with ambiguous sex codes 175s Writing list of these individuals to [ sativas_GWAS.nosex ] 175s 378 individuals read from [ sativas_GWAS.ped ] 175s 0 individuals with nonmissing phenotypes 175s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 175s Missing phenotype value is also -9 175s 0 cases, 0 controls and 378 missing 175s 0 males, 0 females, and 378 of unspecified sex 175s Before frequency and genotyping pruning, there are 36901 SNPs 175s 378 founders and 0 non-founders found 175s Total genotyping rate in remaining individuals is 0.956642 175s 0 SNPs failed missingness test ( GENO > 1 ) 175s 0 SNPs failed frequency test ( MAF < 0 ) 175s After frequency and genotyping pruning, there are 36901 SNPs 175s After filtering, 0 cases, 0 controls and 378 missing 175s After filtering, 0 males, 0 females, and 378 of unspecified sex 175s Writing transposed ped file to [ sativas_GWAS.tped ] 176s Writing family information to [ sativas_GWAS.tfam ] 176s 176s Analysis finished: Sat Mar 16 17:20:59 2024 176s 176s Creating sativas_GWAS.hIBS.kin kinship file using IBS method... 176s /usr/bin/emmax-kin -v -h -s -d 10 sativas_GWAS 176s 176s Reading TFAM file sativas_GWAS.tfam .... 176s 176s Reading TPED file sativas_GWAS.tped .... 176s Reading 0 SNPs 176s Reading 1000 SNPs 176s Reading 2000 SNPs 177s Reading 3000 SNPs 177s Reading 4000 SNPs 177s Reading 5000 SNPs 177s Reading 6000 SNPs 177s Reading 7000 SNPs 177s Reading 8000 SNPs 177s Reading 9000 SNPs 178s Reading 10000 SNPs 178s Reading 11000 SNPs 178s Reading 12000 SNPs 178s Reading 13000 SNPs 178s Reading 14000 SNPs 178s Reading 15000 SNPs 178s Reading 16000 SNPs 179s Reading 17000 SNPs 179s Reading 18000 SNPs 179s Reading 19000 SNPs 179s Reading 20000 SNPs 179s Reading 21000 SNPs 179s Reading 22000 SNPs 180s Reading 23000 SNPs 180s Reading 24000 SNPs 180s Reading 25000 SNPs 180s Reading 26000 SNPs 180s Reading 27000 SNPs 180s Reading 28000 SNPs 180s Reading 29000 SNPs 181s Reading 30000 SNPs 181s Reading 31000 SNPs 181s Reading 32000 SNPs 181s Reading 33000 SNPs 181s Reading 34000 SNPs 181s Reading 35000 SNPs 181s Reading 36000 SNPs 182s Printing the kinship matrix to file 182s Creating phenotype files in sub-directory sativas_GWAS... 182s 182s cd .. 182s removing temp files... 182s pique-run -d -v -i sativas_GWAS -k IBS -c sativas_GWAS.covar -n 16 182s Warning can't run 16 threads on this system - default to max = 2 threads 182s cd sativas_GWAS 182s Starting Q_grain_Co, pid = 7096 182s cd Q_grain_Co 182s processing phenotype Q_grain_Co... 182s 182s 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 182s cd A_Stem_thickness 182s processing phenotype A_Stem_thickness... 182s 182s 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 182s nmiss = 49 , mphenoflag = 1 182s nmiss = 90 , mphenoflag = 1 182s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 182s k = 282, n-q = 282 182s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.474006 182s k = 323, n-q = 323 186s 186s number of SNP ids in Q_grain_Co_sativas_GWAS.ps for 'Q_grain_Co' phenotype: 36901 186s number of SNP ids in Q_grain_Co_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Co' phenotype: 0 186s 186s number of SNP ids in sativas_GWAS.tped: 36901 186s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Co_sativas_GWAS.ps: 0 186s 187s Error in file(filename, "r", encoding = encoding) : 187s cannot open the connection 187s Calls: source -> file 187s In addition: Warning message: 187s In file(filename, "r", encoding = encoding) : 187s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 187s Execution halted 187s cd .. 187s Starting A_Stem_thickness, pid = 7097 187s Finished Q_grain_Co, pid = 7096, exit_code = 0 187s cd H_Root_dry_weight 187s processing phenotype H_Root_dry_weight... 187s 187s 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 187s nmiss = 260 , mphenoflag = 1 187s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 187s k = 112, n-q = 112 187s 187s number of SNP ids in A_Stem_thickness_sativas_GWAS.ps for 'A_Stem_thickness' phenotype: 36901 187s number of SNP ids in A_Stem_thickness_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Stem_thickness' phenotype: 0 187s 187s number of SNP ids in sativas_GWAS.tped: 36901 187s number of SNP ids in sativas_GWAS.tped not present in A_Stem_thickness_sativas_GWAS.ps: 0 187s 188s Error in file(filename, "r", encoding = encoding) : 188s cannot open the connection 188s Calls: source -> file 188s In addition: Warning message: 188s In file(filename, "r", encoding = encoding) : 188s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 188s Execution halted 188s cd .. 188s Starting H_Root_dry_weight, pid = 7112 188s Finished A_Stem_thickness, pid = 7097, exit_code = 0 188s cd Q_FT 188s processing phenotype Q_FT... 188s 188s 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 188s nmiss = 85 , mphenoflag = 1 188s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.399886 188s k = 287, n-q = 287 191s 191s number of SNP ids in H_Root_dry_weight_sativas_GWAS.ps for 'H_Root_dry_weight' phenotype: 36901 191s 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 191s 191s number of SNP ids in sativas_GWAS.tped: 36901 191s number of SNP ids in sativas_GWAS.tped not present in H_Root_dry_weight_sativas_GWAS.ps: 0 191s 191s Error in file(filename, "r", encoding = encoding) : 191s cannot open the connection 191s Calls: source -> file 191s In addition: Warning message: 191s In file(filename, "r", encoding = encoding) : 191s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 191s Execution halted 191s cd .. 192s 192s number of SNP ids in Q_FT_sativas_GWAS.ps for 'Q_FT' phenotype: 36901 192s number of SNP ids in Q_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_FT' phenotype: 0 192s 192s number of SNP ids in sativas_GWAS.tped: 36901 192s number of SNP ids in sativas_GWAS.tped not present in Q_FT_sativas_GWAS.ps: 0 192s 192s Starting Q_FT, pid = 7126 192s Finished H_Root_dry_weight, pid = 7112, exit_code = 0 192s cd Amylose_Content 192s processing phenotype Amylose_Content... 192s 192s 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 192s nmiss = 50 , mphenoflag = 1 193s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.447865 193s k = 322, n-q = 322 193s Error in file(filename, "r", encoding = encoding) : 193s cannot open the connection 193s Calls: source -> file 193s In addition: Warning message: 193s In file(filename, "r", encoding = encoding) : 193s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 193s Execution halted 193s cd .. 193s Starting Amylose_Content, pid = 7146 193s Finished Q_FT, pid = 7126, exit_code = 0 193s cd F_grain_As 193s processing phenotype F_grain_As... 193s 193s 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 193s nmiss = 73 , mphenoflag = 1 193s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 193s k = 299, n-q = 299 197s 197s number of SNP ids in Amylose_Content_sativas_GWAS.ps for 'Amylose_Content' phenotype: 36901 197s number of SNP ids in Amylose_Content_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Amylose_Content' phenotype: 0 197s 197s number of SNP ids in sativas_GWAS.tped: 36901 197s number of SNP ids in sativas_GWAS.tped not present in Amylose_Content_sativas_GWAS.ps: 0 197s 197s Error in file(filename, "r", encoding = encoding) : 197s cannot open the connection 197s Calls: source -> file 197s In addition: Warning message: 197s In file(filename, "r", encoding = encoding) : 197s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 197s Execution halted 197s cd .. 197s Starting F_grain_As, pid = 7154 197s Finished Amylose_Content, pid = 7146, exit_code = 0 197s cd H_R_S 197s processing phenotype H_R_S... 197s 197s 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 197s nmiss = 260 , mphenoflag = 1 197s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 197s k = 112, n-q = 112 197s 197s number of SNP ids in F_grain_As_sativas_GWAS.ps for 'F_grain_As' phenotype: 36901 197s number of SNP ids in F_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_As' phenotype: 0 197s 197s number of SNP ids in sativas_GWAS.tped: 36901 197s number of SNP ids in sativas_GWAS.tped not present in F_grain_As_sativas_GWAS.ps: 0 197s 198s Error in file(filename, "r", encoding = encoding) : 198s cannot open the connection 198s Calls: source -> file 198s In addition: Warning message: 198s In file(filename, "r", encoding = encoding) : 198s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 198s Execution halted 198s cd .. 198s Starting H_R_S, pid = 7168 198s Finished F_grain_As, pid = 7154, exit_code = 0 198s cd Q_shoot_mass 198s processing phenotype Q_shoot_mass... 198s 198s 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 198s nmiss = 87 , mphenoflag = 1 198s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.413538 198s k = 285, n-q = 285 199s 199s number of SNP ids in H_R_S_sativas_GWAS.ps for 'H_R_S' phenotype: 36901 199s number of SNP ids in H_R_S_sativas_GWAS.ps not present in sativas_GWAS.tped for 'H_R_S' phenotype: 0 199s 199s number of SNP ids in sativas_GWAS.tped: 36901 199s number of SNP ids in sativas_GWAS.tped not present in H_R_S_sativas_GWAS.ps: 0 199s 199s Error in file(filename, "r", encoding = encoding) : 199s cannot open the connection 199s Calls: source -> file 199s In addition: Warning message: 199s In file(filename, "r", encoding = encoding) : 199s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 199s Execution halted 199s cd .. 199s Starting Q_shoot_mass, pid = 7182 199s Finished H_R_S, pid = 7168, exit_code = 0 199s cd F_grain_yield 199s processing phenotype F_grain_yield... 199s 199s 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 199s nmiss = 73 , mphenoflag = 1 199s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 199s k = 299, n-q = 299 202s 202s number of SNP ids in Q_shoot_mass_sativas_GWAS.ps for 'Q_shoot_mass' phenotype: 36901 202s number of SNP ids in Q_shoot_mass_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_shoot_mass' phenotype: 0 202s 202s number of SNP ids in sativas_GWAS.tped: 36901 202s number of SNP ids in sativas_GWAS.tped not present in Q_shoot_mass_sativas_GWAS.ps: 0 202s 202s Error in file(filename, "r", encoding = encoding) : 202s cannot open the connection 202s Calls: source -> file 202s In addition: Warning message: 202s In file(filename, "r", encoding = encoding) : 202s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 202s Execution halted 202s cd .. 203s Starting F_grain_yield, pid = 7196 203s Finished Q_shoot_mass, pid = 7182, exit_code = 0 203s cd HULLED_SEED_LENGTH 203s processing phenotype HULLED_SEED_LENGTH... 203s 203s 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 203s nmiss = 34 , mphenoflag = 1 203s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.481982 203s k = 338, n-q = 338 204s 204s number of SNP ids in F_grain_yield_sativas_GWAS.ps for 'F_grain_yield' phenotype: 36901 204s number of SNP ids in F_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_yield' phenotype: 0 204s 204s number of SNP ids in sativas_GWAS.tped: 36901 204s number of SNP ids in sativas_GWAS.tped not present in F_grain_yield_sativas_GWAS.ps: 0 204s 204s Error in file(filename, "r", encoding = encoding) : 204s cannot open the connection 204s Calls: source -> file 204s In addition: Warning message: 204s In file(filename, "r", encoding = encoding) : 204s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 204s Execution halted 204s cd .. 204s Starting HULLED_SEED_LENGTH, pid = 7210 204s Finished F_grain_yield, pid = 7196, exit_code = 0 204s cd A_PH 204s processing phenotype A_PH... 204s 204s 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 204s nmiss = 29 , mphenoflag = 1 204s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.570052 204s k = 343, n-q = 343 208s 208s number of SNP ids in HULLED_SEED_LENGTH_sativas_GWAS.ps for 'HULLED_SEED_LENGTH' phenotype: 36901 208s number of SNP ids in HULLED_SEED_LENGTH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'HULLED_SEED_LENGTH' phenotype: 0 208s 208s number of SNP ids in sativas_GWAS.tped: 36901 208s number of SNP ids in sativas_GWAS.tped not present in HULLED_SEED_LENGTH_sativas_GWAS.ps: 0 208s 208s Error in file(filename, "r", encoding = encoding) : 208s cannot open the connection 208s Calls: source -> file 208s In addition: Warning message: 208s In file(filename, "r", encoding = encoding) : 208s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 208s Execution halted 208s cd .. 208s Starting A_PH, pid = 7224 208s Finished HULLED_SEED_LENGTH, pid = 7210, exit_code = 0 208s cd A_Tiller_no. 208s processing phenotype A_Tiller_no.... 208s 208s 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 208s nmiss = 46 , mphenoflag = 1 208s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.524438 208s k = 326, n-q = 326 209s 209s number of SNP ids in A_PH_sativas_GWAS.ps for 'A_PH' phenotype: 36901 209s number of SNP ids in A_PH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_PH' phenotype: 0 209s 209s number of SNP ids in sativas_GWAS.tped: 36901 209s number of SNP ids in sativas_GWAS.tped not present in A_PH_sativas_GWAS.ps: 0 209s 209s Error in file(filename, "r", encoding = encoding) : 209s cannot open the connection 209s Calls: source -> file 209s In addition: Warning message: 209s In file(filename, "r", encoding = encoding) : 209s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 209s Execution halted 209s cd .. 210s Starting A_Tiller_no., pid = 7238 210s Finished A_PH, pid = 7224, exit_code = 0 210s cd H_Shoot_dry_weight 210s processing phenotype H_Shoot_dry_weight... 210s 210s 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 210s nmiss = 260 , mphenoflag = 1 210s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 210s k = 112, n-q = 112 212s 212s number of SNP ids in H_Shoot_dry_weight_sativas_GWAS.ps for 'H_Shoot_dry_weight' phenotype: 36901 212s 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 212s 212s number of SNP ids in sativas_GWAS.tped: 36901 212s number of SNP ids in sativas_GWAS.tped not present in H_Shoot_dry_weight_sativas_GWAS.ps: 0 212s 212s Error in file(filename, "r", encoding = encoding) : 212s cannot open the connection 212s Calls: source -> file 212s In addition: Warning message: 212s In file(filename, "r", encoding = encoding) : 212s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 212s Execution halted 212s cd .. 212s Starting H_Shoot_dry_weight, pid = 7252 212s Finished H_Shoot_dry_weight, pid = 7252, exit_code = 0 212s cd A_Seed_length 212s processing phenotype A_Seed_length... 212s 212s 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 212s nmiss = 20 , mphenoflag = 1 212s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.577637 212s k = 352, n-q = 352 213s 213s number of SNP ids in A_Tiller_no._sativas_GWAS.ps for 'A_Tiller_no.' phenotype: 36901 213s number of SNP ids in A_Tiller_no._sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Tiller_no.' phenotype: 0 213s 213s number of SNP ids in sativas_GWAS.tped: 36901 213s number of SNP ids in sativas_GWAS.tped not present in A_Tiller_no._sativas_GWAS.ps: 0 213s 213s Error in file(filename, "r", encoding = encoding) : 213s cannot open the connection 213s Calls: source -> file 213s In addition: Warning message: 213s In file(filename, "r", encoding = encoding) : 213s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 213s Execution halted 213s cd .. 213s Starting A_Seed_length, pid = 7266 213s Finished A_Tiller_no., pid = 7238, exit_code = 0 213s cd Daniel_shoot_As 213s processing phenotype Daniel_shoot_As... 213s 213s 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 213s nmiss = 40 , mphenoflag = 1 213s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.552770 213s k = 332, n-q = 332 217s 217s number of SNP ids in A_Seed_length_sativas_GWAS.ps for 'A_Seed_length' phenotype: 36901 217s number of SNP ids in A_Seed_length_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Seed_length' phenotype: 0 217s 217s number of SNP ids in sativas_GWAS.tped: 36901 217s number of SNP ids in sativas_GWAS.tped not present in A_Seed_length_sativas_GWAS.ps: 0 217s 218s Error in file(filename, "r", encoding = encoding) : 218s cannot open the connection 218s Calls: source -> file 218s In addition: Warning message: 218s In file(filename, "r", encoding = encoding) : 218s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 218s Execution halted 218s cd .. 218s 218s number of SNP ids in Daniel_shoot_As_sativas_GWAS.ps for 'Daniel_shoot_As' phenotype: 36901 218s number of SNP ids in Daniel_shoot_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Daniel_shoot_As' phenotype: 0 218s 218s number of SNP ids in sativas_GWAS.tped: 36901 218s number of SNP ids in sativas_GWAS.tped not present in Daniel_shoot_As_sativas_GWAS.ps: 0 218s 218s Error in file(filename, "r", encoding = encoding) : 218s cannot open the connection 218s Calls: source -> file 218s In addition: Warning message: 218s In file(filename, "r", encoding = encoding) : 218s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 218s Execution halted 218s cd .. 218s Starting Daniel_shoot_As, pid = 7280 218s Finished Daniel_shoot_As, pid = 7280, exit_code = 0 218s Finished A_Seed_length, pid = 7266, exit_code = 0 218s Starting F_FT, pid = 7306 218s cd F_FT 218s processing phenotype F_FT... 218s 218s 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 218s cd F_shoot_As 218s processing phenotype F_shoot_As... 218s 218s 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 218s nmiss = 73 , mphenoflag = 1 218s nmiss = 73 , mphenoflag = 1 218s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 218s k = 299, n-q = 299 218s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.459771 218s k = 299, n-q = 299 223s 223s number of SNP ids in F_shoot_As_sativas_GWAS.ps for 'F_shoot_As' phenotype: 36901 223s number of SNP ids in F_shoot_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_shoot_As' phenotype: 0 223s 223s number of SNP ids in sativas_GWAS.tped: 36901 223s number of SNP ids in sativas_GWAS.tped not present in F_shoot_As_sativas_GWAS.ps: 0 223s 223s 223s number of SNP ids in F_FT_sativas_GWAS.ps for 'F_FT' phenotype: 36901 223s number of SNP ids in F_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_FT' phenotype: 0 223s 223s number of SNP ids in sativas_GWAS.tped: 36901 223s number of SNP ids in sativas_GWAS.tped not present in F_FT_sativas_GWAS.ps: 0 223s 223s Error in file(filename, "r", encoding = encoding) : 223s cannot open the connection 223s Calls: source -> file 223s In addition: Warning message: 223s In file(filename, "r", encoding = encoding) : 223s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 223s Execution halted 223s Error in file(filename, "r", encoding = encoding) : 223s cannot open the connection 223s Calls: source -> file 223s In addition: Warning message: 223s In file(filename, "r", encoding = encoding) : 223s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 223s Execution halted 223s cd .. 223s cd .. 223s Starting F_shoot_As, pid = 7307 223s Finished F_FT, pid = 7306, exit_code = 0 223s Finished F_shoot_As, pid = 7307, exit_code = 0 223s Starting A_Seed_weight, pid = 7334 223s cd A_Seed_weight 223s processing phenotype A_Seed_weight... 223s 223s 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 223s cd A_FT 223s processing phenotype A_FT... 223s 223s 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 223s nmiss = 21 , mphenoflag = 1 223s nmiss = 19 , mphenoflag = 1 224s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.575045 224s k = 351, n-q = 351 224s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.578644 224s k = 353, n-q = 353 228s 228s number of SNP ids in A_Seed_weight_sativas_GWAS.ps for 'A_Seed_weight' phenotype: 36901 228s number of SNP ids in A_Seed_weight_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Seed_weight' phenotype: 0 228s 228s number of SNP ids in sativas_GWAS.tped: 36901 228s number of SNP ids in sativas_GWAS.tped not present in A_Seed_weight_sativas_GWAS.ps: 0 228s 229s 229s number of SNP ids in A_FT_sativas_GWAS.ps for 'A_FT' phenotype: 36901 229s number of SNP ids in A_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_FT' phenotype: 0 229s 229s number of SNP ids in sativas_GWAS.tped: 36901 229s number of SNP ids in sativas_GWAS.tped not present in A_FT_sativas_GWAS.ps: 0 229s 229s Error in file(filename, "r", encoding = encoding) : 229s cannot open the connection 229s Calls: source -> file 229s In addition: Warning message: 229s In file(filename, "r", encoding = encoding) : 229s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 229s Execution halted 229s Error in file(filename, "r", encoding = encoding) : 229s cannot open the connection 229s Calls: source -> file 229s In addition: Warning message: 229s In file(filename, "r", encoding = encoding) : 229s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 229s Execution halted 229s cd .. 229s cd .. 229s Starting A_FT, pid = 7335 229s Finished A_FT, pid = 7335, exit_code = 0 229s Finished A_Seed_weight, pid = 7334, exit_code = 0 229s Starting H_Shoot_length_27, pid = 7362 229s cd H_Shoot_length_27 229s processing phenotype H_Shoot_length_27... 229s 229s 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 229s cd Q_grain_Cu 229s processing phenotype Q_grain_Cu... 229s 229s 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 229s nmiss = 260 , mphenoflag = 1 229s nmiss = 90 , mphenoflag = 1 229s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 229s k = 112, n-q = 112 229s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 229s k = 282, n-q = 282 231s 231s number of SNP ids in H_Shoot_length_27_sativas_GWAS.ps for 'H_Shoot_length_27' phenotype: 36901 231s 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 231s 231s number of SNP ids in sativas_GWAS.tped: 36901 231s number of SNP ids in sativas_GWAS.tped not present in H_Shoot_length_27_sativas_GWAS.ps: 0 231s 231s Error in file(filename, "r", encoding = encoding) : 231s cannot open the connection 231s Calls: source -> file 231s In addition: Warning message: 231s In file(filename, "r", encoding = encoding) : 231s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 231s Execution halted 231s cd .. 231s Starting Q_grain_Cu, pid = 7363 231s Finished H_Shoot_length_27, pid = 7362, exit_code = 0 231s cd Q_PH 231s processing phenotype Q_PH... 231s 231s 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 231s nmiss = 87 , mphenoflag = 1 231s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.413538 231s k = 285, n-q = 285 233s 233s number of SNP ids in Q_grain_Cu_sativas_GWAS.ps for 'Q_grain_Cu' phenotype: 36901 233s number of SNP ids in Q_grain_Cu_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Cu' phenotype: 0 233s 233s number of SNP ids in sativas_GWAS.tped: 36901 233s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Cu_sativas_GWAS.ps: 0 233s 233s Error in file(filename, "r", encoding = encoding) : 233s cannot open the connection 233s Calls: source -> file 233s In addition: Warning message: 233s In file(filename, "r", encoding = encoding) : 233s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 233s Execution halted 233s cd .. 233s Starting Q_PH, pid = 7378 233s Finished Q_grain_Cu, pid = 7363, exit_code = 0 233s cd Q_grain_As 233s processing phenotype Q_grain_As... 233s 233s 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 233s nmiss = 90 , mphenoflag = 1 233s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 233s k = 282, n-q = 282 235s 235s number of SNP ids in Q_PH_sativas_GWAS.ps for 'Q_PH' phenotype: 36901 235s number of SNP ids in Q_PH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_PH' phenotype: 0 235s 235s number of SNP ids in sativas_GWAS.tped: 36901 235s number of SNP ids in sativas_GWAS.tped not present in Q_PH_sativas_GWAS.ps: 0 235s 235s Error in file(filename, "r", encoding = encoding) : 235s cannot open the connection 235s Calls: source -> file 235s In addition: Warning message: 235s In file(filename, "r", encoding = encoding) : 235s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 235s Execution halted 235s cd .. 236s Starting Q_grain_As, pid = 7392 236s Finished Q_PH, pid = 7378, exit_code = 0 236s cd F_As_TF 236s processing phenotype F_As_TF... 236s 236s 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 236s nmiss = 75 , mphenoflag = 1 237s evals[0] = -0.000000, evals[1] = 0.000000, evals[n-1] = 2.455247 237s k = 297, n-q = 297 237s 237s number of SNP ids in Q_grain_As_sativas_GWAS.ps for 'Q_grain_As' phenotype: 36901 237s number of SNP ids in Q_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_As' phenotype: 0 237s 237s number of SNP ids in sativas_GWAS.tped: 36901 237s number of SNP ids in sativas_GWAS.tped not present in Q_grain_As_sativas_GWAS.ps: 0 237s 237s Error in file(filename, "r", encoding = encoding) : 237s cannot open the connection 237s Calls: source -> file 237s In addition: Warning message: 237s In file(filename, "r", encoding = encoding) : 237s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 237s Execution halted 237s cd .. 238s Starting F_As_TF, pid = 7406 238s Finished Q_grain_As, pid = 7392, exit_code = 0 238s cd A_grain_yield 238s processing phenotype A_grain_yield... 238s 238s 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 238s nmiss = 49 , mphenoflag = 1 239s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.520537 239s k = 323, n-q = 323 240s 240s number of SNP ids in F_As_TF_sativas_GWAS.ps for 'F_As_TF' phenotype: 36901 240s number of SNP ids in F_As_TF_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_As_TF' phenotype: 0 240s 240s number of SNP ids in sativas_GWAS.tped: 36901 240s number of SNP ids in sativas_GWAS.tped not present in F_As_TF_sativas_GWAS.ps: 0 240s 241s Error in file(filename, "r", encoding = encoding) : 241s cannot open the connection 241s Calls: source -> file 241s In addition: Warning message: 241s In file(filename, "r", encoding = encoding) : 241s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 241s Execution halted 241s cd .. 241s Starting A_grain_yield, pid = 7420 241s Finished F_As_TF, pid = 7406, exit_code = 0 241s cd India_grain_As 241s processing phenotype India_grain_As... 241s 241s 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 241s nmiss = 280 , mphenoflag = 1 241s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.487105 241s k = 92, n-q = 92 243s 243s number of SNP ids in India_grain_As_sativas_GWAS.ps for 'India_grain_As' phenotype: 36901 243s number of SNP ids in India_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'India_grain_As' phenotype: 0 243s 243s number of SNP ids in sativas_GWAS.tped: 36901 243s number of SNP ids in sativas_GWAS.tped not present in India_grain_As_sativas_GWAS.ps: 0 243s 243s 243s number of SNP ids in A_grain_yield_sativas_GWAS.ps for 'A_grain_yield' phenotype: 36901 243s number of SNP ids in A_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_grain_yield' phenotype: 0 243s 243s number of SNP ids in sativas_GWAS.tped: 36901 243s number of SNP ids in sativas_GWAS.tped not present in A_grain_yield_sativas_GWAS.ps: 0 243s 243s Error in file(filename, "r", encoding = encoding) : 243s cannot open the connection 243s Calls: source -> file 243s In addition: Warning message: 243s In file(filename, "r", encoding = encoding) : 243s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 243s Execution halted 243s Error in file(filename, "r", encoding = encoding) : 243s cannot open the connection 243s Calls: source -> file 243s In addition: Warning message: 243s In file(filename, "r", encoding = encoding) : 243s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 243s Execution halted 243s cd .. 243s cd .. 244s Starting India_grain_As, pid = 7434 244s Finished A_grain_yield, pid = 7420, exit_code = 0 244s Finished India_grain_As, pid = 7434, exit_code = 0 244s Starting F_grain_Zn, pid = 7460 244s cd F_grain_Zn 244s processing phenotype F_grain_Zn... 244s 244s 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 244s cd F_grain_Cu 244s processing phenotype F_grain_Cu... 244s 244s 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 244s nmiss = 73 , mphenoflag = 1 244s nmiss = 73 , mphenoflag = 1 245s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 245s k = 299, n-q = 299 245s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 245s k = 299, n-q = 299 249s 249s number of SNP ids in F_grain_Zn_sativas_GWAS.ps for 'F_grain_Zn' phenotype: 36901 249s number of SNP ids in F_grain_Zn_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Zn' phenotype: 0 249s 249s number of SNP ids in sativas_GWAS.tped: 36901 249s number of SNP ids in sativas_GWAS.tped not present in F_grain_Zn_sativas_GWAS.ps: 0 249s 249s 249s number of SNP ids in F_grain_Cu_sativas_GWAS.ps for 'F_grain_Cu' phenotype: 36901 249s number of SNP ids in F_grain_Cu_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Cu' phenotype: 0 249s 249s number of SNP ids in sativas_GWAS.tped: 36901 249s number of SNP ids in sativas_GWAS.tped not present in F_grain_Cu_sativas_GWAS.ps: 0 249s 249s Error in file(filename, "r", encoding = encoding) : 249s cannot open the connection 249s Calls: source -> file 249s In addition: Warning message: 249s In file(filename, "r", encoding = encoding) : 249s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 249s Execution halted 249s cd .. 249s Error in file(filename, "r", encoding = encoding) : 249s cannot open the connection 249s Calls: source -> file 249s In addition: Warning message: 249s In file(filename, "r", encoding = encoding) : 249s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 249s Execution halted 249s cd .. 250s Starting F_grain_Cu, pid = 7461 250s Finished F_grain_Cu, pid = 7461, exit_code = 0 250s Finished F_grain_Zn, pid = 7460, exit_code = 0 250s Starting Q_grain_Zn, pid = 7488 250s cd Q_grain_Zn 250s processing phenotype Q_grain_Zn... 250s 250s 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 250s cd H_Root_Length_27 250s processing phenotype H_Root_Length_27... 250s 250s 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 250s nmiss = 90 , mphenoflag = 1 250s nmiss = 260 , mphenoflag = 1 250s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689 250s k = 112, n-q = 112 250s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 250s k = 282, n-q = 282 251s 251s number of SNP ids in H_Root_Length_27_sativas_GWAS.ps for 'H_Root_Length_27' phenotype: 36901 251s 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 251s 251s number of SNP ids in sativas_GWAS.tped: 36901 251s number of SNP ids in sativas_GWAS.tped not present in H_Root_Length_27_sativas_GWAS.ps: 0 251s 251s Error in file(filename, "r", encoding = encoding) : 251s cannot open the connection 251s Calls: source -> file 251s In addition: Warning message: 251s In file(filename, "r", encoding = encoding) : 251s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 251s Execution halted 251s cd .. 252s Starting H_Root_Length_27, pid = 7489 252s Finished H_Root_Length_27, pid = 7489, exit_code = 0 252s cd Q_grain_Mo 252s processing phenotype Q_grain_Mo... 252s 252s 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 252s nmiss = 90 , mphenoflag = 1 252s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551 252s k = 282, n-q = 282 253s 253s number of SNP ids in Q_grain_Zn_sativas_GWAS.ps for 'Q_grain_Zn' phenotype: 36901 253s number of SNP ids in Q_grain_Zn_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Zn' phenotype: 0 253s 253s number of SNP ids in sativas_GWAS.tped: 36901 253s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Zn_sativas_GWAS.ps: 0 253s 253s Error in file(filename, "r", encoding = encoding) : 253s cannot open the connection 253s Calls: source -> file 253s In addition: Warning message: 253s In file(filename, "r", encoding = encoding) : 253s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 253s Execution halted 253s cd .. 254s Starting Q_grain_Mo, pid = 7504 254s Finished Q_grain_Zn, pid = 7488, exit_code = 0 254s cd F_grain_Mo 254s processing phenotype F_grain_Mo... 254s 254s 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 254s nmiss = 73 , mphenoflag = 1 254s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843 254s k = 299, n-q = 299 256s 256s number of SNP ids in Q_grain_Mo_sativas_GWAS.ps for 'Q_grain_Mo' phenotype: 36901 256s number of SNP ids in Q_grain_Mo_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Mo' phenotype: 0 256s 256s number of SNP ids in sativas_GWAS.tped: 36901 256s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Mo_sativas_GWAS.ps: 0 256s 256s Error in file(filename, "r", encoding = encoding) : 256s cannot open the connection 256s Calls: source -> file 256s In addition: Warning message: 256s In file(filename, "r", encoding = encoding) : 256s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 256s Execution halted 256s cd .. 257s Starting F_grain_Mo, pid = 7518 257s Finished Q_grain_Mo, pid = 7504, exit_code = 0 257s cd Q_grain_yield 257s processing phenotype Q_grain_yield... 257s 257s 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 257s nmiss = 91 , mphenoflag = 1 257s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.399146 257s k = 281, n-q = 281 258s 258s number of SNP ids in F_grain_Mo_sativas_GWAS.ps for 'F_grain_Mo' phenotype: 36901 258s number of SNP ids in F_grain_Mo_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Mo' phenotype: 0 258s 258s number of SNP ids in sativas_GWAS.tped: 36901 258s number of SNP ids in sativas_GWAS.tped not present in F_grain_Mo_sativas_GWAS.ps: 0 258s 258s Error in file(filename, "r", encoding = encoding) : 258s cannot open the connection 258s Calls: source -> file 258s In addition: Warning message: 258s In file(filename, "r", encoding = encoding) : 258s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 258s Execution halted 258s cd .. 260s 260s number of SNP ids in Q_grain_yield_sativas_GWAS.ps for 'Q_grain_yield' phenotype: 36901 260s number of SNP ids in Q_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_yield' phenotype: 0 260s 260s number of SNP ids in sativas_GWAS.tped: 36901 260s number of SNP ids in sativas_GWAS.tped not present in Q_grain_yield_sativas_GWAS.ps: 0 260s 261s Error in file(filename, "r", encoding = encoding) : 261s cannot open the connection 261s Calls: source -> file 261s In addition: Warning message: 261s In file(filename, "r", encoding = encoding) : 261s cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory 261s Execution halted 261s cd .. 262s Starting Q_grain_yield, pid = 7532 262s Finished F_grain_Mo, pid = 7518, exit_code = 0 262s Finished Q_grain_yield, pid = 7532, exit_code = 0 262s Analysis complete 262s 262s autopkgtest [17:22:25]: test run-unit-test: -----------------------] 263s run-unit-test PASS 263s autopkgtest [17:22:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 263s autopkgtest [17:22:26]: @@@@@@@@@@@@@@@@@@@@ summary 263s run-unit-test PASS 281s Creating nova instance adt-noble-arm64-pique-20240316-171803-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...