0s autopkgtest [03:29:32]: starting date: 2024-03-11
  0s autopkgtest [03:29:32]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline
  0s autopkgtest [03:29:32]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wjhnann3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:perl,src:db5.3,src:gdbm,src:mmdebstrap --apt-upgrade pique --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 db5.3/5.3.28+dfsg2-5 gdbm/1.23-5.1 mmdebstrap/1.4.3-6' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-10.secgroup --name adt-noble-arm64-pique-20240311-032931-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 70s autopkgtest [03:30:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 70s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 70s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B]
 70s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [434 kB]
 71s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB]
 71s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2615 kB]
 71s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [581 kB]
 71s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 71s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB]
 71s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 71s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2990 kB]
 71s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 71s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB]
 71s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
 72s Fetched 6850 kB in 1s (4997 kB/s)
 72s Reading package lists...
 75s Reading package lists...
 75s Building dependency tree...
 75s Reading state information...
 75s Calculating upgrade...
 76s The following packages were automatically installed and are no longer required:
 76s   libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38
 76s Use 'sudo apt autoremove' to remove them.
 76s The following packages will be REMOVED:
 76s   dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl
 76s The following NEW packages will be installed:
 76s   libgdbm-compat4t64 libgdbm6t64
 76s The following packages have been kept back:
 76s   libperl5.38
 76s The following packages will be upgraded:
 76s   perl-base perl-modules-5.38
 76s 2 upgraded, 2 newly installed, 5 to remove and 1 not upgraded.
 76s Need to get 4928 kB of archives.
 76s After this operation, 4158 kB disk space will be freed.
 76s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB]
 77s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB]
 77s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B]
 77s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB]
 77s Fetched 4928 kB in 1s (6479 kB/s)
 77s (Reading database ... 
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(Reading database ... 74748 files and directories currently installed.)
 77s Removing dpkg-dev (1.22.4ubuntu5) ...
 77s Removing libdpkg-perl (1.22.4ubuntu5) ...
 77s Removing perl (5.38.2-3) ...
 78s (Reading database ... 
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(Reading database ... 74167 files and directories currently installed.)
 78s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ...
 78s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ...
 78s Setting up perl-base (5.38.2-3.2) ...
 78s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested:
 78s  python3-gdbm:arm64 depends on libgdbm6 (>= 1.16).
 78s  man-db depends on libgdbm6 (>= 1.16).
 78s  libperl5.38:arm64 depends on libgdbm6 (>= 1.21).
 78s  libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16).
 78s 
 78s (Reading database ... 
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(Reading database ... 74167 files and directories currently installed.)
 78s Removing libgdbm6:arm64 (1.23-5) ...
 78s Selecting previously unselected package libgdbm6t64:arm64.
 78s (Reading database ... 
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(Reading database ... 74162 files and directories currently installed.)
 78s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ...
 78s Unpacking libgdbm6t64:arm64 (1.23-5.1) ...
 78s dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested:
 78s  libperl5.38:arm64 depends on libgdbm-compat4 (>= 1.18-3).
 78s 
 78s (Reading database ... 
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(Reading database ... 74168 files and directories currently installed.)
 78s Removing libgdbm-compat4:arm64 (1.23-5) ...
 78s Selecting previously unselected package libgdbm-compat4t64:arm64.
 78s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 74163 files and directories currently installed.)
 78s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_arm64.deb ...
 78s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ...
 78s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ...
 78s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ...
 78s Setting up libgdbm6t64:arm64 (1.23-5.1) ...
 78s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ...
 78s Setting up perl-modules-5.38 (5.38.2-3.2) ...
 78s Processing triggers for man-db (2.12.0-3) ...
 80s Processing triggers for libc-bin (2.39-0ubuntu2) ...
 80s Reading package lists...
 80s Building dependency tree...
 80s Reading state information...
 81s The following packages will be REMOVED:
 81s   libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38*
 81s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded.
 81s After this operation, 52.0 MB disk space will be freed.
 81s (Reading database ... 
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(Reading database ... 74169 files and directories currently installed.)
 81s Removing libperl5.38:arm64 (5.38.2-3) ...
 81s Removing libgdbm-compat4t64:arm64 (1.23-5.1) ...
 81s Removing lto-disabled-list (47) ...
 81s Removing make (4.3-4.1build1) ...
 81s Removing perl-modules-5.38 (5.38.2-3.2) ...
 81s Processing triggers for man-db (2.12.0-3) ...
 81s Processing triggers for libc-bin (2.39-0ubuntu2) ...
 82s sh: Attempting to set up Debian/Ubuntu apt sources automatically
 82s sh: Distribution appears to be Ubuntu
 83s Reading package lists...
 83s Building dependency tree...
 83s Reading state information...
 84s eatmydata is already the newest version (131-1).
 84s dbus is already the newest version (1.14.10-4ubuntu1).
 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 84s Reading package lists...
 84s Building dependency tree...
 84s Reading state information...
 85s rng-tools-debian is already the newest version (2.4).
 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 85s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 85s haveged is already the newest version (1.9.14-1ubuntu1).
 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 85s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 86s The following additional packages will be installed:
 86s   libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list
 86s   make perl perl-modules-5.38
 86s Suggested packages:
 86s   debian-keyring gcc | c-compiler git bzr make-doc perl-doc
 86s   libterm-readline-gnu-perl | libterm-readline-perl-perl
 86s   libtap-harness-archive-perl
 86s Recommended packages:
 86s   build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl
 86s   libfile-fcntllock-perl
 86s The following packages will be REMOVED:
 86s   libdb5.3
 86s The following NEW packages will be installed:
 86s   dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64
 86s   lto-disabled-list make perl perl-modules-5.38
 86s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded.
 86s Need to get 7257 kB/10.4 MB of archives.
 86s After this operation, 56.1 MB of additional disk space will be used.
 86s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB]
 87s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB]
 88s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB]
 88s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.4ubuntu5 [268 kB]
 88s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build1 [177 kB]
 88s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB]
 88s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.4ubuntu5 [1078 kB]
 89s Fetched 7257 kB in 2s (3111 kB/s)
 89s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested:
 89s  libsasl2-modules-db:arm64 depends on libdb5.3.
 89s  libpython3.12-stdlib:arm64 depends on libdb5.3.
 89s  libpam-modules:arm64 depends on libdb5.3.
 89s  iproute2 depends on libdb5.3.
 89s  apt-utils depends on libdb5.3.
 89s 
 89s (Reading database ... 
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(Reading database ... 72198 files and directories currently installed.)
 89s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ...
 89s Selecting previously unselected package libdb5.3t64:arm64.
 89s (Reading database ... 
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(Reading database ... 72192 files and directories currently installed.)
 89s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_arm64.deb ...
 89s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5) ...
 89s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5) ...
 89s Selecting previously unselected package perl-modules-5.38.
 89s (Reading database ... 
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(Reading database ... 72198 files and directories currently installed.)
 89s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ...
 89s Unpacking perl-modules-5.38 (5.38.2-3.2) ...
 89s Selecting previously unselected package libgdbm-compat4t64:arm64.
 89s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_arm64.deb ...
 89s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ...
 89s Selecting previously unselected package libperl5.38t64:arm64.
 89s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_arm64.deb ...
 89s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ...
 89s Selecting previously unselected package perl.
 89s Preparing to unpack .../3-perl_5.38.2-3.2_arm64.deb ...
 90s Unpacking perl (5.38.2-3.2) ...
 90s Selecting previously unselected package libdpkg-perl.
 90s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ...
 90s Unpacking libdpkg-perl (1.22.4ubuntu5) ...
 90s Selecting previously unselected package make.
 90s Preparing to unpack .../5-make_4.3-4.1build1_arm64.deb ...
 90s Unpacking make (4.3-4.1build1) ...
 90s Selecting previously unselected package lto-disabled-list.
 90s Preparing to unpack .../6-lto-disabled-list_47_all.deb ...
 90s Unpacking lto-disabled-list (47) ...
 90s Selecting previously unselected package dpkg-dev.
 90s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ...
 90s Unpacking dpkg-dev (1.22.4ubuntu5) ...
 90s Setting up lto-disabled-list (47) ...
 90s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ...
 90s Setting up make (4.3-4.1build1) ...
 90s Setting up perl-modules-5.38 (5.38.2-3.2) ...
 90s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ...
 90s Setting up perl (5.38.2-3.2) ...
 90s Setting up libdpkg-perl (1.22.4ubuntu5) ...
 90s Setting up dpkg-dev (1.22.4ubuntu5) ...
 90s Processing triggers for man-db (2.12.0-3) ...
 91s Processing triggers for libc-bin (2.39-0ubuntu2) ...
 91s Reading package lists...
 91s Building dependency tree...
 91s Reading state information...
 91s The following packages will be REMOVED:
 91s   cloud-init* python3-configobj* python3-debconf*
 92s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
 92s After this operation, 3248 kB disk space will be freed.
 92s (Reading database ... 
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74750 files and directories currently installed.)
 92s Removing cloud-init (24.1-0ubuntu1) ...
 92s Removing python3-configobj (5.0.8-3) ...
 92s Removing python3-debconf (1.5.86) ...
 92s Processing triggers for man-db (2.12.0-3) ...
 93s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74361 files and directories currently installed.)
 93s Purging configuration files for cloud-init (24.1-0ubuntu1) ...
 93s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
 93s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
 94s Reading package lists...
 94s Building dependency tree...
 94s Reading state information...
 94s linux-generic is already the newest version (6.8.0-11.11+1).
 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 95s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
 95s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
 95s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
 95s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
 96s Reading package lists...
 96s Reading package lists...
 96s Building dependency tree...
 96s Reading state information...
 97s Calculating upgrade...
 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 97s Reading package lists...
 97s Building dependency tree...
 97s Reading state information...
 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 98s autopkgtest [03:31:10]: rebooting testbed after setup commands that affected boot
327s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
333s autopkgtest [03:35:05]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
333s autopkgtest [03:35:05]: testbed dpkg architecture: arm64
334s autopkgtest [03:35:06]: @@@@@@@@@@@@@@@@@@@@ apt-source pique
337s Get:1 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (dsc) [2005 B]
337s Get:2 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (tar) [2017 kB]
337s Get:3 http://ftpmaster.internal/ubuntu noble/universe pique 1.0-7 (diff) [5236 B]
338s gpgv: Signature made Tue Dec 12 20:17:37 2023 UTC
338s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
338s gpgv:                issuer "tille@debian.org"
338s gpgv: Can't check signature: No public key
338s dpkg-source: warning: cannot verify inline signature for ./pique_1.0-7.dsc: no acceptable signature found
338s autopkgtest [03:35:10]: testing package pique version 1.0-7
338s autopkgtest [03:35:10]: build not needed
339s autopkgtest [03:35:11]: test run-unit-test: preparing testbed
341s Reading package lists...
341s Building dependency tree...
341s Reading state information...
341s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
342s Starting 2 pkgProblemResolver with broken count: 0
342s Done
342s  Done
342s Starting pkgProblemResolver with broken count: 0
342s Starting 2 pkgProblemResolver with broken count: 0
342s Done
343s The following additional packages will be installed:
343s   eigensoft emmax fontconfig fontconfig-config fonts-dejavu-core
343s   fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings
343s   fonts-mathjax javascript-common libb-hooks-op-check-perl libblas3 libcairo2
343s   libclass-method-modifiers-perl libclass-xsaccessor-perl libdatrie1
343s   libdeflate0 libdevel-callchecker-perl libdynaloader-functions-perl
343s   libfile-slurp-perl libfontconfig1 libgfortran5 libgomp1 libgraphite2-3
343s   libgsl27 libgslcblas0 libharfbuzz0b libice6 libimport-into-perl libjbig0
343s   libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3
343s   libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables
343s   libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax
343s   libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify
343s   libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 liblapacke
343s   liblerc4 liblua5.4-0 libmodule-runtime-perl libmoo-perl libpango-1.0-0
343s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
343s   libparallel-forkmanager-perl libparams-classify-perl libpixman-1-0
343s   libreadonly-perl librole-tiny-perl libsharpyuv0 libsm6 libsub-quote-perl
343s   libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtmglib3 libwebp7
343s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 littler
343s   node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data
343s   pique pique-doc plink r-base-core r-bioc-biobase r-bioc-biocgenerics
343s   r-bioc-multtest r-cran-acepack r-cran-backports r-cran-base64enc
343s   r-cran-bslib r-cran-cachem r-cran-checkmate r-cran-chron r-cran-cli
343s   r-cran-cluster r-cran-colorspace r-cran-commonmark r-cran-cpp11
343s   r-cran-crayon r-cran-curl r-cran-data.table r-cran-deldir r-cran-digest
343s   r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver
343s   r-cran-fastmap r-cran-fontawesome r-cran-forecast r-cran-foreign
343s   r-cran-formula r-cran-fracdiff r-cran-fs r-cran-generics r-cran-getopt
343s   r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-highr
343s   r-cran-hmisc r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets
343s   r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg r-cran-jquerylib
343s   r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later r-cran-lattice
343s   r-cran-latticeextra r-cran-lifecycle r-cran-littler r-cran-lmtest
343s   r-cran-magrittr r-cran-mass r-cran-matrix r-cran-memoise r-cran-mgcv
343s   r-cran-mime r-cran-munsell r-cran-nlme r-cran-nnet r-cran-optparse
343s   r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-png r-cran-promises
343s   r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 r-cran-rappdirs
343s   r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen
343s   r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass
343s   r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr
343s   r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timedate
343s   r-cran-tinytex r-cran-tseries r-cran-ttr r-cran-urca r-cran-uroot
343s   r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr
343s   r-cran-xfun r-cran-xtable r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common
343s   xdg-utils zip
343s Suggested packages:
343s   apache2 | lighttpd | httpd gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
343s   | gsl-ref-html libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix
343s   libjs-mathjax-doc libscalar-number-perl libxstring-perl tcl8.6 tk8.6 nodejs
343s   texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc
343s   texlive-latex-extra context wkhtmltopdf librsvg2-bin groff ghc php python
343s   ruby libjs-katex citation-style-language-styles elpa-ess r-doc-info
343s   | r-doc-pdf r-mathlib r-base-html r-bioc-all r-cran-runit r-bioc-biocstyle
343s   r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray
343s   r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy
343s   r-bioc-deseq2 r-bioc-annotate r-cran-snow r-cran-kernsmooth r-cran-kernlab
343s   r-cran-mvtnorm r-cran-vcd r-cran-shinyjs r-cran-polyclip r-cran-covr
343s   r-cran-markdown r-cran-sp r-cran-scatterplot3d r-cran-magick r-cran-sf
343s   r-cran-testthat r-cran-httr r-cran-bit64 r-cran-dbi r-cran-formattable
343s   r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-vdiffr
343s   r-cran-roxygen2 r-cran-inline r-cran-bench r-cran-blob r-cran-brio
343s   r-cran-callr r-cran-here r-cran-hms r-cran-pkgbuild r-cran-pkgload
343s   r-cran-plm
343s Recommended packages:
343s   gnuplot node-jquery libnamespace-clean-perl med-config r-recommended
343s   r-base-dev r-doc-html r-cran-testthat r-cran-thematic r-cran-fastmatch
343s   r-cran-devtools r-cran-tinytest r-cran-callr r-cran-covr r-cran-mockery
343s   r-cran-processx r-cran-ps r-cran-rprojroot r-cran-whoami r-cran-xml2
343s   r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr
343s   r-cran-progress r-cran-spelling r-cran-webutils r-cran-bit64 r-cran-bit
343s   r-cran-r.utils r-cran-nanotime r-cran-broom r-cran-dbi r-cran-dbplyr
343s   r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite r-cran-unitizer r-cran-rsvg
343s   r-cran-pkgload r-cran-hexbin r-cran-mapproj r-cran-maps r-cran-multcomp
343s   r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-sf r-cran-svglite
343s   r-cran-vdiffr r-cran-waldo r-cran-testit r-cran-cairo r-cran-markdown
343s   r-cran-httr r-cran-r.rsp r-cran-codetools r-cran-formatr r-cran-gridsvg
343s   r-cran-magick r-cran-reticulate r-cran-rgl r-cran-tikzdevice r-cran-webshot
343s   node-highlight.js r-cran-lintr r-cran-tidyverse r-cran-lubridate
343s   r-cran-future r-cran-usethis r-cran-dygraphs r-cran-rsconnect r-cran-downlit
343s   r-cran-dichromat r-cran-hms r-cran-mockr r-cran-formattable r-cran-readr
343s   r-cran-pkgdown r-cran-zeallot r-cran-remotes r-cran-renv r-cran-timeseries
343s   r-cran-runit libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl
343s   x11-utils x11-xserver-utils
343s The following NEW packages will be installed:
343s   eigensoft emmax fontconfig fontconfig-config fonts-dejavu-core
343s   fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings
343s   fonts-mathjax javascript-common libb-hooks-op-check-perl libblas3 libcairo2
343s   libclass-method-modifiers-perl libclass-xsaccessor-perl libdatrie1
343s   libdeflate0 libdevel-callchecker-perl libdynaloader-functions-perl
343s   libfile-slurp-perl libfontconfig1 libgfortran5 libgomp1 libgraphite2-3
343s   libgsl27 libgslcblas0 libharfbuzz0b libice6 libimport-into-perl libjbig0
343s   libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3
343s   libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables
343s   libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax
343s   libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify
343s   libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 liblapacke
343s   liblerc4 liblua5.4-0 libmodule-runtime-perl libmoo-perl libpango-1.0-0
343s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
343s   libparallel-forkmanager-perl libparams-classify-perl libpixman-1-0
343s   libreadonly-perl librole-tiny-perl libsharpyuv0 libsm6 libsub-quote-perl
343s   libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtmglib3 libwebp7
343s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 littler
343s   node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data
343s   pique pique-doc plink r-base-core r-bioc-biobase r-bioc-biocgenerics
343s   r-bioc-multtest r-cran-acepack r-cran-backports r-cran-base64enc
343s   r-cran-bslib r-cran-cachem r-cran-checkmate r-cran-chron r-cran-cli
343s   r-cran-cluster r-cran-colorspace r-cran-commonmark r-cran-cpp11
343s   r-cran-crayon r-cran-curl r-cran-data.table r-cran-deldir r-cran-digest
343s   r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver
343s   r-cran-fastmap r-cran-fontawesome r-cran-forecast r-cran-foreign
343s   r-cran-formula r-cran-fracdiff r-cran-fs r-cran-generics r-cran-getopt
343s   r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-highr
343s   r-cran-hmisc r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets
343s   r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg r-cran-jquerylib
343s   r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later r-cran-lattice
343s   r-cran-latticeextra r-cran-lifecycle r-cran-littler r-cran-lmtest
343s   r-cran-magrittr r-cran-mass r-cran-matrix r-cran-memoise r-cran-mgcv
343s   r-cran-mime r-cran-munsell r-cran-nlme r-cran-nnet r-cran-optparse
343s   r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-png r-cran-promises
343s   r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 r-cran-rappdirs
343s   r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen
343s   r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass
343s   r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr
343s   r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timedate
343s   r-cran-tinytex r-cran-tseries r-cran-ttr r-cran-urca r-cran-uroot
343s   r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr
343s   r-cran-xfun r-cran-xtable r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common
343s   xdg-utils zip
343s 0 upgraded, 206 newly installed, 0 to remove and 0 not upgraded.
343s 1 not fully installed or removed.
343s Need to get 172 MB of archives.
343s After this operation, 539 MB of additional disk space will be used.
343s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB]
343s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB]
343s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB]
343s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B]
343s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
343s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
343s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
344s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
344s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
344s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
344s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
344s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
344s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
344s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
344s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
344s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
344s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
344s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
344s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
344s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
344s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB]
344s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
344s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
344s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB]
345s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB]
345s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB]
345s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB]
345s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB]
345s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB]
345s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB]
345s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
345s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
345s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
345s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
345s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
345s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
345s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB]
345s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
345s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B]
345s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB]
345s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB]
345s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB]
345s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB]
345s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB]
346s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libtmglib3 arm64 3.12.0-3 [112 kB]
346s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 liblapacke arm64 3.12.0-3 [427 kB]
346s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 emmax arm64 0~beta.20100307-5 [29.9 kB]
346s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 plink arm64 1.07+dfsg-4 [1005 kB]
346s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB]
346s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB]
346s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 eigensoft arm64 8.0.0+dfsg-2 [318 kB]
346s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 libreadonly-perl all 2.050-3 [19.9 kB]
346s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libclass-method-modifiers-perl all 2.15-1 [16.1 kB]
346s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libclass-xsaccessor-perl arm64 1.19-4build2 [33.1 kB]
347s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libb-hooks-op-check-perl arm64 0.22-2build2 [9220 B]
347s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libdynaloader-functions-perl all 0.003-3 [12.1 kB]
347s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libdevel-callchecker-perl arm64 0.008-2build1 [13.7 kB]
347s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libparams-classify-perl arm64 0.015-2build3 [19.6 kB]
347s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libmodule-runtime-perl all 0.016-2 [16.4 kB]
347s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libimport-into-perl all 1.002005-2 [10.7 kB]
347s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 librole-tiny-perl all 2.002004-1 [16.3 kB]
347s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-quote-perl all 2.006008-1ubuntu1 [20.7 kB]
347s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libmoo-perl all 2.005005-1 [47.4 kB]
347s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 libparallel-forkmanager-perl all 2.02-1 [27.7 kB]
347s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 libfile-slurp-perl all 9999.32-2 [21.7 kB]
347s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-getopt all 1.20.4-1 [38.4 kB]
347s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB]
347s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fracdiff arm64 1.5-3-1 [108 kB]
347s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB]
347s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB]
347s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB]
347s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB]
347s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
347s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB]
347s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB]
347s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB]
347s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB]
347s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB]
347s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB]
347s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB]
347s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB]
347s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB]
347s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB]
347s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB]
347s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
347s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB]
347s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB]
347s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB]
347s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB]
347s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB]
347s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB]
347s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB]
347s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
347s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB]
347s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB]
347s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB]
347s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-zoo arm64 1.8-12-2 [984 kB]
347s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lmtest arm64 0.9.40-1 [396 kB]
347s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nnet arm64 7.3-19-2 [111 kB]
347s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB]
347s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B]
348s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB]
348s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB]
348s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-timedate arm64 4032.109-1 [1229 kB]
348s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-quadprog arm64 1.5-8-1build1 [29.8 kB]
348s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xts arm64 0.13.2-1 [770 kB]
348s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-curl arm64 5.2.0+dfsg-1 [189 kB]
348s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ttr arm64 0.24.4-1 [509 kB]
348s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB]
348s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-quantmod all 0.4.26-1 [1027 kB]
348s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tseries arm64 0.10-55-1 [367 kB]
348s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-urca arm64 1.3-3-1 [1071 kB]
348s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpparmadillo arm64 0.12.8.0.0-1 [859 kB]
348s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-forecast arm64 8.21.1-1 [1547 kB]
348s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocgenerics all 0.48.1-2 [595 kB]
348s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biobase arm64 2.62.0-1 [2136 kB]
348s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB]
349s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-multtest arm64 2.58.0-1 [836 kB]
349s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-optparse all 1.7.4-1 [81.6 kB]
349s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-uroot all 2.1-3-1 [1927 kB]
349s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 pique all 1.0-7 [21.3 kB]
349s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 pique-doc all 1.0-7 [1931 kB]
349s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cluster arm64 2.1.6-1 [552 kB]
349s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB]
349s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreign arm64 0.8.86-1 [240 kB]
349s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gridextra all 2.3-3build1 [1024 kB]
349s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-data.table arm64 1.14.10+dfsg-1 [1844 kB]
349s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB]
349s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB]
349s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB]
349s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xfun arm64 0.41+dfsg-1 [415 kB]
349s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
349s Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
349s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-highr all 0.10+dfsg-1 [38.3 kB]
349s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-yaml arm64 2.3.8-1 [107 kB]
349s Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
349s Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
349s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
349s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
349s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
349s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB]
349s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-knitr all 1.45+dfsg-1 [917 kB]
349s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-backports arm64 1.4.1-1 [101 kB]
349s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-checkmate arm64 2.3.1-1 [711 kB]
349s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-base64enc arm64 0.1-3-3 [27.4 kB]
349s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB]
349s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB]
349s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fastmap arm64 1.1.1-1 [69.6 kB]
349s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmltools arm64 0.5.7-1 [369 kB]
349s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cachem arm64 1.0.8-1 [72.3 kB]
349s Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB]
349s Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB]
349s Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mime arm64 0.12-1 [35.8 kB]
349s Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fs arm64 1.6.3+dfsg-1 [227 kB]
349s Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rappdirs arm64 0.3.3-1 [47.5 kB]
349s Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sass arm64 0.4.8+dfsg-1 [952 kB]
349s Get:157 http://ftpmaster.internal/ubuntu noble/universe arm64 node-bootstrap-sass all 3.4.3-2 [187 kB]
349s Get:158 http://ftpmaster.internal/ubuntu noble/main arm64 javascript-common all 11+nmu1 [5936 B]
349s Get:159 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB]
349s Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB]
349s Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bslib all 0.6.1+dfsg-1 [5138 kB]
350s Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fontawesome all 0.5.2-1 [1300 kB]
350s Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tinytex all 0.49-1 [141 kB]
350s Get:164 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
350s Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-modernizr all 2.6.2+ds1-5 [48.3 kB]
350s Get:166 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB]
350s Get:167 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
350s Get:168 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc-data all 3.1.3-1 [92.4 kB]
350s Get:169 http://ftpmaster.internal/ubuntu noble/main arm64 liblua5.4-0 arm64 5.4.6-3 [158 kB]
350s Get:170 http://ftpmaster.internal/ubuntu noble/universe arm64 pandoc arm64 3.1.3+ds-2 [27.7 MB]
350s Get:171 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-later arm64 1.3.2+dfsg-1 [120 kB]
350s Get:172 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-promises arm64 1.2.1+dfsg-1 [282 kB]
350s Get:173 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-httpuv arm64 1.6.14+dfsg-1 [496 kB]
350s Get:174 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB]
350s Get:175 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sourcetools arm64 0.1.7-1-1 [47.2 kB]
350s Get:176 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB]
350s Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-commonmark arm64 1.9.1-1 [127 kB]
350s Get:178 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB]
350s Get:179 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
350s Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
350s Get:181 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
350s Get:182 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B]
350s Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
350s Get:184 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-d3 all 3.5.17-4 [132 kB]
350s Get:185 http://ftpmaster.internal/ubuntu noble/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
350s Get:186 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-shiny all 1.8.0+dfsg-1 [2762 kB]
351s Get:187 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rmarkdown all 2.25+dfsg-3 [1481 kB]
351s Get:188 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB]
351s Get:189 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rstudioapi all 0.15.0-1 [277 kB]
351s Get:190 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB]
351s Get:191 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB]
351s Get:192 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB]
351s Get:193 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB]
351s Get:194 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB]
351s Get:195 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-htmltable all 2.4.2-1 [381 kB]
351s Get:196 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridis all 0.6.5-1 [2770 kB]
351s Get:197 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-formula all 1.2-5-1 [158 kB]
351s Get:198 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-chron arm64 2.3-61-2 [186 kB]
351s Get:199 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-png arm64 0.1-8-1 [39.9 kB]
351s Get:200 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jpeg arm64 0.1-10-1 [30.8 kB]
351s Get:201 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-deldir arm64 2.0-2-1 [270 kB]
351s Get:202 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB]
351s Get:203 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-interp arm64 1.1-6-1 [1433 kB]
351s Get:204 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-latticeextra all 0.6-30-1 [2198 kB]
352s Get:205 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-acepack arm64 1.4.2-1 [60.5 kB]
352s Get:206 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-hmisc arm64 5.1-1-1 [3486 kB]
353s Preconfiguring packages ...
353s Fetched 172 MB in 9s (20.0 MB/s)
353s Selecting previously unselected package zip.
353s (Reading database ... 
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(Reading database ... 55%
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(Reading database ... 65%
(Reading database ... 70%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74306 files and directories currently installed.)
353s Preparing to unpack .../000-zip_3.0-13_arm64.deb ...
353s Unpacking zip (3.0-13) ...
353s Selecting previously unselected package unzip.
353s Preparing to unpack .../001-unzip_6.0-28ubuntu3_arm64.deb ...
353s Unpacking unzip (6.0-28ubuntu3) ...
353s Selecting previously unselected package libpaper1:arm64.
353s Preparing to unpack .../002-libpaper1_1.1.29_arm64.deb ...
353s Unpacking libpaper1:arm64 (1.1.29) ...
353s Selecting previously unselected package libpaper-utils.
353s Preparing to unpack .../003-libpaper-utils_1.1.29_arm64.deb ...
353s Unpacking libpaper-utils (1.1.29) ...
353s Selecting previously unselected package xdg-utils.
353s Preparing to unpack .../004-xdg-utils_1.1.3-4.1ubuntu3_all.deb ...
353s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ...
353s Selecting previously unselected package libblas3:arm64.
353s Preparing to unpack .../005-libblas3_3.12.0-3_arm64.deb ...
353s Unpacking libblas3:arm64 (3.12.0-3) ...
353s Selecting previously unselected package fonts-dejavu-mono.
354s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ...
354s Unpacking fonts-dejavu-mono (2.37-8) ...
354s Selecting previously unselected package fonts-dejavu-core.
354s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ...
354s Unpacking fonts-dejavu-core (2.37-8) ...
354s Selecting previously unselected package fontconfig-config.
354s Preparing to unpack .../008-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
354s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
354s Selecting previously unselected package libfontconfig1:arm64.
354s Preparing to unpack .../009-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
354s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
354s Selecting previously unselected package libpixman-1-0:arm64.
354s Preparing to unpack .../010-libpixman-1-0_0.42.2-1_arm64.deb ...
354s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
354s Selecting previously unselected package libxcb-render0:arm64.
354s Preparing to unpack .../011-libxcb-render0_1.15-1_arm64.deb ...
354s Unpacking libxcb-render0:arm64 (1.15-1) ...
354s Selecting previously unselected package libxcb-shm0:arm64.
354s Preparing to unpack .../012-libxcb-shm0_1.15-1_arm64.deb ...
354s Unpacking libxcb-shm0:arm64 (1.15-1) ...
354s Selecting previously unselected package libxrender1:arm64.
354s Preparing to unpack .../013-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
354s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
354s Selecting previously unselected package libcairo2:arm64.
354s Preparing to unpack .../014-libcairo2_1.18.0-1_arm64.deb ...
354s Unpacking libcairo2:arm64 (1.18.0-1) ...
354s Selecting previously unselected package libgomp1:arm64.
354s Preparing to unpack .../015-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
354s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
354s Selecting previously unselected package libjpeg-turbo8:arm64.
354s Preparing to unpack .../016-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
354s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
354s Selecting previously unselected package libjpeg8:arm64.
354s Preparing to unpack .../017-libjpeg8_8c-2ubuntu11_arm64.deb ...
354s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
354s Selecting previously unselected package libgfortran5:arm64.
354s Preparing to unpack .../018-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
354s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
354s Selecting previously unselected package liblapack3:arm64.
354s Preparing to unpack .../019-liblapack3_3.12.0-3_arm64.deb ...
354s Unpacking liblapack3:arm64 (3.12.0-3) ...
354s Selecting previously unselected package fontconfig.
354s Preparing to unpack .../020-fontconfig_2.15.0-1ubuntu1_arm64.deb ...
354s Unpacking fontconfig (2.15.0-1ubuntu1) ...
354s Selecting previously unselected package libgraphite2-3:arm64.
354s Preparing to unpack .../021-libgraphite2-3_1.3.14-2_arm64.deb ...
354s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
355s Selecting previously unselected package libharfbuzz0b:arm64.
355s Preparing to unpack .../022-libharfbuzz0b_8.3.0-2_arm64.deb ...
355s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
355s Selecting previously unselected package libthai-data.
355s Preparing to unpack .../023-libthai-data_0.1.29-2_all.deb ...
355s Unpacking libthai-data (0.1.29-2) ...
355s Selecting previously unselected package libdatrie1:arm64.
355s Preparing to unpack .../024-libdatrie1_0.2.13-3_arm64.deb ...
355s Unpacking libdatrie1:arm64 (0.2.13-3) ...
355s Selecting previously unselected package libthai0:arm64.
355s Preparing to unpack .../025-libthai0_0.1.29-2_arm64.deb ...
355s Unpacking libthai0:arm64 (0.1.29-2) ...
355s Selecting previously unselected package libpango-1.0-0:arm64.
355s Preparing to unpack .../026-libpango-1.0-0_1.51.0+ds-4_arm64.deb ...
355s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ...
355s Selecting previously unselected package libpangoft2-1.0-0:arm64.
355s Preparing to unpack .../027-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ...
355s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
355s Selecting previously unselected package libpangocairo-1.0-0:arm64.
355s Preparing to unpack .../028-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ...
355s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
355s Selecting previously unselected package libtcl8.6:arm64.
355s Preparing to unpack .../029-libtcl8.6_8.6.13+dfsg-2_arm64.deb ...
355s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ...
355s Selecting previously unselected package libdeflate0:arm64.
355s Preparing to unpack .../030-libdeflate0_1.19-1_arm64.deb ...
355s Unpacking libdeflate0:arm64 (1.19-1) ...
355s Selecting previously unselected package libjbig0:arm64.
355s Preparing to unpack .../031-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
355s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
355s Selecting previously unselected package liblerc4:arm64.
355s Preparing to unpack .../032-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
355s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
355s Selecting previously unselected package libsharpyuv0:arm64.
355s Preparing to unpack .../033-libsharpyuv0_1.3.2-0.4_arm64.deb ...
355s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
355s Selecting previously unselected package libwebp7:arm64.
355s Preparing to unpack .../034-libwebp7_1.3.2-0.4_arm64.deb ...
355s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
355s Selecting previously unselected package libtiff6:arm64.
355s Preparing to unpack .../035-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
355s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
355s Selecting previously unselected package libxft2:arm64.
355s Preparing to unpack .../036-libxft2_2.3.6-1_arm64.deb ...
355s Unpacking libxft2:arm64 (2.3.6-1) ...
355s Selecting previously unselected package x11-common.
355s Preparing to unpack .../037-x11-common_1%3a7.7+23ubuntu2_all.deb ...
355s Unpacking x11-common (1:7.7+23ubuntu2) ...
355s Selecting previously unselected package libxss1:arm64.
355s Preparing to unpack .../038-libxss1_1%3a1.2.3-1build2_arm64.deb ...
355s Unpacking libxss1:arm64 (1:1.2.3-1build2) ...
355s Selecting previously unselected package libtk8.6:arm64.
355s Preparing to unpack .../039-libtk8.6_8.6.13-2_arm64.deb ...
355s Unpacking libtk8.6:arm64 (8.6.13-2) ...
355s Selecting previously unselected package libice6:arm64.
355s Preparing to unpack .../040-libice6_2%3a1.0.10-1build2_arm64.deb ...
355s Unpacking libice6:arm64 (2:1.0.10-1build2) ...
355s Selecting previously unselected package libsm6:arm64.
355s Preparing to unpack .../041-libsm6_2%3a1.2.3-1build2_arm64.deb ...
355s Unpacking libsm6:arm64 (2:1.2.3-1build2) ...
355s Selecting previously unselected package libxt6:arm64.
355s Preparing to unpack .../042-libxt6_1%3a1.2.1-1.1_arm64.deb ...
355s Unpacking libxt6:arm64 (1:1.2.1-1.1) ...
355s Selecting previously unselected package r-base-core.
355s Preparing to unpack .../043-r-base-core_4.3.2-1build1_arm64.deb ...
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356s Selecting previously unselected package libtmglib3:arm64.
356s Preparing to unpack .../044-libtmglib3_3.12.0-3_arm64.deb ...
356s Unpacking libtmglib3:arm64 (3.12.0-3) ...
356s Selecting previously unselected package liblapacke:arm64.
356s Preparing to unpack .../045-liblapacke_3.12.0-3_arm64.deb ...
356s Unpacking liblapacke:arm64 (3.12.0-3) ...
356s Selecting previously unselected package emmax.
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356s Selecting previously unselected package plink.
356s Preparing to unpack .../047-plink_1.07+dfsg-4_arm64.deb ...
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356s Selecting previously unselected package libgslcblas0:arm64.
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356s Selecting previously unselected package libgsl27:arm64.
356s Preparing to unpack .../049-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ...
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356s Selecting previously unselected package eigensoft.
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356s Selecting previously unselected package libreadonly-perl.
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356s Selecting previously unselected package libclass-method-modifiers-perl.
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356s Selecting previously unselected package libclass-xsaccessor-perl.
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356s Selecting previously unselected package libb-hooks-op-check-perl:arm64.
357s Preparing to unpack .../054-libb-hooks-op-check-perl_0.22-2build2_arm64.deb ...
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357s Selecting previously unselected package libdynaloader-functions-perl.
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357s Selecting previously unselected package libdevel-callchecker-perl:arm64.
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357s Selecting previously unselected package libparams-classify-perl:arm64.
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357s Selecting previously unselected package libmodule-runtime-perl.
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357s Selecting previously unselected package libimport-into-perl.
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357s Selecting previously unselected package librole-tiny-perl.
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357s Selecting previously unselected package libsub-quote-perl.
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357s Selecting previously unselected package libmoo-perl.
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357s Selecting previously unselected package libparallel-forkmanager-perl.
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357s Selecting previously unselected package libfile-slurp-perl.
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357s Selecting previously unselected package r-cran-getopt.
357s Preparing to unpack .../065-r-cran-getopt_1.20.4-1_all.deb ...
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357s Selecting previously unselected package r-cran-colorspace.
357s Preparing to unpack .../066-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ...
357s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ...
357s Selecting previously unselected package r-cran-fracdiff.
357s Preparing to unpack .../067-r-cran-fracdiff_1.5-3-1_arm64.deb ...
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357s Selecting previously unselected package r-cran-generics.
357s Preparing to unpack .../068-r-cran-generics_0.1.3-1_all.deb ...
357s Unpacking r-cran-generics (0.1.3-1) ...
357s Selecting previously unselected package r-cran-cli.
358s Preparing to unpack .../069-r-cran-cli_3.6.2-1_arm64.deb ...
358s Unpacking r-cran-cli (3.6.2-1) ...
358s Selecting previously unselected package r-cran-glue.
358s Preparing to unpack .../070-r-cran-glue_1.7.0-1_arm64.deb ...
358s Unpacking r-cran-glue (1.7.0-1) ...
358s Selecting previously unselected package r-cran-rlang.
358s Preparing to unpack .../071-r-cran-rlang_1.1.3-1_arm64.deb ...
358s Unpacking r-cran-rlang (1.1.3-1) ...
358s Selecting previously unselected package r-cran-lifecycle.
358s Preparing to unpack .../072-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ...
358s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ...
358s Selecting previously unselected package r-cran-gtable.
358s Preparing to unpack .../073-r-cran-gtable_0.3.4+dfsg-1_all.deb ...
358s Unpacking r-cran-gtable (0.3.4+dfsg-1) ...
358s Selecting previously unselected package r-cran-isoband.
358s Preparing to unpack .../074-r-cran-isoband_0.2.7-1_arm64.deb ...
358s Unpacking r-cran-isoband (0.2.7-1) ...
358s Selecting previously unselected package r-cran-mass.
358s Preparing to unpack .../075-r-cran-mass_7.3-60.0.1-1_arm64.deb ...
358s Unpacking r-cran-mass (7.3-60.0.1-1) ...
358s Selecting previously unselected package r-cran-lattice.
358s Preparing to unpack .../076-r-cran-lattice_0.22-5-1_arm64.deb ...
358s Unpacking r-cran-lattice (0.22-5-1) ...
358s Selecting previously unselected package r-cran-nlme.
358s Preparing to unpack .../077-r-cran-nlme_3.1.164-1_arm64.deb ...
358s Unpacking r-cran-nlme (3.1.164-1) ...
358s Selecting previously unselected package r-cran-matrix.
358s Preparing to unpack .../078-r-cran-matrix_1.6-5-1_arm64.deb ...
358s Unpacking r-cran-matrix (1.6-5-1) ...
358s Selecting previously unselected package r-cran-mgcv.
358s Preparing to unpack .../079-r-cran-mgcv_1.9-1-1_arm64.deb ...
358s Unpacking r-cran-mgcv (1.9-1-1) ...
358s Selecting previously unselected package r-cran-farver.
358s Preparing to unpack .../080-r-cran-farver_2.1.1-1_arm64.deb ...
358s Unpacking r-cran-farver (2.1.1-1) ...
359s Selecting previously unselected package r-cran-labeling.
359s Preparing to unpack .../081-r-cran-labeling_0.4.3-1_all.deb ...
359s Unpacking r-cran-labeling (0.4.3-1) ...
359s Selecting previously unselected package r-cran-munsell.
359s Preparing to unpack .../082-r-cran-munsell_0.5.0-2build1_all.deb ...
359s Unpacking r-cran-munsell (0.5.0-2build1) ...
359s Selecting previously unselected package r-cran-r6.
359s Preparing to unpack .../083-r-cran-r6_2.5.1-1_all.deb ...
359s Unpacking r-cran-r6 (2.5.1-1) ...
359s Selecting previously unselected package r-cran-rcolorbrewer.
359s Preparing to unpack .../084-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
359s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
359s Selecting previously unselected package r-cran-viridislite.
359s Preparing to unpack .../085-r-cran-viridislite_0.4.2-2_all.deb ...
359s Unpacking r-cran-viridislite (0.4.2-2) ...
359s Selecting previously unselected package r-cran-scales.
359s Preparing to unpack .../086-r-cran-scales_1.3.0-1_all.deb ...
359s Unpacking r-cran-scales (1.3.0-1) ...
359s Selecting previously unselected package r-cran-fansi.
359s Preparing to unpack .../087-r-cran-fansi_1.0.5-1_arm64.deb ...
359s Unpacking r-cran-fansi (1.0.5-1) ...
359s Selecting previously unselected package r-cran-magrittr.
359s Preparing to unpack .../088-r-cran-magrittr_2.0.3-1_arm64.deb ...
359s Unpacking r-cran-magrittr (2.0.3-1) ...
359s Selecting previously unselected package r-cran-utf8.
359s Preparing to unpack .../089-r-cran-utf8_1.2.4-1_arm64.deb ...
359s Unpacking r-cran-utf8 (1.2.4-1) ...
359s Selecting previously unselected package r-cran-vctrs.
359s Preparing to unpack .../090-r-cran-vctrs_0.6.5-1_arm64.deb ...
359s Unpacking r-cran-vctrs (0.6.5-1) ...
359s Selecting previously unselected package r-cran-pillar.
359s Preparing to unpack .../091-r-cran-pillar_1.9.0+dfsg-1_all.deb ...
359s Unpacking r-cran-pillar (1.9.0+dfsg-1) ...
359s Selecting previously unselected package r-cran-pkgconfig.
359s Preparing to unpack .../092-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
359s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
359s Selecting previously unselected package r-cran-tibble.
359s Preparing to unpack .../093-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ...
359s Unpacking r-cran-tibble (3.2.1+dfsg-2) ...
359s Selecting previously unselected package r-cran-withr.
359s Preparing to unpack .../094-r-cran-withr_2.5.0-1_all.deb ...
359s Unpacking r-cran-withr (2.5.0-1) ...
359s Selecting previously unselected package r-cran-ggplot2.
359s Preparing to unpack .../095-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ...
359s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ...
359s Selecting previously unselected package r-cran-zoo.
359s Preparing to unpack .../096-r-cran-zoo_1.8-12-2_arm64.deb ...
359s Unpacking r-cran-zoo (1.8-12-2) ...
359s Selecting previously unselected package r-cran-lmtest.
359s Preparing to unpack .../097-r-cran-lmtest_0.9.40-1_arm64.deb ...
359s Unpacking r-cran-lmtest (0.9.40-1) ...
360s Selecting previously unselected package r-cran-nnet.
360s Preparing to unpack .../098-r-cran-nnet_7.3-19-2_arm64.deb ...
360s Unpacking r-cran-nnet (7.3-19-2) ...
360s Selecting previously unselected package r-cran-littler.
360s Preparing to unpack .../099-r-cran-littler_0.3.19-1_arm64.deb ...
360s Unpacking r-cran-littler (0.3.19-1) ...
360s Selecting previously unselected package littler.
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360s Unpacking littler (0.3.19-1) ...
360s Selecting previously unselected package r-cran-pkgkitten.
360s Preparing to unpack .../101-r-cran-pkgkitten_0.2.3-1_all.deb ...
360s Unpacking r-cran-pkgkitten (0.2.3-1) ...
360s Selecting previously unselected package r-cran-rcpp.
360s Preparing to unpack .../102-r-cran-rcpp_1.0.12-1_arm64.deb ...
360s Unpacking r-cran-rcpp (1.0.12-1) ...
360s Selecting previously unselected package r-cran-timedate.
360s Preparing to unpack .../103-r-cran-timedate_4032.109-1_arm64.deb ...
360s Unpacking r-cran-timedate (4032.109-1) ...
360s Selecting previously unselected package r-cran-quadprog.
360s Preparing to unpack .../104-r-cran-quadprog_1.5-8-1build1_arm64.deb ...
360s Unpacking r-cran-quadprog (1.5-8-1build1) ...
360s Selecting previously unselected package r-cran-xts.
360s Preparing to unpack .../105-r-cran-xts_0.13.2-1_arm64.deb ...
360s Unpacking r-cran-xts (0.13.2-1) ...
360s Selecting previously unselected package r-cran-curl.
360s Preparing to unpack .../106-r-cran-curl_5.2.0+dfsg-1_arm64.deb ...
360s Unpacking r-cran-curl (5.2.0+dfsg-1) ...
360s Selecting previously unselected package r-cran-ttr.
360s Preparing to unpack .../107-r-cran-ttr_0.24.4-1_arm64.deb ...
360s Unpacking r-cran-ttr (0.24.4-1) ...
360s Selecting previously unselected package r-cran-jsonlite.
360s Preparing to unpack .../108-r-cran-jsonlite_1.8.8+dfsg-1_arm64.deb ...
360s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ...
360s Selecting previously unselected package r-cran-quantmod.
360s Preparing to unpack .../109-r-cran-quantmod_0.4.26-1_all.deb ...
360s Unpacking r-cran-quantmod (0.4.26-1) ...
360s Selecting previously unselected package r-cran-tseries.
360s Preparing to unpack .../110-r-cran-tseries_0.10-55-1_arm64.deb ...
360s Unpacking r-cran-tseries (0.10-55-1) ...
360s Selecting previously unselected package r-cran-urca.
360s Preparing to unpack .../111-r-cran-urca_1.3-3-1_arm64.deb ...
360s Unpacking r-cran-urca (1.3-3-1) ...
360s Selecting previously unselected package r-cran-rcpparmadillo.
360s Preparing to unpack .../112-r-cran-rcpparmadillo_0.12.8.0.0-1_arm64.deb ...
360s Unpacking r-cran-rcpparmadillo (0.12.8.0.0-1) ...
360s Selecting previously unselected package r-cran-forecast.
360s Preparing to unpack .../113-r-cran-forecast_8.21.1-1_arm64.deb ...
360s Unpacking r-cran-forecast (8.21.1-1) ...
360s Selecting previously unselected package r-bioc-biocgenerics.
360s Preparing to unpack .../114-r-bioc-biocgenerics_0.48.1-2_all.deb ...
360s Unpacking r-bioc-biocgenerics (0.48.1-2) ...
360s Selecting previously unselected package r-bioc-biobase.
360s Preparing to unpack .../115-r-bioc-biobase_2.62.0-1_arm64.deb ...
360s Unpacking r-bioc-biobase (2.62.0-1) ...
360s Selecting previously unselected package r-cran-survival.
360s Preparing to unpack .../116-r-cran-survival_3.5-8-1_arm64.deb ...
360s Unpacking r-cran-survival (3.5-8-1) ...
361s Selecting previously unselected package r-bioc-multtest.
361s Preparing to unpack .../117-r-bioc-multtest_2.58.0-1_arm64.deb ...
361s Unpacking r-bioc-multtest (2.58.0-1) ...
361s Selecting previously unselected package r-cran-optparse.
361s Preparing to unpack .../118-r-cran-optparse_1.7.4-1_all.deb ...
361s Unpacking r-cran-optparse (1.7.4-1) ...
361s Selecting previously unselected package r-cran-uroot.
361s Preparing to unpack .../119-r-cran-uroot_2.1-3-1_all.deb ...
361s Unpacking r-cran-uroot (2.1-3-1) ...
361s Selecting previously unselected package pique.
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361s Unpacking pique (1.0-7) ...
361s Selecting previously unselected package pique-doc.
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361s Unpacking pique-doc (1.0-7) ...
361s Selecting previously unselected package r-cran-cluster.
361s Preparing to unpack .../122-r-cran-cluster_2.1.6-1_arm64.deb ...
361s Unpacking r-cran-cluster (2.1.6-1) ...
361s Selecting previously unselected package r-cran-rpart.
361s Preparing to unpack .../123-r-cran-rpart_4.1.23-1_arm64.deb ...
361s Unpacking r-cran-rpart (4.1.23-1) ...
361s Selecting previously unselected package r-cran-foreign.
361s Preparing to unpack .../124-r-cran-foreign_0.8.86-1_arm64.deb ...
361s Unpacking r-cran-foreign (0.8.86-1) ...
361s Selecting previously unselected package r-cran-gridextra.
361s Preparing to unpack .../125-r-cran-gridextra_2.3-3build1_all.deb ...
361s Unpacking r-cran-gridextra (2.3-3build1) ...
361s Selecting previously unselected package r-cran-data.table.
361s Preparing to unpack .../126-r-cran-data.table_1.14.10+dfsg-1_arm64.deb ...
361s Unpacking r-cran-data.table (1.14.10+dfsg-1) ...
361s Selecting previously unselected package r-cran-stringi.
361s Preparing to unpack .../127-r-cran-stringi_1.8.3-1_arm64.deb ...
361s Unpacking r-cran-stringi (1.8.3-1) ...
361s Selecting previously unselected package r-cran-stringr.
361s Preparing to unpack .../128-r-cran-stringr_1.5.1-1_all.deb ...
361s Unpacking r-cran-stringr (1.5.1-1) ...
361s Selecting previously unselected package r-cran-evaluate.
361s Preparing to unpack .../129-r-cran-evaluate_0.23-1_all.deb ...
361s Unpacking r-cran-evaluate (0.23-1) ...
361s Selecting previously unselected package r-cran-xfun.
361s Preparing to unpack .../130-r-cran-xfun_0.41+dfsg-1_arm64.deb ...
361s Unpacking r-cran-xfun (0.41+dfsg-1) ...
361s Selecting previously unselected package libjs-highlight.js.
361s Preparing to unpack .../131-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ...
361s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ...
361s Selecting previously unselected package libjs-jquery.
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361s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
361s Selecting previously unselected package r-cran-highr.
361s Preparing to unpack .../133-r-cran-highr_0.10+dfsg-1_all.deb ...
361s Unpacking r-cran-highr (0.10+dfsg-1) ...
362s Selecting previously unselected package r-cran-yaml.
362s Preparing to unpack .../134-r-cran-yaml_2.3.8-1_arm64.deb ...
362s Unpacking r-cran-yaml (2.3.8-1) ...
362s Selecting previously unselected package fonts-mathjax.
362s Preparing to unpack .../135-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
362s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
362s Selecting previously unselected package libjs-mathjax.
362s Preparing to unpack .../136-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
362s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
362s Selecting previously unselected package fonts-glyphicons-halflings.
362s Preparing to unpack .../137-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ...
362s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
362s Selecting previously unselected package libjs-bootstrap.
362s Preparing to unpack .../138-libjs-bootstrap_3.4.1+dfsg-3_all.deb ...
362s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ...
363s Selecting previously unselected package libjs-jquery-datatables.
363s Preparing to unpack .../139-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ...
363s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ...
363s Selecting previously unselected package node-normalize.css.
363s Preparing to unpack .../140-node-normalize.css_8.0.1-5_all.deb ...
363s Unpacking node-normalize.css (8.0.1-5) ...
363s Selecting previously unselected package r-cran-knitr.
363s Preparing to unpack .../141-r-cran-knitr_1.45+dfsg-1_all.deb ...
363s Unpacking r-cran-knitr (1.45+dfsg-1) ...
363s Selecting previously unselected package r-cran-backports.
363s Preparing to unpack .../142-r-cran-backports_1.4.1-1_arm64.deb ...
363s Unpacking r-cran-backports (1.4.1-1) ...
363s Selecting previously unselected package r-cran-checkmate.
363s Preparing to unpack .../143-r-cran-checkmate_2.3.1-1_arm64.deb ...
363s Unpacking r-cran-checkmate (2.3.1-1) ...
363s Selecting previously unselected package r-cran-base64enc.
363s Preparing to unpack .../144-r-cran-base64enc_0.1-3-3_arm64.deb ...
363s Unpacking r-cran-base64enc (0.1-3-3) ...
363s Selecting previously unselected package r-cran-digest.
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363s Selecting previously unselected package r-cran-ellipsis.
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363s Selecting previously unselected package r-cran-fastmap.
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363s Selecting previously unselected package r-cran-htmltools.
363s Preparing to unpack .../148-r-cran-htmltools_0.5.7-1_arm64.deb ...
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363s Selecting previously unselected package r-cran-cachem.
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363s Selecting previously unselected package r-cran-jquerylib.
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363s Selecting previously unselected package r-cran-memoise.
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363s Selecting previously unselected package r-cran-mime.
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363s Unpacking r-cran-mime (0.12-1) ...
363s Selecting previously unselected package r-cran-fs.
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363s Unpacking r-cran-fs (1.6.3+dfsg-1) ...
363s Selecting previously unselected package r-cran-rappdirs.
363s Preparing to unpack .../154-r-cran-rappdirs_0.3.3-1_arm64.deb ...
363s Unpacking r-cran-rappdirs (0.3.3-1) ...
363s Selecting previously unselected package r-cran-sass.
363s Preparing to unpack .../155-r-cran-sass_0.4.8+dfsg-1_arm64.deb ...
363s Unpacking r-cran-sass (0.4.8+dfsg-1) ...
363s Selecting previously unselected package node-bootstrap-sass.
363s Preparing to unpack .../156-node-bootstrap-sass_3.4.3-2_all.deb ...
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363s Selecting previously unselected package javascript-common.
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363s Selecting previously unselected package libjs-popper.js.
363s Preparing to unpack .../158-libjs-popper.js_1.16.1+ds-6_all.deb ...
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363s Selecting previously unselected package libjs-bootstrap4.
363s Preparing to unpack .../159-libjs-bootstrap4_4.6.1+dfsg1-4_all.deb ...
363s Unpacking libjs-bootstrap4 (4.6.1+dfsg1-4) ...
364s Selecting previously unselected package r-cran-bslib.
364s Preparing to unpack .../160-r-cran-bslib_0.6.1+dfsg-1_all.deb ...
364s Unpacking r-cran-bslib (0.6.1+dfsg-1) ...
364s Selecting previously unselected package r-cran-fontawesome.
364s Preparing to unpack .../161-r-cran-fontawesome_0.5.2-1_all.deb ...
364s Unpacking r-cran-fontawesome (0.5.2-1) ...
364s Selecting previously unselected package r-cran-tinytex.
364s Preparing to unpack .../162-r-cran-tinytex_0.49-1_all.deb ...
364s Unpacking r-cran-tinytex (0.49-1) ...
364s Selecting previously unselected package libjs-jquery-ui.
364s Preparing to unpack .../163-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
364s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
364s Selecting previously unselected package libjs-modernizr.
364s Preparing to unpack .../164-libjs-modernizr_2.6.2+ds1-5_all.deb ...
364s Unpacking libjs-modernizr (2.6.2+ds1-5) ...
364s Selecting previously unselected package libjs-prettify.
364s Preparing to unpack .../165-libjs-prettify_2015.12.04+dfsg-1.1_all.deb ...
364s Unpacking libjs-prettify (2015.12.04+dfsg-1.1) ...
364s Selecting previously unselected package fonts-font-awesome.
364s Preparing to unpack .../166-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
364s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
364s Selecting previously unselected package pandoc-data.
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364s Unpacking pandoc-data (3.1.3-1) ...
364s Selecting previously unselected package liblua5.4-0:arm64.
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364s Unpacking liblua5.4-0:arm64 (5.4.6-3) ...
364s Selecting previously unselected package pandoc.
364s Preparing to unpack .../169-pandoc_3.1.3+ds-2_arm64.deb ...
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365s Selecting previously unselected package r-cran-later.
365s Preparing to unpack .../170-r-cran-later_1.3.2+dfsg-1_arm64.deb ...
365s Unpacking r-cran-later (1.3.2+dfsg-1) ...
365s Selecting previously unselected package r-cran-promises.
365s Preparing to unpack .../171-r-cran-promises_1.2.1+dfsg-1_arm64.deb ...
365s Unpacking r-cran-promises (1.2.1+dfsg-1) ...
365s Selecting previously unselected package r-cran-httpuv.
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365s Unpacking r-cran-httpuv (1.6.14+dfsg-1) ...
365s Selecting previously unselected package r-cran-xtable.
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365s Unpacking r-cran-xtable (1:1.8-4-2) ...
365s Selecting previously unselected package r-cran-sourcetools.
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365s Unpacking r-cran-sourcetools (0.1.7-1-1) ...
365s Selecting previously unselected package r-cran-crayon.
365s Preparing to unpack .../175-r-cran-crayon_1.5.2-1_all.deb ...
365s Unpacking r-cran-crayon (1.5.2-1) ...
365s Selecting previously unselected package r-cran-commonmark.
365s Preparing to unpack .../176-r-cran-commonmark_1.9.1-1_arm64.deb ...
365s Unpacking r-cran-commonmark (1.9.1-1) ...
366s Selecting previously unselected package libjs-json.
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366s Unpacking libjs-json (0~20221030+~1.0.8-1) ...
366s Selecting previously unselected package libjs-es5-shim.
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366s Selecting previously unselected package libjs-twitter-bootstrap-datepicker.
366s Preparing to unpack .../179-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ...
366s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ...
366s Selecting previously unselected package libjs-sifter.js.
366s Preparing to unpack .../180-libjs-sifter.js_0.6.0+dfsg-3_all.deb ...
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366s Selecting previously unselected package libjs-microplugin.js.
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366s Selecting previously unselected package libjs-jquery-selectize.js.
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366s Selecting previously unselected package libjs-d3.
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366s Selecting previously unselected package node-html5shiv.
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366s Selecting previously unselected package r-cran-shiny.
366s Preparing to unpack .../185-r-cran-shiny_1.8.0+dfsg-1_all.deb ...
366s Unpacking r-cran-shiny (1.8.0+dfsg-1) ...
366s Selecting previously unselected package r-cran-rmarkdown.
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366s Unpacking r-cran-rmarkdown (2.25+dfsg-3) ...
366s Selecting previously unselected package r-cran-htmlwidgets.
366s Preparing to unpack .../187-r-cran-htmlwidgets_1.6.4+dfsg-1_all.deb ...
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366s Selecting previously unselected package r-cran-rstudioapi.
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366s Selecting previously unselected package r-cran-tidyselect.
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366s Selecting previously unselected package r-cran-dplyr.
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366s Selecting previously unselected package r-cran-purrr.
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366s Selecting previously unselected package r-cran-cpp11.
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366s Selecting previously unselected package r-cran-tidyr.
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367s Selecting previously unselected package r-cran-viridis.
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367s Setting up libjs-json (0~20221030+~1.0.8-1) ...
367s Setting up javascript-common (11+nmu1) ...
367s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
367s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
367s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
367s Setting up libpaper1:arm64 (1.1.29) ...
368s 
368s Creating config file /etc/papersize with new version
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368s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
368s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
368s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
368s Setting up pique-doc (1.0-7) ...
368s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
368s Setting up libdynaloader-functions-perl (0.003-3) ...
368s Setting up libdatrie1:arm64 (0.2.13-3) ...
368s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ...
368s Setting up libclass-method-modifiers-perl (2.15-1) ...
368s Setting up libjs-popper.js (1.16.1+ds-6) ...
368s Setting up libxcb-render0:arm64 (1.15-1) ...
368s Setting up libjs-sifter.js (0.6.0+dfsg-3) ...
368s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
368s Setting up unzip (6.0-28ubuntu3) ...
368s Setting up x11-common (1:7.7+23ubuntu2) ...
369s Setting up node-html5shiv (3.7.3+dfsg-5) ...
369s Setting up libdeflate0:arm64 (1.19-1) ...
369s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ...
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369s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
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369s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
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369s Setting up node-bootstrap-sass (3.4.3-2) ...
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369s Setting up libjs-prettify (2015.12.04+dfsg-1.1) ...
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369s Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ...
369s Setting up pandoc-data (3.1.3-1) ...
369s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
369s Setting up node-normalize.css (8.0.1-5) ...
369s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
369s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
369s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
369s Setting up libjs-bootstrap (3.4.1+dfsg-3) ...
369s Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ...
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369s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
369s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
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369s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ...
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369s Setting up pandoc (3.1.3+ds-2) ...
369s Setting up liblapacke:arm64 (3.12.0-3) ...
369s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
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371s Setting up libtk8.6:arm64 (8.6.13-2) ...
371s Setting up libparams-classify-perl:arm64 (0.015-2build3) ...
371s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ...
371s Setting up libcairo2:arm64 (1.18.0-1) ...
371s Setting up libmodule-runtime-perl (0.016-2) ...
371s Setting up libxt6:arm64 (1:1.2.1-1.1) ...
371s Setting up emmax (0~beta.20100307-5) ...
371s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
371s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
371s Setting up libimport-into-perl (1.002005-2) ...
371s Setting up libmoo-perl (2.005005-1) ...
371s Setting up r-base-core (4.3.2-1build1) ...
372s 
372s Creating config file /etc/R/Renviron with new version
372s Setting up r-cran-crayon (1.5.2-1) ...
372s Setting up libparallel-forkmanager-perl (2.02-1) ...
372s Setting up r-cran-labeling (0.4.3-1) ...
372s Setting up r-cran-sourcetools (0.1.7-1-1) ...
372s Setting up r-cran-lattice (0.22-5-1) ...
372s Setting up r-cran-nlme (3.1.164-1) ...
372s Setting up r-cran-farver (2.1.1-1) ...
372s Setting up r-cran-formula (1.2-5-1) ...
372s Setting up r-cran-viridislite (0.4.2-2) ...
372s Setting up r-cran-cluster (2.1.6-1) ...
372s Setting up r-cran-nnet (7.3-19-2) ...
372s Setting up r-cran-commonmark (1.9.1-1) ...
372s Setting up r-cran-r6 (2.5.1-1) ...
372s Setting up r-cran-pkgkitten (0.2.3-1) ...
372s Setting up r-cran-jpeg (0.1-10-1) ...
372s Setting up r-cran-chron (2.3-61-2) ...
372s Setting up r-cran-magrittr (2.0.3-1) ...
372s Setting up r-cran-rappdirs (0.3.3-1) ...
372s Setting up r-cran-quadprog (1.5-8-1build1) ...
372s Setting up r-cran-littler (0.3.19-1) ...
372s Setting up r-cran-fs (1.6.3+dfsg-1) ...
372s Setting up r-cran-rcpp (1.0.12-1) ...
372s Setting up r-cran-curl (5.2.0+dfsg-1) ...
372s Setting up r-bioc-biocgenerics (0.48.1-2) ...
372s Setting up r-cran-rlang (1.1.3-1) ...
372s Setting up littler (0.3.19-1) ...
372s Setting up r-cran-uroot (2.1-3-1) ...
372s Setting up r-cran-xfun (0.41+dfsg-1) ...
372s Setting up r-cran-urca (1.3-3-1) ...
372s Setting up r-cran-withr (2.5.0-1) ...
372s Setting up r-cran-backports (1.4.1-1) ...
372s Setting up r-cran-mime (0.12-1) ...
372s Setting up r-cran-generics (0.1.3-1) ...
372s Setting up r-cran-base64enc (0.1-3-3) ...
372s Setting up r-cran-digest (0.6.34-1) ...
372s Setting up r-cran-yaml (2.3.8-1) ...
372s Setting up r-cran-evaluate (0.23-1) ...
372s Setting up r-cran-timedate (4032.109-1) ...
372s Setting up r-cran-highr (0.10+dfsg-1) ...
372s Setting up r-cran-fansi (1.0.5-1) ...
372s Setting up r-cran-mass (7.3-60.0.1-1) ...
372s Setting up r-cran-checkmate (2.3.1-1) ...
372s Setting up r-cran-acepack (1.4.2-1) ...
372s Setting up r-cran-data.table (1.14.10+dfsg-1) ...
372s Setting up r-cran-glue (1.7.0-1) ...
372s Setting up r-cran-foreign (0.8.86-1) ...
372s Setting up r-cran-fracdiff (1.5-3-1) ...
372s Setting up r-cran-xtable (1:1.8-4-2) ...
372s Setting up r-cran-cli (3.6.2-1) ...
372s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
372s Setting up r-cran-deldir (2.0-2-1) ...
372s Setting up r-cran-fastmap (1.1.1-1) ...
372s Setting up r-cran-png (0.1-8-1) ...
372s Setting up r-bioc-biobase (2.62.0-1) ...
372s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ...
372s Setting up r-cran-rstudioapi (0.15.0-1) ...
372s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
372s Setting up r-cran-getopt (1.20.4-1) ...
372s Setting up r-cran-utf8 (1.2.4-1) ...
372s Setting up r-cran-colorspace (2.1-0+dfsg-1) ...
372s Setting up r-cran-stringi (1.8.3-1) ...
372s Setting up r-cran-cpp11 (0.4.7-1) ...
372s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
372s Setting up r-cran-isoband (0.2.7-1) ...
372s Setting up r-cran-gtable (0.3.4+dfsg-1) ...
372s Setting up r-cran-zoo (1.8-12-2) ...
372s Setting up r-cran-later (1.3.2+dfsg-1) ...
372s Setting up r-cran-matrix (1.6-5-1) ...
372s Setting up r-cran-tinytex (0.49-1) ...
372s Setting up r-cran-knitr (1.45+dfsg-1) ...
372s Setting up r-cran-mgcv (1.9-1-1) ...
372s Setting up r-cran-cachem (1.0.8-1) ...
372s Setting up r-cran-lmtest (0.9.40-1) ...
372s Setting up r-cran-rcpparmadillo (0.12.8.0.0-1) ...
372s Setting up r-cran-optparse (1.7.4-1) ...
372s Setting up r-cran-vctrs (0.6.5-1) ...
372s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ...
372s Setting up r-cran-pillar (1.9.0+dfsg-1) ...
372s Setting up r-cran-ellipsis (0.3.2-2) ...
372s Setting up r-cran-stringr (1.5.1-1) ...
372s Setting up r-cran-munsell (0.5.0-2build1) ...
372s Setting up r-cran-tibble (3.2.1+dfsg-2) ...
372s Setting up r-cran-survival (3.5-8-1) ...
372s Setting up r-cran-xts (0.13.2-1) ...
372s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ...
372s Setting up r-cran-interp (1.1-6-1) ...
372s Setting up r-cran-gridextra (2.3-3build1) ...
372s Setting up r-cran-scales (1.3.0-1) ...
372s Setting up r-cran-memoise (2.0.1-1) ...
372s Setting up r-cran-promises (1.2.1+dfsg-1) ...
372s Setting up r-cran-purrr (1.0.2-1) ...
372s Setting up r-cran-htmltools (0.5.7-1) ...
372s Setting up r-cran-sass (0.4.8+dfsg-1) ...
372s Setting up r-cran-dplyr (1.1.4-1) ...
372s Setting up r-cran-ttr (0.24.4-1) ...
372s Setting up r-bioc-multtest (2.58.0-1) ...
372s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ...
372s Setting up r-cran-httpuv (1.6.14+dfsg-1) ...
372s Setting up r-cran-rpart (4.1.23-1) ...
372s Setting up r-cran-fontawesome (0.5.2-1) ...
372s Setting up r-cran-latticeextra (0.6-30-1) ...
372s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ...
372s Setting up r-cran-viridis (0.6.5-1) ...
372s Setting up r-cran-bslib (0.6.1+dfsg-1) ...
372s Setting up r-cran-tidyr (1.3.1-1) ...
372s Setting up r-cran-quantmod (0.4.26-1) ...
372s Setting up r-cran-shiny (1.8.0+dfsg-1) ...
372s Setting up r-cran-tseries (0.10-55-1) ...
372s Setting up r-cran-rmarkdown (2.25+dfsg-3) ...
372s Setting up r-cran-forecast (8.21.1-1) ...
372s Setting up r-cran-htmlwidgets (1.6.4+dfsg-1) ...
372s Setting up pique (1.0-7) ...
372s Setting up r-cran-htmltable (2.4.2-1) ...
372s Setting up r-cran-hmisc (5.1-1-1) ...
372s Setting up autopkgtest-satdep (0) ...
372s Processing triggers for man-db (2.12.0-3) ...
373s Processing triggers for install-info (7.1-3) ...
373s Processing triggers for libc-bin (2.39-0ubuntu2) ...
383s (Reading database ... 94498 files and directories currently installed.)
383s Removing autopkgtest-satdep (0) ...
384s autopkgtest [03:35:56]: test run-unit-test: [-----------------------
384s wget --no-check-certificate  http://ricediversity.org/data/sets/44kgwas/RiceDiversity.44K.MSU6.Genotypes_PLINK.zip
384s --2024-03-11 03:35:56--  http://ricediversity.org/data/sets/44kgwas/RiceDiversity.44K.MSU6.Genotypes_PLINK.zip
385s Resolving squid.internal (squid.internal)... 185.125.188.85, 185.125.188.86
385s Connecting to squid.internal (squid.internal)|185.125.188.85|:3128... connected.
385s Proxy request sent, awaiting response... 200 OK
385s Length: 7107854 (6.8M) [application/zip]
385s Saving to: ‘RiceDiversity.44K.MSU6.Genotypes_PLINK.zip’
385s 
385s      0K .......... .......... .......... .......... ..........  0%  284K 24s
385s     50K .......... .......... .......... .......... ..........  1%  347K 22s
385s    100K .......... .......... .......... .......... ..........  2% 93.1T 15s
385s    150K .......... .......... .......... .......... ..........  2% 1.44M 12s
385s    200K .......... .......... .......... .......... ..........  3% 10.1M 10s
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385s    900K .......... .......... .......... .......... .......... 13% 8.75M 3s
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386s   1250K .......... .......... .......... .......... .......... 18% 14.7M 2s
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386s   1650K .......... .......... .......... .......... .......... 24% 11.5M 2s
386s   1700K .......... .......... .......... .......... .......... 25% 11.9M 2s
386s   1750K .......... .......... .......... .......... .......... 25% 2.01M 2s
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386s   1850K .......... .......... .......... .......... .......... 27% 30.5M 2s
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386s   2500K .......... .......... .......... .......... .......... 36% 23.0M 1s
386s   2550K .......... .......... .......... .......... .......... 37% 36.1M 1s
386s   2600K .......... .......... .......... .......... .......... 38% 27.4M 1s
386s   2650K .......... .......... .......... .......... .......... 38% 26.5M 1s
386s   2700K .......... .......... .......... .......... .......... 39% 38.0M 1s
386s   2750K .......... .......... .......... .......... .......... 40% 31.7M 1s
386s   2800K .......... .......... .......... .......... .......... 41% 33.9M 1s
386s   2850K .......... .......... .......... .......... .......... 41% 26.9M 1s
386s   2900K .......... .......... .......... .......... .......... 42% 45.5M 1s
386s   2950K .......... .......... .......... .......... .......... 43% 28.3M 1s
386s   3000K .......... .......... .......... .......... .......... 43% 31.2M 1s
386s   3050K .......... .......... .......... .......... .......... 44% 31.6M 1s
386s   3100K .......... .......... .......... .......... .......... 45% 27.9M 1s
386s   3150K .......... .......... .......... .......... .......... 46% 45.0M 1s
386s   3200K .......... .......... .......... .......... .......... 46% 27.5M 1s
386s   3250K .......... .......... .......... .......... .......... 47% 38.9M 1s
386s   3300K .......... .......... .......... .......... .......... 48% 20.6M 1s
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386s   3400K .......... .......... .......... .......... .......... 49% 58.3M 1s
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386s   3800K .......... .......... .......... .......... .......... 55% 34.4M 1s
386s   3850K .......... .......... .......... .......... .......... 56% 51.5M 1s
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386s   3950K .......... .......... .......... .......... .......... 57% 42.4M 1s
386s   4000K .......... .......... .......... .......... .......... 58% 49.2M 1s
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386s   4150K .......... .......... .......... .......... .......... 60% 46.9M 0s
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386s   4250K .......... .......... .......... .......... .......... 61% 42.1M 0s
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386s   5000K .......... .......... .......... .......... .......... 72%  134M 0s
386s   5050K .......... .......... .......... .......... .......... 73% 47.4M 0s
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386s   5150K .......... .......... .......... .......... .......... 74% 40.0M 0s
386s   5200K .......... .......... .......... .......... .......... 75% 45.6M 0s
386s   5250K .......... .......... .......... .......... .......... 76% 93.1M 0s
386s   5300K .......... .......... .......... .......... .......... 77% 54.9M 0s
386s   5350K .......... .......... .......... .......... .......... 77% 44.5M 0s
386s   5400K .......... .......... .......... .......... .......... 78% 41.4M 0s
386s   5450K .......... .......... .......... .......... .......... 79% 90.1M 0s
386s   5500K .......... .......... .......... .......... .......... 79% 52.8M 0s
386s   5550K .......... .......... .......... .......... .......... 80% 70.5M 0s
386s   5600K .......... .......... .......... .......... .......... 81% 2.93M 0s
386s   5650K .......... .......... .......... .......... .......... 82% 40.7M 0s
386s   5700K .......... .......... .......... .......... .......... 82%  172M 0s
386s   5750K .......... .......... .......... .......... .......... 83%  149M 0s
386s   5800K .......... .......... .......... .......... .......... 84% 45.2M 0s
386s   5850K .......... .......... .......... .......... .......... 84% 42.0M 0s
386s   5900K .......... .......... .......... .......... .......... 85%  117M 0s
386s   5950K .......... .......... .......... .......... .......... 86%  123M 0s
386s   6000K .......... .......... .......... .......... .......... 87% 63.0M 0s
386s   6050K .......... .......... .......... .......... .......... 87% 51.5M 0s
386s   6100K .......... .......... .......... .......... .......... 88% 52.5M 0s
386s   6150K .......... .......... .......... .......... .......... 89% 46.9M 0s
386s   6200K .......... .......... .......... .......... .......... 90% 93.1T 0s
386s   6250K .......... .......... .......... .......... .......... 90% 64.2M 0s
386s   6300K .......... .......... .......... .......... .......... 91% 39.2M 0s
386s   6350K .......... .......... .......... .......... .......... 92% 3.90M 0s
386s   6400K .......... .......... .......... .......... .......... 92% 33.2M 0s
386s   6450K .......... .......... .......... .......... .......... 93% 93.1T 0s
386s   6500K .......... .......... .......... .......... .......... 94% 81.1M 0s
386s   6550K .......... .......... .......... .......... .......... 95% 51.0M 0s
386s   6600K .......... .......... .......... .......... .......... 95% 58.9M 0s
386s   6650K .......... .......... .......... .......... .......... 96% 47.7M 0s
386s   6700K .......... .......... .......... .......... .......... 97% 93.1T 0s
386s   6750K .......... .......... .......... .......... .......... 97% 59.4M 0s
386s   6800K .......... .......... .......... .......... .......... 98% 51.8M 0s
386s   6850K .......... .......... .......... .......... .......... 99% 46.9M 0s
386s   6900K .......... .......... .......... .......... .         100% 76.9T=0.8s
386s 
386s 2024-03-11 03:35:58 (8.47 MB/s) - ‘RiceDiversity.44K.MSU6.Genotypes_PLINK.zip’ saved [7107854/7107854]
386s 
386s unzip RiceDiversity.44K.MSU6.Genotypes_PLINK.zip
386s Archive:  RiceDiversity.44K.MSU6.Genotypes_PLINK.zip
386s    creating: RiceDiversity_44K_Genotypes_PLINK/
386s   inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.fam  
386s    creating: __MACOSX/
386s    creating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/
386s   inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.fam  
386s   inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.map  
386s   inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.map  
386s   inflating: RiceDiversity_44K_Genotypes_PLINK/sativas413.ped  
386s   inflating: __MACOSX/RiceDiversity_44K_Genotypes_PLINK/._sativas413.ped  
386s mv -i ./RiceDiversity_44K_Genotypes_PLINK/sativas* .
386s rmdir RiceDiversity_44K_Genotypes_PLINK
386s rm RiceDiversity.44K.MSU6.Genotypes_PLINK.zip
386s pique-input -d -v -i sativas413 -o sativas_GWAS -p rice_phenotype.txt -k -c -e 5
387s Pre-process input data...
387s /usr/bin/p-link --missing-genotype 0 --recode12 --file sativas413 --out sativas413_recode12
387s 
387s @----------------------------------------------------------@
387s |        PLINK!       |     v1.07      |   10/Aug/2009     |
387s |----------------------------------------------------------|
387s |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
387s |----------------------------------------------------------|
387s |  For documentation, citation & bug-report instructions:  |
387s |        http://pngu.mgh.harvard.edu/purcell/plink/        |
387s @----------------------------------------------------------@
387s 
387s Web-based version check ( --noweb to skip )
387s Connecting to web...  failed connection
387s 
387s Problem connecting to web
387s 
387s Writing this text to log file [ sativas413_recode12.log ]
387s Analysis started: Mon Mar 11 03:35:59 2024
387s 
387s Options in effect:
387s 	--missing-genotype 0
387s 	--recode12
387s 	--file sativas413
387s 	--out sativas413_recode12
387s 
387s 36901 (of 36901) markers to be included from [ sativas413.map ]
388s Warning, found 413 individuals with ambiguous sex codes
388s Writing list of these individuals to [ sativas413_recode12.nosex ]
388s 413 individuals read from [ sativas413.ped ] 
388s 0 individuals with nonmissing phenotypes
388s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
388s Missing phenotype value is also -9
388s 0 cases, 0 controls and 413 missing
388s 0 males, 0 females, and 413 of unspecified sex
388s Before frequency and genotyping pruning, there are 36901 SNPs
388s 413 founders and 0 non-founders found
388s Total genotyping rate in remaining individuals is 0.956644
388s 0 SNPs failed missingness test ( GENO > 1 )
388s 0 SNPs failed frequency test ( MAF < 0 )
388s After frequency and genotyping pruning, there are 36901 SNPs
388s After filtering, 0 cases, 0 controls and 413 missing
388s After filtering, 0 males, 0 females, and 413 of unspecified sex
388s Writing recoded ped file to [ sativas413_recode12.ped ] 
389s Writing new map file to [ sativas413_recode12.map ] 
389s 
389s Analysis finished: Mon Mar 11 03:36:01 2024
389s 
390s Store phenotype data indexed by genotype...
390s cd sativas_GWAS
390s Filter accessions for phenotype from ../sativas413_recode12...
390s Checking concurrence of id's in .ped and .pheno input files...
390s 
390s Total number of accession ids in ../sativas413_recode12.ped: 413
390s Number of accession id's in ../sativas413_recode12.ped not present in rice_phenotype.txt: 35
390s '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' 
390s Total number of accession id's in rice_phenotype.txt: 378
390s Number of accession id's in rice_phenotype.txt not present in ../sativas413_recode12.ped: 0
390s 
390s Quality control sativas_GWAS...
390s 
390s Calculating MAF...
390s /usr/bin/p-link --missing-genotype 0 --freq --file sativas_GWAS --out sativas_GWAS
390s 
390s @----------------------------------------------------------@
390s |        PLINK!       |     v1.07      |   10/Aug/2009     |
390s |----------------------------------------------------------|
390s |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
390s |----------------------------------------------------------|
390s |  For documentation, citation & bug-report instructions:  |
390s |        http://pngu.mgh.harvard.edu/purcell/plink/        |
390s @----------------------------------------------------------@
390s 
390s Web-based version check ( --noweb to skip )
390s Connecting to web...  failed connection
390s 
390s Problem connecting to web
390s 
390s Writing this text to log file [ sativas_GWAS.log ]
390s Analysis started: Mon Mar 11 03:36:01 2024
390s 
390s Options in effect:
390s 	--missing-genotype 0
390s 	--freq
390s 	--file sativas_GWAS
390s 	--out sativas_GWAS
390s 
390s 36901 (of 36901) markers to be included from [ sativas_GWAS.map ]
391s Warning, found 378 individuals with ambiguous sex codes
391s These individuals will be set to missing ( or use --allow-no-sex )
391s Writing list of these individuals to [ sativas_GWAS.nosex ]
391s 378 individuals read from [ sativas_GWAS.ped ] 
391s 0 individuals with nonmissing phenotypes
391s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
391s Missing phenotype value is also -9
391s 0 cases, 0 controls and 378 missing
391s 0 males, 0 females, and 378 of unspecified sex
391s Before frequency and genotyping pruning, there are 36901 SNPs
391s 378 founders and 0 non-founders found
391s Writing allele frequencies (founders-only) to [ sativas_GWAS.frq ] 
391s 
391s Analysis finished: Mon Mar 11 03:36:03 2024
391s 
391s Create sativas_GWAS.covar file...
391s /usr/lib/eigensoft/smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log
399s Transpose sativas_GWAS...
399s /usr/bin/p-link --missing-genotype 0 --recode --transpose --file sativas_GWAS --out sativas_GWAS
399s 
399s @----------------------------------------------------------@
399s |        PLINK!       |     v1.07      |   10/Aug/2009     |
399s |----------------------------------------------------------|
399s |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
399s |----------------------------------------------------------|
399s |  For documentation, citation & bug-report instructions:  |
399s |        http://pngu.mgh.harvard.edu/purcell/plink/        |
399s @----------------------------------------------------------@
399s 
399s Web-based version check ( --noweb to skip )
399s Recent cached web-check found...Problem connecting to web
399s 
399s Writing this text to log file [ sativas_GWAS.log ]
399s Analysis started: Mon Mar 11 03:36:11 2024
399s 
399s Options in effect:
399s 	--missing-genotype 0
399s 	--recode
399s 	--transpose
399s 	--file sativas_GWAS
399s 	--out sativas_GWAS
399s 
399s 36901 (of 36901) markers to be included from [ sativas_GWAS.map ]
400s Warning, found 378 individuals with ambiguous sex codes
400s Writing list of these individuals to [ sativas_GWAS.nosex ]
400s 378 individuals read from [ sativas_GWAS.ped ] 
400s 0 individuals with nonmissing phenotypes
400s Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
400s Missing phenotype value is also -9
400s 0 cases, 0 controls and 378 missing
400s 0 males, 0 females, and 378 of unspecified sex
400s Before frequency and genotyping pruning, there are 36901 SNPs
400s 378 founders and 0 non-founders found
400s Total genotyping rate in remaining individuals is 0.956642
400s 0 SNPs failed missingness test ( GENO > 1 )
400s 0 SNPs failed frequency test ( MAF < 0 )
400s After frequency and genotyping pruning, there are 36901 SNPs
400s After filtering, 0 cases, 0 controls and 378 missing
400s After filtering, 0 males, 0 females, and 378 of unspecified sex
400s Writing transposed ped file to [ sativas_GWAS.tped ] 
401s Writing family information to [ sativas_GWAS.tfam ] 
401s 
401s Analysis finished: Mon Mar 11 03:36:13 2024
401s 
401s Creating sativas_GWAS.hIBS.kin kinship file using IBS method...
401s /usr/bin/emmax-kin -v -h -s -d 10 sativas_GWAS
401s 
401s Reading TFAM file sativas_GWAS.tfam ....
401s 
401s Reading TPED file sativas_GWAS.tped ....
401s Reading 0 SNPs
401s Reading 1000 SNPs
402s Reading 2000 SNPs
402s Reading 3000 SNPs
402s Reading 4000 SNPs
402s Reading 5000 SNPs
402s Reading 6000 SNPs
402s Reading 7000 SNPs
402s Reading 8000 SNPs
403s Reading 9000 SNPs
403s Reading 10000 SNPs
403s Reading 11000 SNPs
403s Reading 12000 SNPs
403s Reading 13000 SNPs
403s Reading 14000 SNPs
404s Reading 15000 SNPs
404s Reading 16000 SNPs
404s Reading 17000 SNPs
404s Reading 18000 SNPs
404s Reading 19000 SNPs
404s Reading 20000 SNPs
404s Reading 21000 SNPs
405s Reading 22000 SNPs
405s Reading 23000 SNPs
405s Reading 24000 SNPs
405s Reading 25000 SNPs
405s Reading 26000 SNPs
405s Reading 27000 SNPs
405s Reading 28000 SNPs
406s Reading 29000 SNPs
406s Reading 30000 SNPs
406s Reading 31000 SNPs
406s Reading 32000 SNPs
406s Reading 33000 SNPs
406s Reading 34000 SNPs
406s Reading 35000 SNPs
407s Reading 36000 SNPs
407s Printing the kinship matrix to file
407s Creating phenotype files in sub-directory sativas_GWAS...
407s 
407s cd ..
407s removing temp files...
407s pique-run -d -v -i sativas_GWAS -k IBS -c sativas_GWAS.covar -n 16
407s Warning can't run 16 threads on this system - default to max = 2 threads
407s cd sativas_GWAS
407s Starting Q_grain_Co, pid = 5744
407s cd A_Stem_thickness
407s processing phenotype A_Stem_thickness...
407s 
407s 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
407s cd Q_grain_Co
407s processing phenotype Q_grain_Co...
407s 
407s 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
407s nmiss = 49 , mphenoflag = 1
407s nmiss = 90 , mphenoflag = 1
407s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551
407s k = 282,  n-q = 282
408s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.474006
408s k = 323,  n-q = 323
411s 
411s number of SNP ids in Q_grain_Co_sativas_GWAS.ps for 'Q_grain_Co' phenotype: 36901
411s number of SNP ids in Q_grain_Co_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Co' phenotype: 0
411s 
411s number of SNP ids in sativas_GWAS.tped: 36901
411s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Co_sativas_GWAS.ps: 0
411s 
412s Error in file(filename, "r", encoding = encoding) : 
412s   cannot open the connection
412s Calls: source -> file
412s In addition: Warning message:
412s In file(filename, "r", encoding = encoding) :
412s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
412s Execution halted
412s cd ..
412s 
412s number of SNP ids in A_Stem_thickness_sativas_GWAS.ps for 'A_Stem_thickness' phenotype: 36901
412s number of SNP ids in A_Stem_thickness_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Stem_thickness' phenotype: 0
412s 
412s number of SNP ids in sativas_GWAS.tped: 36901
412s number of SNP ids in sativas_GWAS.tped not present in A_Stem_thickness_sativas_GWAS.ps: 0
412s 
412s Error in file(filename, "r", encoding = encoding) : 
412s   cannot open the connection
412s Calls: source -> file
412s In addition: Warning message:
412s In file(filename, "r", encoding = encoding) :
412s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
412s Execution halted
412s cd ..
412s Starting A_Stem_thickness, pid = 5745
412s Finished Q_grain_Co, pid = 5744, exit_code = 0
412s Finished A_Stem_thickness, pid = 5745, exit_code = 0
412s Starting H_Root_dry_weight, pid = 5772
412s cd H_Root_dry_weight
412s processing phenotype H_Root_dry_weight...
412s 
412s 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
412s cd Q_FT
412s processing phenotype Q_FT...
412s 
412s 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
412s nmiss = 260 , mphenoflag = 1
412s nmiss = 85 , mphenoflag = 1
412s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689
412s k = 112,  n-q = 112
412s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.399886
412s k = 287,  n-q = 287
414s 
414s number of SNP ids in H_Root_dry_weight_sativas_GWAS.ps for 'H_Root_dry_weight' phenotype: 36901
414s 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
414s 
414s number of SNP ids in sativas_GWAS.tped: 36901
414s number of SNP ids in sativas_GWAS.tped not present in H_Root_dry_weight_sativas_GWAS.ps: 0
414s 
414s Error in file(filename, "r", encoding = encoding) : 
414s   cannot open the connection
414s Calls: source -> file
414s In addition: Warning message:
414s In file(filename, "r", encoding = encoding) :
414s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
414s Execution halted
414s cd ..
414s Starting Q_FT, pid = 5773
414s Finished H_Root_dry_weight, pid = 5772, exit_code = 0
414s cd Amylose_Content
414s processing phenotype Amylose_Content...
414s 
414s 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
414s nmiss = 50 , mphenoflag = 1
414s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.447865
414s k = 322,  n-q = 322
416s 
416s number of SNP ids in Q_FT_sativas_GWAS.ps for 'Q_FT' phenotype: 36901
416s number of SNP ids in Q_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_FT' phenotype: 0
416s 
416s number of SNP ids in sativas_GWAS.tped: 36901
416s number of SNP ids in sativas_GWAS.tped not present in Q_FT_sativas_GWAS.ps: 0
416s 
416s Error in file(filename, "r", encoding = encoding) : 
416s   cannot open the connection
416s Calls: source -> file
416s In addition: Warning message:
416s In file(filename, "r", encoding = encoding) :
416s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
416s Execution halted
416s cd ..
416s Starting Amylose_Content, pid = 5788
416s Finished Q_FT, pid = 5773, exit_code = 0
416s cd F_grain_As
416s processing phenotype F_grain_As...
416s 
416s 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
416s nmiss = 73 , mphenoflag = 1
416s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843
416s k = 299,  n-q = 299
419s 
419s number of SNP ids in Amylose_Content_sativas_GWAS.ps for 'Amylose_Content' phenotype: 36901
419s number of SNP ids in Amylose_Content_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Amylose_Content' phenotype: 0
419s 
419s number of SNP ids in sativas_GWAS.tped: 36901
419s number of SNP ids in sativas_GWAS.tped not present in Amylose_Content_sativas_GWAS.ps: 0
419s 
419s Error in file(filename, "r", encoding = encoding) : 
419s   cannot open the connection
419s Calls: source -> file
419s In addition: Warning message:
419s In file(filename, "r", encoding = encoding) :
419s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
419s Execution halted
419s cd ..
419s Starting F_grain_As, pid = 5802
419s Finished Amylose_Content, pid = 5788, exit_code = 0
419s cd H_R_S
419s processing phenotype H_R_S...
419s 
419s 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
419s nmiss = 260 , mphenoflag = 1
419s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689
419s k = 112,  n-q = 112
420s 
420s number of SNP ids in F_grain_As_sativas_GWAS.ps for 'F_grain_As' phenotype: 36901
420s number of SNP ids in F_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_As' phenotype: 0
420s 
420s number of SNP ids in sativas_GWAS.tped: 36901
420s number of SNP ids in sativas_GWAS.tped not present in F_grain_As_sativas_GWAS.ps: 0
420s 
421s Error in file(filename, "r", encoding = encoding) : 
421s   cannot open the connection
421s Calls: source -> file
421s In addition: Warning message:
421s In file(filename, "r", encoding = encoding) :
421s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
421s Execution halted
421s cd ..
421s 
421s number of SNP ids in H_R_S_sativas_GWAS.ps for 'H_R_S' phenotype: 36901
421s number of SNP ids in H_R_S_sativas_GWAS.ps not present in sativas_GWAS.tped for 'H_R_S' phenotype: 0
421s 
421s number of SNP ids in sativas_GWAS.tped: 36901
421s number of SNP ids in sativas_GWAS.tped not present in H_R_S_sativas_GWAS.ps: 0
421s 
421s Error in file(filename, "r", encoding = encoding) : 
421s   cannot open the connection
421s Calls: source -> file
421s In addition: Warning message:
421s In file(filename, "r", encoding = encoding) :
421s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
421s Execution halted
421s cd ..
421s Starting H_R_S, pid = 5816
421s Finished H_R_S, pid = 5816, exit_code = 0
421s Finished F_grain_As, pid = 5802, exit_code = 0
421s Starting Q_shoot_mass, pid = 5842
421s cd Q_shoot_mass
421s processing phenotype Q_shoot_mass...
421s 
421s 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
421s cd F_grain_yield
421s processing phenotype F_grain_yield...
421s 
421s 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
421s nmiss = 87 , mphenoflag = 1
421s nmiss = 73 , mphenoflag = 1
421s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.413538
421s k = 285,  n-q = 285
421s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843
421s k = 299,  n-q = 299
425s 
425s number of SNP ids in Q_shoot_mass_sativas_GWAS.ps for 'Q_shoot_mass' phenotype: 36901
425s number of SNP ids in Q_shoot_mass_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_shoot_mass' phenotype: 0
425s 
425s number of SNP ids in sativas_GWAS.tped: 36901
425s number of SNP ids in sativas_GWAS.tped not present in Q_shoot_mass_sativas_GWAS.ps: 0
425s 
425s Error in file(filename, "r", encoding = encoding) : 
425s   cannot open the connection
425s Calls: source -> file
425s In addition: Warning message:
425s In file(filename, "r", encoding = encoding) :
425s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
425s Execution halted
425s cd ..
425s Starting F_grain_yield, pid = 5843
425s Finished Q_shoot_mass, pid = 5842, exit_code = 0
425s cd HULLED_SEED_LENGTH
425s processing phenotype HULLED_SEED_LENGTH...
425s 
425s 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
425s nmiss = 34 , mphenoflag = 1
425s 
425s number of SNP ids in F_grain_yield_sativas_GWAS.ps for 'F_grain_yield' phenotype: 36901
425s number of SNP ids in F_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_yield' phenotype: 0
425s 
425s number of SNP ids in sativas_GWAS.tped: 36901
425s number of SNP ids in sativas_GWAS.tped not present in F_grain_yield_sativas_GWAS.ps: 0
425s 
425s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.481982
425s k = 338,  n-q = 338
426s Error in file(filename, "r", encoding = encoding) : 
426s   cannot open the connection
426s Calls: source -> file
426s In addition: Warning message:
426s In file(filename, "r", encoding = encoding) :
426s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
426s Execution halted
426s cd ..
427s Starting HULLED_SEED_LENGTH, pid = 5858
427s Finished F_grain_yield, pid = 5843, exit_code = 0
427s nmiss = 29 , mphenoflag = 1
427s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.570052
427s k = 343,  n-q = 343
427s cd A_PH
427s processing phenotype A_PH...
427s 
427s 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
430s 
430s number of SNP ids in HULLED_SEED_LENGTH_sativas_GWAS.ps for 'HULLED_SEED_LENGTH' phenotype: 36901
430s number of SNP ids in HULLED_SEED_LENGTH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'HULLED_SEED_LENGTH' phenotype: 0
430s 
430s number of SNP ids in sativas_GWAS.tped: 36901
430s number of SNP ids in sativas_GWAS.tped not present in HULLED_SEED_LENGTH_sativas_GWAS.ps: 0
430s 
430s Error in file(filename, "r", encoding = encoding) : 
430s   cannot open the connection
430s Calls: source -> file
430s In addition: Warning message:
430s In file(filename, "r", encoding = encoding) :
430s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
430s Execution halted
430s cd ..
431s 
431s number of SNP ids in A_PH_sativas_GWAS.ps for 'A_PH' phenotype: 36901
431s number of SNP ids in A_PH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_PH' phenotype: 0
431s 
431s number of SNP ids in sativas_GWAS.tped: 36901
431s number of SNP ids in sativas_GWAS.tped not present in A_PH_sativas_GWAS.ps: 0
431s 
431s Starting A_PH, pid = 5872
431s Finished HULLED_SEED_LENGTH, pid = 5858, exit_code = 0
431s cd A_Tiller_no.
431s processing phenotype A_Tiller_no....
431s 
431s 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
431s nmiss = 46 , mphenoflag = 1
432s Error in file(filename, "r", encoding = encoding) : 
432s   cannot open the connection
432s Calls: source -> file
432s In addition: Warning message:
432s In file(filename, "r", encoding = encoding) :
432s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
432s Execution halted
432s cd ..
432s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.524438
432s k = 326,  n-q = 326
432s Starting A_Tiller_no., pid = 5892
432s Finished A_PH, pid = 5872, exit_code = 0
432s cd H_Shoot_dry_weight
432s processing phenotype H_Shoot_dry_weight...
432s 
432s 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
432s nmiss = 260 , mphenoflag = 1
432s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689
432s k = 112,  n-q = 112
434s 
434s number of SNP ids in H_Shoot_dry_weight_sativas_GWAS.ps for 'H_Shoot_dry_weight' phenotype: 36901
434s 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
434s 
434s number of SNP ids in sativas_GWAS.tped: 36901
434s number of SNP ids in sativas_GWAS.tped not present in H_Shoot_dry_weight_sativas_GWAS.ps: 0
434s 
434s Error in file(filename, "r", encoding = encoding) : 
434s   cannot open the connection
434s Calls: source -> file
434s In addition: Warning message:
434s In file(filename, "r", encoding = encoding) :
434s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
434s Execution halted
434s cd ..
435s Starting H_Shoot_dry_weight, pid = 5900
435s Finished H_Shoot_dry_weight, pid = 5900, exit_code = 0
435s cd A_Seed_length
435s processing phenotype A_Seed_length...
435s 
435s 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
435s nmiss = 20 , mphenoflag = 1
436s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.577637
436s k = 352,  n-q = 352
436s 
436s number of SNP ids in A_Tiller_no._sativas_GWAS.ps for 'A_Tiller_no.' phenotype: 36901
436s number of SNP ids in A_Tiller_no._sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Tiller_no.' phenotype: 0
436s 
436s number of SNP ids in sativas_GWAS.tped: 36901
436s number of SNP ids in sativas_GWAS.tped not present in A_Tiller_no._sativas_GWAS.ps: 0
436s 
436s Error in file(filename, "r", encoding = encoding) : 
436s   cannot open the connection
436s Calls: source -> file
436s In addition: Warning message:
436s In file(filename, "r", encoding = encoding) :
436s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
436s Execution halted
436s cd ..
436s Starting A_Seed_length, pid = 5914
436s Finished A_Tiller_no., pid = 5892, exit_code = 0
436s cd Daniel_shoot_As
436s processing phenotype Daniel_shoot_As...
436s 
436s 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
436s nmiss = 40 , mphenoflag = 1
437s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.552770
437s k = 332,  n-q = 332
441s 
441s number of SNP ids in A_Seed_length_sativas_GWAS.ps for 'A_Seed_length' phenotype: 36901
441s number of SNP ids in A_Seed_length_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Seed_length' phenotype: 0
441s 
441s number of SNP ids in sativas_GWAS.tped: 36901
441s number of SNP ids in sativas_GWAS.tped not present in A_Seed_length_sativas_GWAS.ps: 0
441s 
441s Error in file(filename, "r", encoding = encoding) : 
441s   cannot open the connection
441s Calls: source -> file
441s In addition: Warning message:
441s In file(filename, "r", encoding = encoding) :
441s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
441s Execution halted
441s cd ..
441s 
441s number of SNP ids in Daniel_shoot_As_sativas_GWAS.ps for 'Daniel_shoot_As' phenotype: 36901
441s number of SNP ids in Daniel_shoot_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Daniel_shoot_As' phenotype: 0
441s 
441s number of SNP ids in sativas_GWAS.tped: 36901
441s number of SNP ids in sativas_GWAS.tped not present in Daniel_shoot_As_sativas_GWAS.ps: 0
441s 
441s Starting Daniel_shoot_As, pid = 5928
441s Finished A_Seed_length, pid = 5914, exit_code = 0
441s cd F_FT
441s processing phenotype F_FT...
441s 
441s 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
442s nmiss = 73 , mphenoflag = 1
442s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843
442s k = 299,  n-q = 299
442s Error in file(filename, "r", encoding = encoding) : 
442s   cannot open the connection
442s Calls: source -> file
442s In addition: Warning message:
442s In file(filename, "r", encoding = encoding) :
442s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
442s Execution halted
442s cd ..
443s Starting F_FT, pid = 5948
443s Finished Daniel_shoot_As, pid = 5928, exit_code = 0
443s cd F_shoot_As
443s processing phenotype F_shoot_As...
443s 
443s 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
443s nmiss = 73 , mphenoflag = 1
443s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.459771
443s k = 299,  n-q = 299
446s 
446s number of SNP ids in F_FT_sativas_GWAS.ps for 'F_FT' phenotype: 36901
446s number of SNP ids in F_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_FT' phenotype: 0
446s 
446s number of SNP ids in sativas_GWAS.tped: 36901
446s number of SNP ids in sativas_GWAS.tped not present in F_FT_sativas_GWAS.ps: 0
446s 
446s Error in file(filename, "r", encoding = encoding) : 
446s   cannot open the connection
446s Calls: source -> file
446s In addition: Warning message:
446s In file(filename, "r", encoding = encoding) :
446s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
446s Execution halted
446s cd ..
447s Starting F_shoot_As, pid = 5956
447s Finished F_FT, pid = 5948, exit_code = 0
447s cd A_Seed_weight
447s processing phenotype A_Seed_weight...
447s 
447s 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
447s 
447s number of SNP ids in F_shoot_As_sativas_GWAS.ps for 'F_shoot_As' phenotype: 36901
447s number of SNP ids in F_shoot_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_shoot_As' phenotype: 0
447s 
447s number of SNP ids in sativas_GWAS.tped: 36901
447s number of SNP ids in sativas_GWAS.tped not present in F_shoot_As_sativas_GWAS.ps: 0
447s 
447s nmiss = 21 , mphenoflag = 1
447s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.575045
447s k = 351,  n-q = 351
447s Error in file(filename, "r", encoding = encoding) : 
447s   cannot open the connection
447s Calls: source -> file
447s In addition: Warning message:
447s In file(filename, "r", encoding = encoding) :
447s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
447s Execution halted
447s cd ..
448s Starting A_Seed_weight, pid = 5970
448s Finished F_shoot_As, pid = 5956, exit_code = 0
448s cd A_FT
448s processing phenotype A_FT...
448s 
448s 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
448s nmiss = 19 , mphenoflag = 1
448s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.578644
448s k = 353,  n-q = 353
451s 
451s number of SNP ids in A_Seed_weight_sativas_GWAS.ps for 'A_Seed_weight' phenotype: 36901
451s number of SNP ids in A_Seed_weight_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_Seed_weight' phenotype: 0
451s 
451s number of SNP ids in sativas_GWAS.tped: 36901
451s number of SNP ids in sativas_GWAS.tped not present in A_Seed_weight_sativas_GWAS.ps: 0
451s 
452s Error in file(filename, "r", encoding = encoding) : 
452s   cannot open the connection
452s Calls: source -> file
452s In addition: Warning message:
452s In file(filename, "r", encoding = encoding) :
452s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
452s Execution halted
452s cd ..
452s 
452s number of SNP ids in A_FT_sativas_GWAS.ps for 'A_FT' phenotype: 36901
452s number of SNP ids in A_FT_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_FT' phenotype: 0
452s 
452s number of SNP ids in sativas_GWAS.tped: 36901
452s number of SNP ids in sativas_GWAS.tped not present in A_FT_sativas_GWAS.ps: 0
452s 
453s Starting A_FT, pid = 5984
453s Finished A_Seed_weight, pid = 5970, exit_code = 0
453s cd H_Shoot_length_27
453s processing phenotype H_Shoot_length_27...
453s 
453s 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
453s nmiss = 260 , mphenoflag = 1
453s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689
453s k = 112,  n-q = 112
453s Error in file(filename, "r", encoding = encoding) : 
453s   cannot open the connection
453s Calls: source -> file
453s In addition: Warning message:
453s In file(filename, "r", encoding = encoding) :
453s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
453s Execution halted
453s cd ..
454s Starting H_Shoot_length_27, pid = 6004
454s Finished A_FT, pid = 5984, exit_code = 0
454s nmiss = 90 , mphenoflag = 1
454s cd Q_grain_Cu
454s processing phenotype Q_grain_Cu...
454s 
454s 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
454s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551
454s k = 282,  n-q = 282
454s 
454s number of SNP ids in H_Shoot_length_27_sativas_GWAS.ps for 'H_Shoot_length_27' phenotype: 36901
454s 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
454s 
454s number of SNP ids in sativas_GWAS.tped: 36901
454s number of SNP ids in sativas_GWAS.tped not present in H_Shoot_length_27_sativas_GWAS.ps: 0
454s 
454s Error in file(filename, "r", encoding = encoding) : 
454s   cannot open the connection
454s Calls: source -> file
454s In addition: Warning message:
454s In file(filename, "r", encoding = encoding) :
454s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
454s Execution halted
454s cd ..
455s Starting Q_grain_Cu, pid = 6012
455s Finished H_Shoot_length_27, pid = 6004, exit_code = 0
455s cd Q_PH
455s processing phenotype Q_PH...
455s 
455s 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
455s nmiss = 87 , mphenoflag = 1
455s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.413538
455s k = 285,  n-q = 285
458s 
458s number of SNP ids in Q_grain_Cu_sativas_GWAS.ps for 'Q_grain_Cu' phenotype: 36901
458s number of SNP ids in Q_grain_Cu_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Cu' phenotype: 0
458s 
458s number of SNP ids in sativas_GWAS.tped: 36901
458s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Cu_sativas_GWAS.ps: 0
458s 
458s Error in file(filename, "r", encoding = encoding) : 
458s   cannot open the connection
458s Calls: source -> file
458s In addition: Warning message:
458s In file(filename, "r", encoding = encoding) :
458s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
458s Execution halted
458s cd ..
458s 
458s number of SNP ids in Q_PH_sativas_GWAS.ps for 'Q_PH' phenotype: 36901
458s number of SNP ids in Q_PH_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_PH' phenotype: 0
458s 
458s number of SNP ids in sativas_GWAS.tped: 36901
458s number of SNP ids in sativas_GWAS.tped not present in Q_PH_sativas_GWAS.ps: 0
458s 
459s Starting Q_PH, pid = 6026
459s Finished Q_grain_Cu, pid = 6012, exit_code = 0
459s nmiss = 90 , mphenoflag = 1
459s cd Q_grain_As
459s processing phenotype Q_grain_As...
459s 
459s 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
459s cd ..
459s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551
459s k = 282,  n-q = 282
459s Error in file(filename, "r", encoding = encoding) : 
459s   cannot open the connection
459s Calls: source -> file
459s In addition: Warning message:
459s In file(filename, "r", encoding = encoding) :
459s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
459s Execution halted
460s Starting Q_grain_As, pid = 6046
460s Finished Q_PH, pid = 6026, exit_code = 0
460s cd F_As_TF
460s processing phenotype F_As_TF...
460s 
460s 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
460s nmiss = 75 , mphenoflag = 1
460s evals[0] = -0.000000, evals[1] = 0.000000, evals[n-1] = 2.455247
460s k = 297,  n-q = 297
462s 
462s number of SNP ids in Q_grain_As_sativas_GWAS.ps for 'Q_grain_As' phenotype: 36901
462s number of SNP ids in Q_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_As' phenotype: 0
462s 
462s number of SNP ids in sativas_GWAS.tped: 36901
462s number of SNP ids in sativas_GWAS.tped not present in Q_grain_As_sativas_GWAS.ps: 0
462s 
462s Error in file(filename, "r", encoding = encoding) : 
462s   cannot open the connection
462s Calls: source -> file
462s In addition: Warning message:
462s In file(filename, "r", encoding = encoding) :
462s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
462s Execution halted
462s cd ..
463s Starting F_As_TF, pid = 6054
463s Finished Q_grain_As, pid = 6046, exit_code = 0
463s cd A_grain_yield
463s processing phenotype A_grain_yield...
463s 
463s 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
463s nmiss = 49 , mphenoflag = 1
463s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.520537
463s k = 323,  n-q = 323
463s 
463s number of SNP ids in F_As_TF_sativas_GWAS.ps for 'F_As_TF' phenotype: 36901
463s number of SNP ids in F_As_TF_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_As_TF' phenotype: 0
463s 
463s number of SNP ids in sativas_GWAS.tped: 36901
463s number of SNP ids in sativas_GWAS.tped not present in F_As_TF_sativas_GWAS.ps: 0
463s 
464s Error in file(filename, "r", encoding = encoding) : 
464s   cannot open the connection
464s Calls: source -> file
464s In addition: Warning message:
464s In file(filename, "r", encoding = encoding) :cd ..
464s 
464s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
464s Execution halted
465s Starting A_grain_yield, pid = 6068
465s Finished F_As_TF, pid = 6054, exit_code = 0
465s cd India_grain_As
465s processing phenotype India_grain_As...
465s 
465s 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
465s nmiss = 280 , mphenoflag = 1
465s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.487105
465s k = 92,  n-q = 92
466s 
466s number of SNP ids in India_grain_As_sativas_GWAS.ps for 'India_grain_As' phenotype: 36901
466s number of SNP ids in India_grain_As_sativas_GWAS.ps not present in sativas_GWAS.tped for 'India_grain_As' phenotype: 0
466s 
466s number of SNP ids in sativas_GWAS.tped: 36901
466s number of SNP ids in sativas_GWAS.tped not present in India_grain_As_sativas_GWAS.ps: 0
466s 
467s Error in file(filename, "r", encoding = encoding) : 
467s   cannot open the connection
467s Calls: source -> file
467s In addition: Warning message:
467s In file(filename, "r", encoding = encoding) :
467s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
467s Execution halted
467s cd ..
467s 
467s number of SNP ids in A_grain_yield_sativas_GWAS.ps for 'A_grain_yield' phenotype: 36901
467s number of SNP ids in A_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'A_grain_yield' phenotype: 0
467s 
467s number of SNP ids in sativas_GWAS.tped: 36901
467s number of SNP ids in sativas_GWAS.tped not present in A_grain_yield_sativas_GWAS.ps: 0
467s 
467s Error in file(filename, "r", encoding = encoding) : 
467s   cannot open the connection
467s Calls: source -> file
467s In addition: Warning message:
467s In file(filename, "r", encoding = encoding) :
467s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
467s Execution halted
467s cd ..
468s Starting India_grain_As, pid = 6082
468s Finished A_grain_yield, pid = 6068, exit_code = 0
468s Finished India_grain_As, pid = 6082, exit_code = 0
468s Starting F_grain_Zn, pid = 6108
468s cd F_grain_Zn
468s processing phenotype F_grain_Zn...
468s 
468s 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
468s cd F_grain_Cu
468s processing phenotype F_grain_Cu...
468s 
468s 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
468s nmiss = 73 , mphenoflag = 1
468s nmiss = 73 , mphenoflag = 1
468s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843
468s k = 299,  n-q = 299
468s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843
468s k = 299,  n-q = 299
472s 
472s number of SNP ids in F_grain_Zn_sativas_GWAS.ps for 'F_grain_Zn' phenotype: 36901
472s number of SNP ids in F_grain_Zn_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Zn' phenotype: 0
472s 
472s number of SNP ids in sativas_GWAS.tped: 36901
472s number of SNP ids in sativas_GWAS.tped not present in F_grain_Zn_sativas_GWAS.ps: 0
472s 
472s 
472s number of SNP ids in F_grain_Cu_sativas_GWAS.ps for 'F_grain_Cu' phenotype: 36901
472s number of SNP ids in F_grain_Cu_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Cu' phenotype: 0
472s 
472s number of SNP ids in sativas_GWAS.tped: 36901
472s number of SNP ids in sativas_GWAS.tped not present in F_grain_Cu_sativas_GWAS.ps: 0
472s 
472s Error in file(filename, "r", encoding = encoding) : 
472s   cannot open the connection
472s Calls: source -> file
472s In addition: Warning message:
472s In file(filename, "r", encoding = encoding) :
472s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
472s Execution halted
472s cd ..
472s Error in file(filename, "r", encoding = encoding) : 
472s   cannot open the connection
472s Calls: source -> file
472s In addition: Warning message:
472s In file(filename, "r", encoding = encoding) :
472s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
472s Execution halted
472s cd ..
473s Starting F_grain_Cu, pid = 6109
473s Finished F_grain_Cu, pid = 6109, exit_code = 0
473s Finished F_grain_Zn, pid = 6108, exit_code = 0
473s Starting Q_grain_Zn, pid = 6136
473s cd Q_grain_Zn
473s processing phenotype Q_grain_Zn...
473s 
473s 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
473s cd H_Root_Length_27
473s processing phenotype H_Root_Length_27...
473s 
473s 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
473s nmiss = 90 , mphenoflag = 1
473s nmiss = 260 , mphenoflag = 1
473s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 1.929689
473s k = 112,  n-q = 112
473s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551
473s k = 282,  n-q = 282
475s 
475s number of SNP ids in H_Root_Length_27_sativas_GWAS.ps for 'H_Root_Length_27' phenotype: 36901
475s 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
475s 
475s number of SNP ids in sativas_GWAS.tped: 36901
475s number of SNP ids in sativas_GWAS.tped not present in H_Root_Length_27_sativas_GWAS.ps: 0
475s 
475s Error in file(filename, "r", encoding = encoding) : 
475s   cannot open the connection
475s Calls: source -> file
475s In addition: Warning message:
475s In file(filename, "r", encoding = encoding) :
475s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
475s Execution halted
475s cd ..
476s Starting H_Root_Length_27, pid = 6137
476s Finished H_Root_Length_27, pid = 6137, exit_code = 0
476s cd Q_grain_Mo
476s processing phenotype Q_grain_Mo...
476s 
476s 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
476s nmiss = 90 , mphenoflag = 1
476s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.444551
476s k = 282,  n-q = 282
477s 
477s number of SNP ids in Q_grain_Zn_sativas_GWAS.ps for 'Q_grain_Zn' phenotype: 36901
477s number of SNP ids in Q_grain_Zn_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Zn' phenotype: 0
477s 
477s number of SNP ids in sativas_GWAS.tped: 36901
477s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Zn_sativas_GWAS.ps: 0
477s 
477s Error in file(filename, "r", encoding = encoding) : 
477s   cannot open the connection
477s Calls: source -> file
477s In addition: Warning message:
477s In file(filename, "r", encoding = encoding) :
477s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
477s Execution halted
477s cd ..
478s Starting Q_grain_Mo, pid = 6152
478s Finished Q_grain_Zn, pid = 6136, exit_code = 0
478s cd F_grain_Mo
478s processing phenotype F_grain_Mo...
478s 
478s 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
478s nmiss = 73 , mphenoflag = 1
478s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.476843
478s k = 299,  n-q = 299
479s 
479s number of SNP ids in Q_grain_Mo_sativas_GWAS.ps for 'Q_grain_Mo' phenotype: 36901
479s number of SNP ids in Q_grain_Mo_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_Mo' phenotype: 0
479s 
479s number of SNP ids in sativas_GWAS.tped: 36901
479s number of SNP ids in sativas_GWAS.tped not present in Q_grain_Mo_sativas_GWAS.ps: 0
479s 
480s Error in file(filename, "r", encoding = encoding) : 
480s   cannot open the connection
480s Calls: source -> file
480s In addition: Warning message:
480s In file(filename, "r", encoding = encoding) :
480s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
480s Execution halted
480s cd ..
480s Starting F_grain_Mo, pid = 6166
480s Finished Q_grain_Mo, pid = 6152, exit_code = 0
480s cd Q_grain_yield
480s processing phenotype Q_grain_yield...
480s 
480s 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
480s nmiss = 91 , mphenoflag = 1
480s evals[0] = -0.000000, evals[1] = -0.000000, evals[n-1] = 2.399146
480s k = 281,  n-q = 281
482s 
482s number of SNP ids in F_grain_Mo_sativas_GWAS.ps for 'F_grain_Mo' phenotype: 36901
482s number of SNP ids in F_grain_Mo_sativas_GWAS.ps not present in sativas_GWAS.tped for 'F_grain_Mo' phenotype: 0
482s 
482s number of SNP ids in sativas_GWAS.tped: 36901
482s number of SNP ids in sativas_GWAS.tped not present in F_grain_Mo_sativas_GWAS.ps: 0
482s 
482s Error in file(filename, "r", encoding = encoding) : 
482s   cannot open the connection
482s Calls: source -> file
482s In addition: Warning message:
482s In file(filename, "r", encoding = encoding) :
482s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
482s Execution halted
482s cd ..
483s 
483s number of SNP ids in Q_grain_yield_sativas_GWAS.ps for 'Q_grain_yield' phenotype: 36901
483s number of SNP ids in Q_grain_yield_sativas_GWAS.ps not present in sativas_GWAS.tped for 'Q_grain_yield' phenotype: 0
483s 
483s number of SNP ids in sativas_GWAS.tped: 36901
483s number of SNP ids in sativas_GWAS.tped not present in Q_grain_yield_sativas_GWAS.ps: 0
483s 
484s Error in file(filename, "r", encoding = encoding) : 
484s   cannot open the connection
484s Calls: source -> file
484s In addition: Warning message:
484s In file(filename, "r", encoding = encoding) :
484s   cannot open file '/usr/bin/GWAS_manhattanplots.R': No such file or directory
484s Execution halted
484s cd ..
484s Starting Q_grain_yield, pid = 6180
484s Finished F_grain_Mo, pid = 6166, exit_code = 0
484s Finished Q_grain_yield, pid = 6180, exit_code = 0
484s Analysis complete
484s 
484s autopkgtest [03:37:36]: test run-unit-test: -----------------------]
485s run-unit-test        PASS
485s autopkgtest [03:37:37]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
485s autopkgtest [03:37:37]: @@@@@@@@@@@@@@@@@@@@ summary
485s run-unit-test        PASS
503s Creating nova instance adt-noble-arm64-pique-20240311-032931-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240311.img (UUID 900cfff9-7f1a-42c7-81a7-22635cd2a5f9)...