0s autopkgtest [01:45:16]: starting date and time: 2024-03-23 01:45:16+0000 0s autopkgtest [01:45:16]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [01:45:16]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w4if_19b/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed --apt-upgrade r-cran-pscbs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 -- lxd -r lxd-armhf-10.145.243.126 lxd-armhf-10.145.243.126:autopkgtest/ubuntu/noble/armhf 22s autopkgtest [01:45:38]: testbed dpkg architecture: armhf 24s autopkgtest [01:45:40]: testbed apt version: 2.7.12 24s autopkgtest [01:45:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 31s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 31s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4035 kB] 32s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 32s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 32s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 32s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [637 kB] 32s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 32s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 32s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 32s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [4061 kB] 32s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 32s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [49.1 kB] 32s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 34s Fetched 9471 kB in 2s (5386 kB/s) 35s Reading package lists... 43s tee: /proc/self/fd/2: Permission denied 66s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 66s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 66s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 66s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 68s Reading package lists... 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 69s Calculating upgrade... 69s The following packages were automatically installed and are no longer required: 69s linux-headers-6.8.0-11 python3-lib2to3 69s Use 'apt autoremove' to remove them. 69s The following packages will be REMOVED: 69s libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1 69s libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11 69s libhogweed6 libmagic1 libnetplan0 libnettle8 libnpth0 libnvme1 libparted2 69s libpcap0.8 libperl5.38 libpng16-16 libpsl5 libreadline8 libreiserfscore0 69s libssl3 libtirpc3 libuv1 linux-headers-6.8.0-11-generic python3-distutils 69s The following NEW packages will be installed: 69s libapt-pkg6.0t64 libarchive13t64 libatm1t64 libcurl3t64-gnutls libcurl4t64 69s libdb5.3t64 libelf1t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 69s libglib2.0-0t64 libgnutls30t64 libgpgme11t64 libhogweed6t64 libmagic1t64 70s libnetplan1 libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64 70s libpcap0.8t64 libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64 70s libreiserfscore0t64 libssl3t64 libtirpc3t64 libuv1t64 linux-headers-6.8.0-20 70s linux-headers-6.8.0-20-generic xdg-user-dirs 70s The following packages have been kept back: 70s multipath-tools 70s The following packages will be upgraded: 70s apparmor apt apt-utils bind9-dnsutils bind9-host bind9-libs binutils 70s binutils-arm-linux-gnueabihf binutils-common bolt bsdextrautils bsdutils 70s btrfs-progs coreutils cryptsetup-bin curl dbus dbus-bin dbus-daemon 70s dbus-session-bus-common dbus-system-bus-common dbus-user-session dhcpcd-base 70s dirmngr dmsetup dpkg dpkg-dev e2fsprogs e2fsprogs-l10n eject fdisk file ftp 70s fwupd gawk gcc-13-base gcc-14-base gir1.2-girepository-2.0 gir1.2-glib-2.0 70s gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv 70s groff-base ibverbs-providers inetutils-telnet info initramfs-tools 70s initramfs-tools-bin initramfs-tools-core install-info iproute2 jq keyboxd 70s kmod kpartx krb5-locales libapparmor1 libaudit-common libaudit1 libbinutils 70s libblkid1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 70s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 70s libblockdev-utils3 libblockdev3 libbpf1 libbrotli1 libc-bin libc6 libcap-ng0 70s libcom-err2 libcryptsetup12 libctf-nobfd0 libctf0 libdbus-1-3 70s libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libevent-core-2.1-7 70s libexpat1 libfdisk1 libfido2-1 libftdi1-2 libfwupd2 libgcc-s1 70s libgirepository-1.0-1 libglib2.0-data libgssapi-krb5-2 libgudev-1.0-0 70s libgusb2 libibverbs1 libjcat1 libjq1 libjson-glib-1.0-0 70s libjson-glib-1.0-common libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 70s libldap-common libldap2 liblocale-gettext-perl liblzma5 libmagic-mgc 70s libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 libnghttp2-14 libnsl2 70s libnss-systemd libpam-modules libpam-modules-bin libpam-runtime 70s libpam-systemd libpam0g libplymouth5 libpolkit-agent-1-0 70s libpolkit-gobject-1-0 libprotobuf-c1 libpython3-stdlib libpython3.11-minimal 70s libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libqmi-glib5 70s libqmi-proxy libqrtr-glib0 librtmp1 libsasl2-2 libsasl2-modules 70s libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 70s libsframe1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssh-4 libstdc++6 70s libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl 70s libtirpc-common libudev1 libudisks2-0 libusb-1.0-0 libuuid1 libvolume-key1 70s libxml2 libxmlb2 libxmuu1 linux-headers-generic locales logsave lshw lsof 70s man-db mount mtr-tiny netplan-generator netplan.io openssh-client 70s openssh-server openssh-sftp-server openssl parted perl perl-base 70s perl-modules-5.38 pinentry-curses plymouth plymouth-theme-ubuntu-text psmisc 70s python-apt-common python3 python3-apt python3-cryptography python3-dbus 70s python3-gdbm python3-gi python3-lib2to3 python3-minimal python3-netplan 70s python3-pkg-resources python3-pyrsistent python3-setuptools 70s python3-typing-extensions python3-yaml python3.11 python3.11-minimal 70s python3.12 python3.12-minimal readline-common rsync shared-mime-info sudo 70s systemd systemd-dev systemd-resolved systemd-sysv systemd-timesyncd tcpdump 70s telnet tnftp ubuntu-pro-client ubuntu-pro-client-l10n udev udisks2 usb.ids 70s util-linux uuid-runtime vim-common vim-tiny wget xxd xz-utils zlib1g 70s 233 upgraded, 32 newly installed, 31 to remove and 1 not upgraded. 70s Need to get 106 MB of archives. 70s After this operation, 84.4 MB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu2 [102 kB] 70s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240315-1ubuntu1 [47.0 kB] 70s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240315-1ubuntu1 [41.5 kB] 70s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240315-1ubuntu1 [714 kB] 70s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.39-0ubuntu6 [2827 kB] 70s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbrotli1 armhf 1.1.0-2build1 [319 kB] 70s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-5.1ubuntu1 [119 kB] 70s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5-3 armhf 1.20.1-5.1ubuntu1 [321 kB] 70s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5support0 armhf 1.20.1-5.1ubuntu1 [31.4 kB] 70s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libk5crypto3 armhf 1.20.1-5.1ubuntu1 [78.6 kB] 70s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB] 70s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu1 [49.2 kB] 70s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build6 [51.3 kB] 70s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udisks2 armhf 2.10.1-6 [276 kB] 70s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudisks2-0 armhf 2.10.1-6 [143 kB] 70s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu2 [160 kB] 70s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma5 armhf 5.6.0-0.2 [117 kB] 70s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kmod armhf 31+20240202-2ubuntu4 [91.8 kB] 70s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu4 [44.9 kB] 70s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.4-1ubuntu5 [103 kB] 70s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-timesyncd armhf 255.4-1ubuntu5 [36.0 kB] 70s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB] 70s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit-common all 1:3.1.2-2.1 [5674 B] 70s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.4-2build1 [13.5 kB] 70s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit1 armhf 1:3.1.2-2.1 [44.3 kB] 70s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.3-5ubuntu3 [62.0 kB] 70s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2ubuntu1 [70.9 kB] 70s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl4t64 armhf 8.5.0-2ubuntu7 [296 kB] 70s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf curl armhf 8.5.0-2ubuntu7 [219 kB] 70s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.7 kB] 70s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf wget armhf 1.21.4-1ubuntu2 [317 kB] 70s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tnftp armhf 20230507-2build1 [98.6 kB] 70s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpcap0.8t64 armhf 1.10.4-4.1ubuntu1 [137 kB] 70s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tcpdump armhf 4.99.4-3ubuntu2 [425 kB] 71s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.4-1ubuntu5 [2009 kB] 71s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-resolved armhf 255.4-1ubuntu5 [289 kB] 71s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sudo armhf 1.9.15p5-3ubuntu3 [936 kB] 71s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf rsync armhf 3.2.7-1build1 [413 kB] 71s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-cryptography armhf 41.0.7-4build2 [788 kB] 71s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.13-0ubuntu2 [975 kB] 71s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu11 [35.5 kB] 71s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-client armhf 1:9.6p1-3ubuntu11 [890 kB] 71s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-server armhf 1:9.6p1-3ubuntu11 [503 kB] 71s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20 all 6.8.0-20.20 [13.6 MB] 71s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20-generic armhf 6.8.0-20.20 [1287 kB] 71s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-generic armhf 6.8.0-20.20+1 [9610 B] 71s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3t64 armhf 3.0.13-0ubuntu2 [1558 kB] 71s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnss-systemd armhf 255.4-1ubuntu5 [148 kB] 71s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.4-1ubuntu5 [166 kB] 71s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.4-1ubuntu5 [3502 kB] 71s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udev armhf 255.4-1ubuntu5 [1852 kB] 71s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.4-1ubuntu5 [11.9 kB] 71s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-systemd armhf 255.4-1ubuntu5 [216 kB] 71s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.4-1ubuntu5 [410 kB] 71s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu3 [47.0 kB] 71s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.3-5ubuntu3 [261 kB] 71s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] 71s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-user-session armhf 1.14.10-4ubuntu2 [9962 B] 71s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapparmor1 armhf 4.0.0-beta3-0ubuntu2 [45.0 kB] 71s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libexpat1 armhf 2.6.1-2 [65.9 kB] 71s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB] 71s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-bin armhf 1.14.10-4ubuntu2 [37.1 kB] 71s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus armhf 1.14.10-4ubuntu2 [28.1 kB] 71s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-daemon armhf 1.14.10-4ubuntu2 [109 kB] 71s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdbus-1-3 armhf 1.14.10-4ubuntu2 [190 kB] 71s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu2 [171 kB] 71s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.5-1ubuntu2 [49.5 kB] 71s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu2 [135 kB] 71s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu2 [34.4 kB] 71s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu2 [238 kB] 71s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu2 [196 kB] 71s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu2 [134 kB] 71s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-utils3 armhf 3.1.0-1build1 [16.9 kB] 71s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libvolume-key1 armhf 0.3.12-7build1 [38.4 kB] 71s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjcat1 armhf 0.2.0-2build2 [30.4 kB] 71s Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf parted armhf 3.6-3.1build2 [39.4 kB] 71s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libparted2t64 armhf 3.6-3.1build2 [143 kB] 71s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12 armhf 3.12.2-4build3 [645 kB] 71s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12-minimal armhf 3.12.2-4build3 [1942 kB] 72s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-stdlib armhf 3.12.2-4build3 [1906 kB] 72s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-minimal armhf 3.12.2-4build3 [816 kB] 72s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-5ubuntu1 [19.0 kB] 72s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11 armhf 3.11.8-1build4 [589 kB] 72s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11-minimal armhf 3.11.8-1build4 [1795 kB] 72s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-stdlib armhf 3.11.8-1build4 [1810 kB] 72s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-minimal armhf 3.11.8-1build4 [826 kB] 72s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu1 [599 kB] 72s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build2 [12.7 kB] 72s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build2 [8962 B] 72s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 72s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-6 [661 kB] 72s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gdbm armhf 3.12.2-3ubuntu2 [17.1 kB] 72s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main armhf man-db armhf 2.12.0-3build4 [1196 kB] 72s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm6t64 armhf 1.23-5.1 [30.3 kB] 72s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm-compat4t64 armhf 1.23-5.1 [6208 B] 72s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38t64 armhf 5.38.2-3.2 [4101 kB] 72s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3.2 [231 kB] 72s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3.2 [1671 kB] 72s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu4 [15.0 kB] 72s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnettle8t64 armhf 3.9.1-2.2 [187 kB] 72s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libhogweed6t64 armhf 3.9.1-2.2 [187 kB] 72s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu2 [1046 kB] 73s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap2 armhf 2.6.7+dfsg-1~exp1ubuntu6 [172 kB] 73s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu7 [290 kB] 73s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main armhf shared-mime-info armhf 2.4-1build1 [470 kB] 73s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-girepository-2.0 armhf 1.79.1-1ubuntu6 [24.8 kB] 73s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-glib-2.0 armhf 2.79.3-3ubuntu5 [182 kB] 73s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgirepository-1.0-1 armhf 1.79.1-1ubuntu6 [106 kB] 73s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gi armhf 3.47.0-3build1 [219 kB] 73s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dbus armhf 1.3.2-5build2 [94.7 kB] 73s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnetplan1 armhf 1.0-1 [113 kB] 73s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-netplan armhf 1.0-1 [22.5 kB] 73s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan-generator armhf 1.0-1 [58.7 kB] 73s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-bin armhf 0.142ubuntu23 [20.3 kB] 73s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-core all 0.142ubuntu23 [50.1 kB] 73s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools all 0.142ubuntu23 [9058 B] 73s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan.io armhf 1.0-1 [64.3 kB] 73s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmlb2 armhf 0.3.15-1build1 [57.0 kB] 73s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqrtr-glib0 armhf 1.2.2-1ubuntu3 [15.4 kB] 73s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-glib5 armhf 1.35.2-0ubuntu1 [908 kB] 73s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-proxy armhf 1.35.2-0ubuntu1 [5732 B] 73s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-agent-1-0 armhf 124-1ubuntu1 [15.3 kB] 73s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-gobject-1-0 armhf 124-1ubuntu1 [44.1 kB] 73s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-0t64 armhf 2.79.3-3ubuntu5 [1414 kB] 73s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfwupd2 armhf 1.9.15-1 [123 kB] 73s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libarchive13t64 armhf 3.7.2-1.1ubuntu2 [330 kB] 73s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fwupd armhf 1.9.15-1 [4349 kB] 73s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.14 [210 kB] 73s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0t64 armhf 2.7.14 [986 kB] 73s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.14 [1368 kB] 73s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client-l10n armhf 31.2.1 [19.4 kB] 73s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client armhf 31.2.1 [216 kB] 73s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main armhf keyboxd armhf 2.4.4-2ubuntu15 [111 kB] 73s Get:134 http://ftpmaster.internal/ubuntu noble/main armhf libnpth0t64 armhf 1.6-3.1 [6940 B] 73s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu15 [224 kB] 73s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu15 [524 kB] 73s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-wks-client armhf 2.4.4-2ubuntu15 [87.4 kB] 73s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-utils armhf 2.4.4-2ubuntu15 [158 kB] 73s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu15 [235 kB] 73s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgsm armhf 2.4.4-2ubuntu15 [241 kB] 73s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreadline8t64 armhf 8.2-3.1build1 [129 kB] 73s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gawk armhf 1:5.2.1-2build2 [415 kB] 73s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fdisk armhf 2.39.3-9ubuntu2 [135 kB] 73s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu15 [115 kB] 73s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dirmngr armhf 2.4.4-2ubuntu15 [346 kB] 73s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg all 2.4.4-2ubuntu15 [359 kB] 73s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-apt armhf 2.7.6build1 [162 kB] 73s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main armhf pinentry-curses armhf 1.2.1-3ubuntu4 [36.7 kB] 73s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-yaml armhf 6.0.1-2build1 [117 kB] 73s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python-apt-common all 2.7.6build1 [19.8 kB] 73s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-setuptools all 68.1.2-2ubuntu1 [396 kB] 73s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB] 73s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.6ubuntu4 [1229 kB] 73s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-minimal armhf 3.12.2-0ubuntu1 [27.1 kB] 73s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3 armhf 3.12.2-0ubuntu1 [24.1 kB] 73s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-stdlib armhf 3.12.2-0ubuntu1 [9802 B] 73s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu2 [117 kB] 73s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu2 [78.7 kB] 73s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf groff-base armhf 1.23.0-3build1 [946 kB] 73s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-3.1build1 [56.5 kB] 73s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpgme11t64 armhf 1.18.0-4.1ubuntu3 [120 kB] 73s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-crypto3 armhf 3.1.0-1build1 [20.3 kB] 73s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B] 73s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB] 73s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dhcpcd-base armhf 1:10.0.6-1ubuntu2 [186 kB] 73s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-fs3 armhf 3.1.0-1build1 [34.4 kB] 73s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreiserfscore0t64 armhf 1:3.6.27-7.1 [66.2 kB] 74s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main armhf btrfs-progs armhf 6.6.3-1.1build1 [852 kB] 74s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu2 [201 kB] 74s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu2 [571 kB] 74s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-loop3 armhf 3.1.0-1build1 [6502 B] 74s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-mdraid3 armhf 3.1.0-1build1 [13.3 kB] 74s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-nvme3 armhf 3.1.0-1build1 [17.5 kB] 74s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnvme1t64 armhf 1.8-3 [67.5 kB] 74s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-part3 armhf 3.1.0-1build1 [16.4 kB] 74s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-swap3 armhf 3.1.0-1build1 [8894 B] 74s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev3 armhf 3.1.0-1build1 [42.9 kB] 74s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgudev-1.0-0 armhf 1:238-3ubuntu2 [13.6 kB] 74s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.3ubuntu2 [595 kB] 74s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbpf1 armhf 1:1.3.0-2build1 [146 kB] 74s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main armhf iproute2 armhf 6.1.0-1ubuntu5 [1060 kB] 74s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libelf1t64 armhf 0.190-1.1build2 [49.9 kB] 74s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1 [8018 B] 74s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lsof armhf 4.95.0-1build2 [248 kB] 74s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl2 armhf 1.3.0-3build2 [36.5 kB] 74s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1 [73.2 kB] 74s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-proxy armhf 1.31.2-0ubuntu2 [5748 B] 74s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-glib4 armhf 1.31.2-0ubuntu2 [216 kB] 74s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-common all 1.8.0-2build1 [4210 B] 74s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-0 armhf 1.8.0-2build1 [61.2 kB] 74s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnghttp2-14 armhf 1.59.0-1build1 [68.1 kB] 74s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssh-4 armhf 0.10.6-2build1 [169 kB] 74s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libusb-1.0-0 armhf 2:1.0.27-1 [48.7 kB] 74s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgusb2 armhf 0.4.8-1build1 [34.6 kB] 74s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmm-glib0 armhf 1.23.4-0ubuntu1 [214 kB] 74s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libprotobuf-c1 armhf 1.4.1-1ubuntu3 [17.7 kB] 74s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-2 armhf 2.1.28+dfsg1-5ubuntu1 [49.7 kB] 74s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libibverbs1 armhf 50.0-2build1 [57.9 kB] 74s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfido2-1 armhf 1.14.0-1build1 [75.8 kB] 74s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-3ubuntu3 [1280 kB] 74s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu2 [1216 kB] 74s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.39-0ubuntu6 [530 kB] 74s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main armhf file armhf 1:5.45-3 [21.1 kB] 74s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic-mgc armhf 1:5.45-3 [307 kB] 74s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic1t64 armhf 1:5.45-3 [81.4 kB] 74s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libplymouth5 armhf 24.004.60-1ubuntu6 [140 kB] 75s Get:207 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng16-16t64 armhf 1.6.43-3 [166 kB] 75s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-host armhf 1:9.18.24-0ubuntu3 [47.4 kB] 75s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-dnsutils armhf 1:9.18.24-0ubuntu3 [149 kB] 75s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-libs armhf 1:9.18.24-0ubuntu3 [1148 kB] 75s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuv1t64 armhf 1.48.0-1.1 [82.9 kB] 75s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu2 [41.7 kB] 75s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebconfclient0 armhf 0.271ubuntu2 [10.8 kB] 75s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage-common all 3.5-1build4 [10.1 kB] 75s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage2 armhf 3.5-1build4 [84.5 kB] 75s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main armhf install-info armhf 7.1-3build1 [60.5 kB] 75s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-19ubuntu1 [47.7 kB] 75s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu2 [14.7 kB] 75s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dmsetup armhf 2:1.02.185-3ubuntu2 [81.1 kB] 75s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main armhf eject armhf 2.39.3-9ubuntu2 [43.2 kB] 75s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main armhf krb5-locales all 1.20.1-5.1ubuntu1 [13.9 kB] 75s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 75s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libslang2 armhf 2.3.3-3build1 [478 kB] 75s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main armhf locales all 2.39-0ubuntu6 [4232 kB] 75s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-tiny armhf 2:9.1.0016-1ubuntu5 [665 kB] 75s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-common all 2:9.1.0016-1ubuntu5 [385 kB] 75s Get:227 http://ftpmaster.internal/ubuntu noble/main armhf xdg-user-dirs armhf 0.18-1 [17.3 kB] 75s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xxd armhf 2:9.1.0016-1ubuntu5 [62.4 kB] 75s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apparmor armhf 4.0.0-beta3-0ubuntu2 [562 kB] 75s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ftp all 20230507-2build1 [4724 B] 75s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main armhf inetutils-telnet armhf 2:2.5-3ubuntu3 [90.7 kB] 75s Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main armhf info armhf 7.1-3build1 [127 kB] 75s Get:233 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmuu1 armhf 2:1.1.3-3build1 [8004 B] 75s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lshw armhf 02.19.git.2021.06.19.996aaad9c7-2build2 [310 kB] 75s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mtr-tiny armhf 0.95-1.1build1 [51.7 kB] 75s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu6 [9818 B] 75s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth armhf 24.004.60-1ubuntu6 [142 kB] 75s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.7-1 [176 kB] 75s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main armhf telnet all 0.17+2.5-3ubuntu3 [3682 B] 75s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main armhf usb.ids all 2024.03.18-1 [223 kB] 75s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xz-utils armhf 5.6.0-0.2 [271 kB] 75s Get:242 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf0 armhf 2.42-4ubuntu1 [87.7 kB] 75s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf-nobfd0 armhf 2.42-4ubuntu1 [88.0 kB] 75s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.42-4ubuntu1 [2925 kB] 75s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbinutils armhf 2.42-4ubuntu1 [464 kB] 75s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils armhf 2.42-4ubuntu1 [3078 B] 75s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-common armhf 2.42-4ubuntu1 [217 kB] 75s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsframe1 armhf 2.42-4ubuntu1 [13.1 kB] 75s Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bolt armhf 0.9.6-2build1 [138 kB] 75s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cryptsetup-bin armhf 2:2.7.0-1ubuntu2 [214 kB] 75s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.6ubuntu4 [1074 kB] 75s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.6ubuntu4 [268 kB] 75s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB] 75s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ibverbs-providers armhf 50.0-2build1 [27.4 kB] 75s Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main armhf jq armhf 1.7.1-3 [65.2 kB] 75s Get:256 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjq1 armhf 1.7.1-3 [156 kB] 75s Get:257 http://ftpmaster.internal/ubuntu noble/main armhf libatm1t64 armhf 1:2.5.1-5.1 [20.0 kB] 75s Get:258 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB] 75s Get:259 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libftdi1-2 armhf 1.5-6build4 [25.7 kB] 75s Get:260 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB] 75s Get:261 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules armhf 2.1.28+dfsg1-5ubuntu1 [61.3 kB] 75s Get:262 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-lib2to3 all 3.12.2-3ubuntu2 [79.3 kB] 75s Get:263 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pyrsistent armhf 0.20.0-1build1 [53.0 kB] 75s Get:264 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-typing-extensions all 4.10.0-1 [60.7 kB] 75s Get:265 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kpartx armhf 0.9.4-5ubuntu6 [31.5 kB] 76s Preconfiguring packages ... 77s Fetched 106 MB in 6s (17.8 MB/s) 77s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 77s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_armhf.deb ... 77s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ... 77s Setting up bsdutils (1:2.39.3-9ubuntu2) ... 77s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 77s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_armhf.deb ... 77s Unpacking gcc-14-base:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 77s Setting up gcc-14-base:armhf (14-20240315-1ubuntu1) ... 77s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 77s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_armhf.deb ... 77s Unpacking libgcc-s1:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 77s Setting up libgcc-s1:armhf (14-20240315-1ubuntu1) ... 77s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 77s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_armhf.deb ... 77s Unpacking libstdc++6:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 77s Setting up libstdc++6:armhf (14-20240315-1ubuntu1) ... 77s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 77s Preparing to unpack .../libc6_2.39-0ubuntu6_armhf.deb ... 77s Unpacking libc6:armhf (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 78s Setting up libc6:armhf (2.39-0ubuntu6) ... 78s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 78s Preparing to unpack .../0-libbrotli1_1.1.0-2build1_armhf.deb ... 78s Unpacking libbrotli1:armhf (1.1.0-2build1) over (1.1.0-2) ... 78s Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-5.1ubuntu1_armhf.deb ... 78s Unpacking libgssapi-krb5-2:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 78s Preparing to unpack .../2-libkrb5-3_1.20.1-5.1ubuntu1_armhf.deb ... 78s Unpacking libkrb5-3:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 78s Preparing to unpack .../3-libkrb5support0_1.20.1-5.1ubuntu1_armhf.deb ... 78s Unpacking libkrb5support0:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 78s Preparing to unpack .../4-libk5crypto3_1.20.1-5.1ubuntu1_armhf.deb ... 78s Unpacking libk5crypto3:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 78s Preparing to unpack .../5-libcom-err2_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 78s Unpacking libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 78s Preparing to unpack .../6-zlib1g_1%3a1.3.dfsg-3.1ubuntu1_armhf.deb ... 78s Unpacking zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ... 78s Setting up zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) ... 78s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 78s Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-2build6_armhf.deb ... 78s Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ... 79s Preparing to unpack .../udisks2_2.10.1-6_armhf.deb ... 79s Unpacking udisks2 (2.10.1-6) over (2.10.1-1ubuntu2) ... 79s Preparing to unpack .../libudisks2-0_2.10.1-6_armhf.deb ... 79s Unpacking libudisks2-0:armhf (2.10.1-6) over (2.10.1-1ubuntu2) ... 79s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_armhf.deb ... 79s Unpacking libblkid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 79s Setting up libblkid1:armhf (2.39.3-9ubuntu2) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 79s Preparing to unpack .../liblzma5_5.6.0-0.2_armhf.deb ... 79s Unpacking liblzma5:armhf (5.6.0-0.2) over (5.4.5-0.3) ... 79s Setting up liblzma5:armhf (5.6.0-0.2) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 79s Preparing to unpack .../0-kmod_31+20240202-2ubuntu4_armhf.deb ... 79s Unpacking kmod (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 79s dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty 79s Preparing to unpack .../1-libkmod2_31+20240202-2ubuntu4_armhf.deb ... 79s Unpacking libkmod2:armhf (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 79s Preparing to unpack .../2-systemd-dev_255.4-1ubuntu5_all.deb ... 79s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 79s Preparing to unpack .../3-systemd-timesyncd_255.4-1ubuntu5_armhf.deb ... 79s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 79s Preparing to unpack .../4-dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ... 79s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 79s Preparing to unpack .../5-libaudit-common_1%3a3.1.2-2.1_all.deb ... 79s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ... 79s Setting up libaudit-common (1:3.1.2-2.1) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 79s Preparing to unpack .../libcap-ng0_0.8.4-2build1_armhf.deb ... 79s Unpacking libcap-ng0:armhf (0.8.4-2build1) over (0.8.4-2) ... 79s Setting up libcap-ng0:armhf (0.8.4-2build1) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 79s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_armhf.deb ... 79s Unpacking libaudit1:armhf (1:3.1.2-2.1) over (1:3.1.2-2) ... 79s Setting up libaudit1:armhf (1:3.1.2-2.1) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 79s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_armhf.deb ... 79s Unpacking libpam0g:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 79s Setting up libpam0g:armhf (1.5.3-5ubuntu3) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 79s Preparing to unpack .../libselinux1_3.5-2ubuntu1_armhf.deb ... 79s Unpacking libselinux1:armhf (3.5-2ubuntu1) over (3.5-2build1) ... 79s Setting up libselinux1:armhf (3.5-2ubuntu1) ... 80s dpkg: libcurl4:armhf: dependency problems, but removing anyway as you requested: 80s curl depends on libcurl4 (= 8.5.0-2ubuntu2). 80s 80s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 80s Removing libcurl4:armhf (8.5.0-2ubuntu2) ... 80s Selecting previously unselected package libcurl4t64:armhf. 80s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58613 files and directories currently installed.) 80s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_armhf.deb ... 80s Unpacking libcurl4t64:armhf (8.5.0-2ubuntu7) ... 80s Preparing to unpack .../curl_8.5.0-2ubuntu7_armhf.deb ... 80s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 80s dpkg: libpsl5:armhf: dependency problems, but removing anyway as you requested: 80s wget depends on libpsl5 (>= 0.16.0). 80s libcurl3-gnutls:armhf depends on libpsl5 (>= 0.16.0). 80s 80s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 80s Removing libpsl5:armhf (0.21.2-1build1) ... 80s Selecting previously unselected package libpsl5t64:armhf. 80s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58614 files and directories currently installed.) 80s Preparing to unpack .../libpsl5t64_0.21.2-1.1_armhf.deb ... 80s Unpacking libpsl5t64:armhf (0.21.2-1.1) ... 80s Preparing to unpack .../wget_1.21.4-1ubuntu2_armhf.deb ... 80s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ... 80s Preparing to unpack .../tnftp_20230507-2build1_armhf.deb ... 80s Unpacking tnftp (20230507-2build1) over (20230507-2) ... 80s dpkg: libpcap0.8:armhf: dependency problems, but removing anyway as you requested: 80s tcpdump depends on libpcap0.8 (>= 1.9.1). 80s 80s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58620 files and directories currently installed.) 80s Removing libpcap0.8:armhf (1.10.4-4ubuntu3) ... 80s Selecting previously unselected package libpcap0.8t64:armhf. 80s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58609 files and directories currently installed.) 80s Preparing to unpack .../00-libpcap0.8t64_1.10.4-4.1ubuntu1_armhf.deb ... 80s Unpacking libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ... 80s Preparing to unpack .../01-tcpdump_4.99.4-3ubuntu2_armhf.deb ... 80s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ... 80s Preparing to unpack .../02-libsystemd-shared_255.4-1ubuntu5_armhf.deb ... 80s Unpacking libsystemd-shared:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 80s Preparing to unpack .../03-systemd-resolved_255.4-1ubuntu5_armhf.deb ... 80s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 80s Preparing to unpack .../04-sudo_1.9.15p5-3ubuntu3_armhf.deb ... 80s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ... 80s Preparing to unpack .../05-rsync_3.2.7-1build1_armhf.deb ... 80s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ... 80s Preparing to unpack .../06-python3-cryptography_41.0.7-4build2_armhf.deb ... 80s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ... 80s Preparing to unpack .../07-openssl_3.0.13-0ubuntu2_armhf.deb ... 80s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 81s Preparing to unpack .../08-openssh-sftp-server_1%3a9.6p1-3ubuntu11_armhf.deb ... 81s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 81s Preparing to unpack .../09-openssh-client_1%3a9.6p1-3ubuntu11_armhf.deb ... 81s Unpacking openssh-client (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 81s Preparing to unpack .../10-openssh-server_1%3a9.6p1-3ubuntu11_armhf.deb ... 81s Unpacking openssh-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 81s Selecting previously unselected package linux-headers-6.8.0-20. 81s Preparing to unpack .../11-linux-headers-6.8.0-20_6.8.0-20.20_all.deb ... 81s Unpacking linux-headers-6.8.0-20 (6.8.0-20.20) ... 84s Selecting previously unselected package linux-headers-6.8.0-20-generic. 84s Preparing to unpack .../12-linux-headers-6.8.0-20-generic_6.8.0-20.20_armhf.deb ... 84s Unpacking linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 85s Preparing to unpack .../13-linux-headers-generic_6.8.0-20.20+1_armhf.deb ... 85s Unpacking linux-headers-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 85s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 89772 files and directories currently installed.) 85s Removing linux-headers-6.8.0-11-generic (6.8.0-11.11) ... 86s dpkg: libssl3:armhf: dependency problems, but removing anyway as you requested: 86s systemd depends on libssl3 (>= 3.0.0). 86s libssh-4:armhf depends on libssl3 (>= 3.0.0). 86s libsasl2-modules:armhf depends on libssl3 (>= 3.0.0). 86s libsasl2-2:armhf depends on libssl3 (>= 3.0.0). 86s libpython3.12-minimal:armhf depends on libssl3 (>= 3.0.0). 86s libpython3.11-minimal:armhf depends on libssl3 (>= 3.0.0). 86s libnvme1 depends on libssl3 (>= 3.0.0). 86s libfido2-1:armhf depends on libssl3 (>= 3.0.0). 86s libcryptsetup12:armhf depends on libssl3 (>= 3.0.0). 86s dhcpcd-base depends on libssl3 (>= 3.0.0). 86s bind9-libs:armhf depends on libssl3 (>= 3.0.0). 86s 86s Removing libssl3:armhf (3.0.10-1ubuntu4) ... 86s Selecting previously unselected package libssl3t64:armhf. 86s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78622 files and directories currently installed.) 86s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_armhf.deb ... 86s Unpacking libssl3t64:armhf (3.0.13-0ubuntu2) ... 86s Setting up libssl3t64:armhf (3.0.13-0ubuntu2) ... 86s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78635 files and directories currently installed.) 86s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_armhf.deb ... 86s Unpacking libnss-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 86s Preparing to unpack .../libudev1_255.4-1ubuntu5_armhf.deb ... 86s Unpacking libudev1:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 86s Setting up libudev1:armhf (255.4-1ubuntu5) ... 86s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78635 files and directories currently installed.) 86s Preparing to unpack .../systemd_255.4-1ubuntu5_armhf.deb ... 86s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 87s Preparing to unpack .../udev_255.4-1ubuntu5_armhf.deb ... 87s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 87s Preparing to unpack .../libsystemd0_255.4-1ubuntu5_armhf.deb ... 87s Unpacking libsystemd0:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 87s Setting up libsystemd0:armhf (255.4-1ubuntu5) ... 87s Setting up libkmod2:armhf (31+20240202-2ubuntu4) ... 87s Setting up libsystemd-shared:armhf (255.4-1ubuntu5) ... 87s Setting up systemd-dev (255.4-1ubuntu5) ... 87s Setting up systemd (255.4-1ubuntu5) ... 88s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78635 files and directories currently installed.) 88s Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_armhf.deb ... 88s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 88s Preparing to unpack .../libpam-systemd_255.4-1ubuntu5_armhf.deb ... 88s Unpacking libpam-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 88s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_armhf.deb ... 88s Unpacking libpam-modules-bin (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 88s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ... 89s pam_namespace.service is a disabled or a static unit not running, not starting it. 89s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78635 files and directories currently installed.) 89s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu3_armhf.deb ... 89s Unpacking libpam-modules:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 89s Setting up libpam-modules:armhf (1.5.3-5ubuntu3) ... 89s Installing new version of config file /etc/security/namespace.init ... 89s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 89s Preparing to unpack .../0-dbus-user-session_1.14.10-4ubuntu2_armhf.deb ... 89s Unpacking dbus-user-session (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 89s Preparing to unpack .../1-libapparmor1_4.0.0-beta3-0ubuntu2_armhf.deb ... 89s Unpacking libapparmor1:armhf (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 89s Preparing to unpack .../2-libexpat1_2.6.1-2_armhf.deb ... 89s Unpacking libexpat1:armhf (2.6.1-2) over (2.6.0-1) ... 89s Preparing to unpack .../3-dbus-system-bus-common_1.14.10-4ubuntu2_all.deb ... 89s Unpacking dbus-system-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 89s Preparing to unpack .../4-dbus-bin_1.14.10-4ubuntu2_armhf.deb ... 89s Unpacking dbus-bin (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 89s Preparing to unpack .../5-dbus_1.14.10-4ubuntu2_armhf.deb ... 89s Unpacking dbus (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 90s Preparing to unpack .../6-dbus-daemon_1.14.10-4ubuntu2_armhf.deb ... 90s Unpacking dbus-daemon (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 90s Preparing to unpack .../7-libdbus-1-3_1.14.10-4ubuntu2_armhf.deb ... 90s Unpacking libdbus-1-3:armhf (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 90s Preparing to unpack .../8-libmount1_2.39.3-9ubuntu2_armhf.deb ... 90s Unpacking libmount1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 90s Setting up libmount1:armhf (2.39.3-9ubuntu2) ... 90s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 90s Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_armhf.deb ... 90s Unpacking libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 90s Preparing to unpack .../libuuid1_2.39.3-9ubuntu2_armhf.deb ... 90s Unpacking libuuid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 90s Setting up libuuid1:armhf (2.39.3-9ubuntu2) ... 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 90s Preparing to unpack .../0-libcryptsetup12_2%3a2.7.0-1ubuntu2_armhf.deb ... 90s Unpacking libcryptsetup12:armhf (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 90s Preparing to unpack .../1-libfdisk1_2.39.3-9ubuntu2_armhf.deb ... 90s Unpacking libfdisk1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 90s Preparing to unpack .../2-mount_2.39.3-9ubuntu2_armhf.deb ... 90s Unpacking mount (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 90s Preparing to unpack .../3-libblockdev-utils3_3.1.0-1build1_armhf.deb ... 90s Unpacking libblockdev-utils3:armhf (3.1.0-1build1) over (3.1.0-1) ... 90s Preparing to unpack .../4-libvolume-key1_0.3.12-7build1_armhf.deb ... 90s Unpacking libvolume-key1:armhf (0.3.12-7build1) over (0.3.12-5build2) ... 90s Preparing to unpack .../5-libjcat1_0.2.0-2build2_armhf.deb ... 90s Unpacking libjcat1:armhf (0.2.0-2build2) over (0.2.0-2) ... 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 90s Removing libgpgme11:armhf (1.18.0-4ubuntu1) ... 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78627 files and directories currently installed.) 90s Preparing to unpack .../parted_3.6-3.1build2_armhf.deb ... 90s Unpacking parted (3.6-3.1build2) over (3.6-3) ... 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78627 files and directories currently installed.) 90s Removing libparted2:armhf (3.6-3) ... 90s Selecting previously unselected package libparted2t64:armhf. 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 90s Preparing to unpack .../00-libparted2t64_3.6-3.1build2_armhf.deb ... 90s Unpacking libparted2t64:armhf (3.6-3.1build2) ... 90s Preparing to unpack .../01-python3.12_3.12.2-4build3_armhf.deb ... 90s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ... 91s Preparing to unpack .../02-python3.12-minimal_3.12.2-4build3_armhf.deb ... 91s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ... 91s Preparing to unpack .../03-libpython3.12-stdlib_3.12.2-4build3_armhf.deb ... 91s Unpacking libpython3.12-stdlib:armhf (3.12.2-4build3) over (3.12.2-1) ... 91s Preparing to unpack .../04-libpython3.12-minimal_3.12.2-4build3_armhf.deb ... 91s Unpacking libpython3.12-minimal:armhf (3.12.2-4build3) over (3.12.2-1) ... 92s Preparing to unpack .../05-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu1_armhf.deb ... 92s Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 92s Preparing to unpack .../06-python3.11_3.11.8-1build4_armhf.deb ... 92s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ... 92s Preparing to unpack .../07-python3.11-minimal_3.11.8-1build4_armhf.deb ... 92s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ... 92s Preparing to unpack .../08-libpython3.11-stdlib_3.11.8-1build4_armhf.deb ... 92s Unpacking libpython3.11-stdlib:armhf (3.11.8-1build4) over (3.11.8-1) ... 92s Preparing to unpack .../09-libpython3.11-minimal_3.11.8-1build4_armhf.deb ... 92s Unpacking libpython3.11-minimal:armhf (3.11.8-1build4) over (3.11.8-1) ... 93s Preparing to unpack .../10-libsqlite3-0_3.45.1-1ubuntu1_armhf.deb ... 93s Unpacking libsqlite3-0:armhf (3.45.1-1ubuntu1) over (3.45.1-1) ... 93s Preparing to unpack .../11-libtext-iconv-perl_1.7-8build2_armhf.deb ... 93s Unpacking libtext-iconv-perl:armhf (1.7-8build2) over (1.7-8build1) ... 93s Preparing to unpack .../12-libtext-charwidth-perl_0.04-11build2_armhf.deb ... 93s Unpacking libtext-charwidth-perl:armhf (0.04-11build2) over (0.04-11build1) ... 93s Preparing to unpack .../13-perl-modules-5.38_5.38.2-3.2_all.deb ... 93s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 93s dpkg: libperl5.38:armhf: dependency problems, but removing anyway as you requested: 93s perl depends on libperl5.38 (= 5.38.2-3). 93s 93s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78624 files and directories currently installed.) 93s Removing libperl5.38:armhf (5.38.2-3) ... 93s dpkg: libdb5.3:armhf: dependency problems, but removing anyway as you requested: 93s iproute2 depends on libdb5.3. 93s apt-utils depends on libdb5.3. 93s 93s Removing libdb5.3:armhf (5.3.28+dfsg2-4) ... 93s Selecting previously unselected package libdb5.3t64:armhf. 93s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78099 files and directories currently installed.) 93s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_armhf.deb ... 93s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-6) ... 93s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu2_armhf.deb ... 93s Unpacking python3-gdbm:armhf (3.12.2-3ubuntu2) over (3.11.5-1) ... 93s Preparing to unpack .../man-db_2.12.0-3build4_armhf.deb ... 93s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ... 94s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78105 files and directories currently installed.) 94s Removing libgdbm-compat4:armhf (1.23-5) ... 94s Removing libgdbm6:armhf (1.23-5) ... 94s Selecting previously unselected package libgdbm6t64:armhf. 94s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78095 files and directories currently installed.) 94s Preparing to unpack .../libgdbm6t64_1.23-5.1_armhf.deb ... 94s Unpacking libgdbm6t64:armhf (1.23-5.1) ... 94s Selecting previously unselected package libgdbm-compat4t64:armhf. 94s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_armhf.deb ... 94s Unpacking libgdbm-compat4t64:armhf (1.23-5.1) ... 94s Selecting previously unselected package libperl5.38t64:armhf. 94s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_armhf.deb ... 94s Unpacking libperl5.38t64:armhf (5.38.2-3.2) ... 94s Preparing to unpack .../perl_5.38.2-3.2_armhf.deb ... 94s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ... 94s Preparing to unpack .../perl-base_5.38.2-3.2_armhf.deb ... 94s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 94s Setting up perl-base (5.38.2-3.2) ... 94s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78626 files and directories currently installed.) 94s Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu4_armhf.deb ... 94s Unpacking liblocale-gettext-perl (1.07-6ubuntu4) over (1.07-6build1) ... 94s dpkg: libnettle8:armhf: dependency problems, but removing anyway as you requested: 94s libhogweed6:armhf depends on libnettle8. 94s libgnutls30:armhf depends on libnettle8 (>= 3.9~). 94s libcurl3-gnutls:armhf depends on libnettle8. 94s libarchive13:armhf depends on libnettle8. 94s 94s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78626 files and directories currently installed.) 94s Removing libnettle8:armhf (3.9.1-2) ... 95s Selecting previously unselected package libnettle8t64:armhf. 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78619 files and directories currently installed.) 95s Preparing to unpack .../libnettle8t64_3.9.1-2.2_armhf.deb ... 95s Unpacking libnettle8t64:armhf (3.9.1-2.2) ... 95s Setting up libnettle8t64:armhf (3.9.1-2.2) ... 95s dpkg: libhogweed6:armhf: dependency problems, but removing anyway as you requested: 95s libgnutls30:armhf depends on libhogweed6 (>= 3.6). 95s 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78627 files and directories currently installed.) 95s Removing libhogweed6:armhf (3.9.1-2) ... 95s Selecting previously unselected package libhogweed6t64:armhf. 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78622 files and directories currently installed.) 95s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_armhf.deb ... 95s Unpacking libhogweed6t64:armhf (3.9.1-2.2) ... 95s Setting up libhogweed6t64:armhf (3.9.1-2.2) ... 95s dpkg: libgnutls30:armhf: dependency problems, but removing anyway as you requested: 95s libldap2:armhf depends on libgnutls30 (>= 3.8.2). 95s libcurl3-gnutls:armhf depends on libgnutls30 (>= 3.8.2). 95s fwupd depends on libgnutls30 (>= 3.7.3). 95s dirmngr depends on libgnutls30 (>= 3.8.1). 95s apt depends on libgnutls30 (>= 3.8.1). 95s 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78628 files and directories currently installed.) 95s Removing libgnutls30:armhf (3.8.3-1ubuntu1) ... 95s Selecting previously unselected package libgnutls30t64:armhf. 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78619 files and directories currently installed.) 95s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_armhf.deb ... 95s Unpacking libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ... 95s Setting up libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ... 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78647 files and directories currently installed.) 95s Preparing to unpack .../libldap2_2.6.7+dfsg-1~exp1ubuntu6_armhf.deb ... 95s Unpacking libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 95s dpkg: libcurl3-gnutls:armhf: dependency problems, but removing anyway as you requested: 95s libfwupd2:armhf depends on libcurl3-gnutls (>= 7.63.0). 95s fwupd depends on libcurl3-gnutls (>= 7.63.0). 95s 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78647 files and directories currently installed.) 95s Removing libcurl3-gnutls:armhf (8.5.0-2ubuntu2) ... 95s Selecting previously unselected package libcurl3t64-gnutls:armhf. 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78640 files and directories currently installed.) 95s Preparing to unpack .../00-libcurl3t64-gnutls_8.5.0-2ubuntu7_armhf.deb ... 95s Unpacking libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ... 95s Preparing to unpack .../01-shared-mime-info_2.4-1build1_armhf.deb ... 95s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ... 95s Preparing to unpack .../02-gir1.2-girepository-2.0_1.79.1-1ubuntu6_armhf.deb ... 95s Unpacking gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ... 95s Preparing to unpack .../03-gir1.2-glib-2.0_2.79.3-3ubuntu5_armhf.deb ... 95s Unpacking gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 95s Preparing to unpack .../04-libgirepository-1.0-1_1.79.1-1ubuntu6_armhf.deb ... 95s Unpacking libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ... 95s Preparing to unpack .../05-python3-gi_3.47.0-3build1_armhf.deb ... 96s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ... 96s Preparing to unpack .../06-python3-dbus_1.3.2-5build2_armhf.deb ... 96s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ... 96s Selecting previously unselected package libnetplan1:armhf. 96s Preparing to unpack .../07-libnetplan1_1.0-1_armhf.deb ... 96s Unpacking libnetplan1:armhf (1.0-1) ... 96s Preparing to unpack .../08-python3-netplan_1.0-1_armhf.deb ... 96s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ... 96s Preparing to unpack .../09-netplan-generator_1.0-1_armhf.deb ... 96s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 96s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ... 96s Preparing to unpack .../10-initramfs-tools-bin_0.142ubuntu23_armhf.deb ... 96s Unpacking initramfs-tools-bin (0.142ubuntu23) over (0.142ubuntu20) ... 96s Preparing to unpack .../11-initramfs-tools-core_0.142ubuntu23_all.deb ... 96s Unpacking initramfs-tools-core (0.142ubuntu23) over (0.142ubuntu20) ... 96s Preparing to unpack .../12-initramfs-tools_0.142ubuntu23_all.deb ... 96s Unpacking initramfs-tools (0.142ubuntu23) over (0.142ubuntu20) ... 96s Preparing to unpack .../13-netplan.io_1.0-1_armhf.deb ... 96s Unpacking netplan.io (1.0-1) over (0.107.1-3) ... 96s Preparing to unpack .../14-libxmlb2_0.3.15-1build1_armhf.deb ... 96s Unpacking libxmlb2:armhf (0.3.15-1build1) over (0.3.15-1) ... 96s Preparing to unpack .../15-libqrtr-glib0_1.2.2-1ubuntu3_armhf.deb ... 96s Unpacking libqrtr-glib0:armhf (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ... 96s Preparing to unpack .../16-libqmi-glib5_1.35.2-0ubuntu1_armhf.deb ... 96s Unpacking libqmi-glib5:armhf (1.35.2-0ubuntu1) over (1.34.0-2) ... 96s Preparing to unpack .../17-libqmi-proxy_1.35.2-0ubuntu1_armhf.deb ... 96s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ... 96s Preparing to unpack .../18-libpolkit-agent-1-0_124-1ubuntu1_armhf.deb ... 96s Unpacking libpolkit-agent-1-0:armhf (124-1ubuntu1) over (124-1) ... 96s Preparing to unpack .../19-libpolkit-gobject-1-0_124-1ubuntu1_armhf.deb ... 96s Unpacking libpolkit-gobject-1-0:armhf (124-1ubuntu1) over (124-1) ... 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78651 files and directories currently installed.) 97s Removing libnetplan0:armhf (0.107.1-3) ... 97s dpkg: libglib2.0-0:armhf: dependency problems, but removing anyway as you requested: 97s libmm-glib0:armhf depends on libglib2.0-0 (>= 2.62.0). 97s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 97s libmbim-glib4:armhf depends on libglib2.0-0 (>= 2.56). 97s libjson-glib-1.0-0:armhf depends on libglib2.0-0 (>= 2.75.3). 97s libgusb2:armhf depends on libglib2.0-0 (>= 2.75.3). 97s libgudev-1.0-0:armhf depends on libglib2.0-0 (>= 2.38.0). 97s libfwupd2:armhf depends on libglib2.0-0 (>= 2.79.0). 97s libblockdev3:armhf depends on libglib2.0-0 (>= 2.42.2). 97s libblockdev-swap3:armhf depends on libglib2.0-0 (>= 2.42.2). 97s libblockdev-part3:armhf depends on libglib2.0-0 (>= 2.42.2). 97s libblockdev-nvme3:armhf depends on libglib2.0-0 (>= 2.42.2). 97s libblockdev-mdraid3:armhf depends on libglib2.0-0 (>= 2.42.2). 97s libblockdev-loop3:armhf depends on libglib2.0-0 (>= 2.42.2). 97s libblockdev-fs3:armhf depends on libglib2.0-0 (>= 2.42.2). 97s libblockdev-crypto3:armhf depends on libglib2.0-0 (>= 2.42.2). 97s fwupd depends on libglib2.0-0 (>= 2.79.0). 97s bolt depends on libglib2.0-0 (>= 2.56.0). 97s 97s Removing libglib2.0-0:armhf (2.79.2-1~ubuntu1) ... 97s Selecting previously unselected package libglib2.0-0t64:armhf. 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78622 files and directories currently installed.) 97s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_armhf.deb ... 97s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:armhf.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 97s removed '/var/lib/dpkg/info/libglib2.0-0:armhf.postrm' 97s Unpacking libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ... 97s Preparing to unpack .../libfwupd2_1.9.15-1_armhf.deb ... 97s Unpacking libfwupd2:armhf (1.9.15-1) over (1.9.14-1) ... 97s dpkg: libarchive13:armhf: dependency problems, but removing anyway as you requested: 97s fwupd depends on libarchive13 (>= 3.2.1). 97s 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78647 files and directories currently installed.) 97s Removing libarchive13:armhf (3.7.2-1ubuntu2) ... 97s Selecting previously unselected package libarchive13t64:armhf. 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78641 files and directories currently installed.) 97s Preparing to unpack .../libarchive13t64_3.7.2-1.1ubuntu2_armhf.deb ... 97s Unpacking libarchive13t64:armhf (3.7.2-1.1ubuntu2) ... 97s Preparing to unpack .../fwupd_1.9.15-1_armhf.deb ... 97s Unpacking fwupd (1.9.15-1) over (1.9.14-1) ... 97s Preparing to unpack .../apt-utils_2.7.14_armhf.deb ... 97s Unpacking apt-utils (2.7.14) over (2.7.12) ... 97s dpkg: libapt-pkg6.0:armhf: dependency problems, but removing anyway as you requested: 97s ubuntu-pro-client depends on libapt-pkg6.0 (>= 1.9~). 97s python3-apt depends on libapt-pkg6.0 (>= 2.7.11). 97s apt depends on libapt-pkg6.0 (>= 2.7.12). 97s 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78648 files and directories currently installed.) 97s Removing libapt-pkg6.0:armhf (2.7.12) ... 97s Selecting previously unselected package libapt-pkg6.0t64:armhf. 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78599 files and directories currently installed.) 97s Preparing to unpack .../libapt-pkg6.0t64_2.7.14_armhf.deb ... 97s Unpacking libapt-pkg6.0t64:armhf (2.7.14) ... 97s Setting up libapt-pkg6.0t64:armhf (2.7.14) ... 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78649 files and directories currently installed.) 97s Preparing to unpack .../archives/apt_2.7.14_armhf.deb ... 98s Unpacking apt (2.7.14) over (2.7.12) ... 98s Setting up apt (2.7.14) ... 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78649 files and directories currently installed.) 98s Preparing to unpack .../ubuntu-pro-client-l10n_31.2.1_armhf.deb ... 98s Unpacking ubuntu-pro-client-l10n (31.2.1) over (31.1) ... 98s Preparing to unpack .../ubuntu-pro-client_31.2.1_armhf.deb ... 98s Unpacking ubuntu-pro-client (31.2.1) over (31.1) ... 99s Preparing to unpack .../keyboxd_2.4.4-2ubuntu15_armhf.deb ... 99s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 99s dpkg: libnpth0:armhf: dependency problems, but removing anyway as you requested: 99s gpgv depends on libnpth0 (>= 0.90). 99s gpgsm depends on libnpth0 (>= 0.90). 99s gpg-agent depends on libnpth0 (>= 0.90). 99s gpg depends on libnpth0 (>= 0.90). 99s dirmngr depends on libnpth0 (>= 0.90). 99s 99s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78649 files and directories currently installed.) 99s Removing libnpth0:armhf (1.6-3build2) ... 99s Selecting previously unselected package libnpth0t64:armhf. 99s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78644 files and directories currently installed.) 99s Preparing to unpack .../libnpth0t64_1.6-3.1_armhf.deb ... 99s Unpacking libnpth0t64:armhf (1.6-3.1) ... 99s Setting up libnpth0t64:armhf (1.6-3.1) ... 99s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78650 files and directories currently installed.) 99s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_armhf.deb ... 99s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 99s Setting up gpgv (2.4.4-2ubuntu15) ... 99s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78650 files and directories currently installed.) 99s Preparing to unpack .../gpg_2.4.4-2ubuntu15_armhf.deb ... 99s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 99s Preparing to unpack .../gpg-wks-client_2.4.4-2ubuntu15_armhf.deb ... 99s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 99s Preparing to unpack .../gnupg-utils_2.4.4-2ubuntu15_armhf.deb ... 99s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 99s Preparing to unpack .../gpg-agent_2.4.4-2ubuntu15_armhf.deb ... 99s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 99s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_armhf.deb ... 99s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 99s dpkg: libreadline8:armhf: dependency problems, but removing anyway as you requested: 99s gpgconf depends on libreadline8 (>= 6.0). 99s gawk depends on libreadline8 (>= 6.0). 99s fdisk depends on libreadline8 (>= 6.0). 99s 99s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78650 files and directories currently installed.) 99s Removing libreadline8:armhf (8.2-3) ... 99s Selecting previously unselected package libreadline8t64:armhf. 99s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78638 files and directories currently installed.) 99s Preparing to unpack .../libreadline8t64_8.2-3.1build1_armhf.deb ... 99s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' 99s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' 99s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' 99s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' 99s Unpacking libreadline8t64:armhf (8.2-3.1build1) ... 99s Setting up libreadline8t64:armhf (8.2-3.1build1) ... 99s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78658 files and directories currently installed.) 99s Preparing to unpack .../00-gawk_1%3a5.2.1-2build2_armhf.deb ... 99s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ... 99s Preparing to unpack .../01-fdisk_2.39.3-9ubuntu2_armhf.deb ... 99s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 100s Preparing to unpack .../02-gpgconf_2.4.4-2ubuntu15_armhf.deb ... 100s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 100s Preparing to unpack .../03-dirmngr_2.4.4-2ubuntu15_armhf.deb ... 100s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 100s Preparing to unpack .../04-gnupg_2.4.4-2ubuntu15_all.deb ... 100s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 100s Preparing to unpack .../05-python3-apt_2.7.6build1_armhf.deb ... 100s Unpacking python3-apt (2.7.6build1) over (2.7.6) ... 100s Preparing to unpack .../06-pinentry-curses_1.2.1-3ubuntu4_armhf.deb ... 100s Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-3ubuntu1) ... 100s Preparing to unpack .../07-python3-yaml_6.0.1-2build1_armhf.deb ... 100s Unpacking python3-yaml (6.0.1-2build1) over (6.0.1-2) ... 100s Preparing to unpack .../08-python-apt-common_2.7.6build1_all.deb ... 100s Unpacking python-apt-common (2.7.6build1) over (2.7.6) ... 100s Preparing to unpack .../09-python3-setuptools_68.1.2-2ubuntu1_all.deb ... 100s Unpacking python3-setuptools (68.1.2-2ubuntu1) over (68.1.2-2) ... 101s Preparing to unpack .../10-python3-pkg-resources_68.1.2-2ubuntu1_all.deb ... 101s Unpacking python3-pkg-resources (68.1.2-2ubuntu1) over (68.1.2-2) ... 101s Preparing to unpack .../11-dpkg_1.22.6ubuntu4_armhf.deb ... 101s Unpacking dpkg (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 101s Setting up dpkg (1.22.6ubuntu4) ... 101s Setting up libpython3.12-minimal:armhf (3.12.2-4build3) ... 101s Setting up libexpat1:armhf (2.6.1-2) ... 101s Setting up python3.12-minimal (3.12.2-4build3) ... 102s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78655 files and directories currently installed.) 102s Preparing to unpack .../python3-minimal_3.12.2-0ubuntu1_armhf.deb ... 102s Unpacking python3-minimal (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 102s Setting up python3-minimal (3.12.2-0ubuntu1) ... 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78655 files and directories currently installed.) 103s Preparing to unpack .../python3_3.12.2-0ubuntu1_armhf.deb ... 103s Unpacking python3 (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 103s Preparing to unpack .../libpython3-stdlib_3.12.2-0ubuntu1_armhf.deb ... 103s Unpacking libpython3-stdlib:armhf (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 103s Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu2_armhf.deb ... 103s Unpacking libsmartcols1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 103s Setting up libsmartcols1:armhf (2.39.3-9ubuntu2) ... 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78655 files and directories currently installed.) 103s Preparing to unpack .../0-bsdextrautils_2.39.3-9ubuntu2_armhf.deb ... 103s Unpacking bsdextrautils (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 103s Preparing to unpack .../1-groff-base_1.23.0-3build1_armhf.deb ... 103s Unpacking groff-base (1.23.0-3build1) over (1.23.0-3) ... 103s Preparing to unpack .../2-readline-common_8.2-3.1build1_all.deb ... 103s Unpacking readline-common (8.2-3.1build1) over (8.2-3) ... 103s Selecting previously unselected package libgpgme11t64:armhf. 103s Preparing to unpack .../3-libgpgme11t64_1.18.0-4.1ubuntu3_armhf.deb ... 103s Unpacking libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ... 103s Preparing to unpack .../4-libblockdev-crypto3_3.1.0-1build1_armhf.deb ... 103s Unpacking libblockdev-crypto3:armhf (3.1.0-1build1) over (3.1.0-1) ... 103s Preparing to unpack .../5-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ... 103s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 103s Preparing to unpack .../6-logsave_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 103s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 103s Preparing to unpack .../7-dhcpcd-base_1%3a10.0.6-1ubuntu2_armhf.deb ... 103s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ... 103s Preparing to unpack .../8-libblockdev-fs3_3.1.0-1build1_armhf.deb ... 103s Unpacking libblockdev-fs3:armhf (3.1.0-1build1) over (3.1.0-1) ... 103s dpkg: libreiserfscore0: dependency problems, but removing anyway as you requested: 103s btrfs-progs depends on libreiserfscore0 (>= 1:3.6.27). 103s 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78662 files and directories currently installed.) 103s Removing libreiserfscore0 (1:3.6.27-7) ... 103s Selecting previously unselected package libreiserfscore0t64. 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78657 files and directories currently installed.) 103s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_armhf.deb ... 103s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ... 103s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_armhf.deb ... 103s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ... 104s dpkg: libext2fs2:armhf: dependency problems, but removing anyway as you requested: 104s e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1). 104s 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78663 files and directories currently installed.) 104s Removing libext2fs2:armhf (1.47.0-2ubuntu1) ... 104s Selecting previously unselected package libext2fs2t64:armhf. 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78656 files and directories currently installed.) 104s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 104s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64' 104s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64' 104s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64' 104s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' 104s Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ... 104s Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) ... 104s Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ... 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78672 files and directories currently installed.) 104s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 104s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 104s Preparing to unpack .../libblockdev-loop3_3.1.0-1build1_armhf.deb ... 104s Unpacking libblockdev-loop3:armhf (3.1.0-1build1) over (3.1.0-1) ... 104s Preparing to unpack .../libblockdev-mdraid3_3.1.0-1build1_armhf.deb ... 104s Unpacking libblockdev-mdraid3:armhf (3.1.0-1build1) over (3.1.0-1) ... 104s Preparing to unpack .../libblockdev-nvme3_3.1.0-1build1_armhf.deb ... 104s Unpacking libblockdev-nvme3:armhf (3.1.0-1build1) over (3.1.0-1) ... 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78672 files and directories currently installed.) 104s Removing libnvme1 (1.8-2) ... 104s Selecting previously unselected package libnvme1t64. 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78665 files and directories currently installed.) 104s Preparing to unpack .../0-libnvme1t64_1.8-3_armhf.deb ... 104s Unpacking libnvme1t64 (1.8-3) ... 104s Preparing to unpack .../1-libblockdev-part3_3.1.0-1build1_armhf.deb ... 104s Unpacking libblockdev-part3:armhf (3.1.0-1build1) over (3.1.0-1) ... 104s Preparing to unpack .../2-libblockdev-swap3_3.1.0-1build1_armhf.deb ... 104s Unpacking libblockdev-swap3:armhf (3.1.0-1build1) over (3.1.0-1) ... 104s Preparing to unpack .../3-libblockdev3_3.1.0-1build1_armhf.deb ... 104s Unpacking libblockdev3:armhf (3.1.0-1build1) over (3.1.0-1) ... 104s Preparing to unpack .../4-libgudev-1.0-0_1%3a238-3ubuntu2_armhf.deb ... 104s Unpacking libgudev-1.0-0:armhf (1:238-3ubuntu2) over (1:238-3) ... 105s Preparing to unpack .../5-libxml2_2.9.14+dfsg-1.3ubuntu2_armhf.deb ... 105s Unpacking libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) over (2.9.14+dfsg-1.3ubuntu1) ... 105s Preparing to unpack .../6-libbpf1_1%3a1.3.0-2build1_armhf.deb ... 105s Unpacking libbpf1:armhf (1:1.3.0-2build1) over (1:1.3.0-2) ... 105s Preparing to unpack .../7-iproute2_6.1.0-1ubuntu5_armhf.deb ... 105s Unpacking iproute2 (6.1.0-1ubuntu5) over (6.1.0-1ubuntu2) ... 105s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78673 files and directories currently installed.) 105s Removing libelf1:armhf (0.190-1) ... 105s Selecting previously unselected package libelf1t64:armhf. 105s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78668 files and directories currently installed.) 105s Preparing to unpack .../libelf1t64_0.190-1.1build2_armhf.deb ... 105s Unpacking libelf1t64:armhf (0.190-1.1build2) ... 105s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 105s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 105s Preparing to unpack .../lsof_4.95.0-1build2_armhf.deb ... 105s Unpacking lsof (4.95.0-1build2) over (4.95.0-1build1) ... 105s Preparing to unpack .../libnsl2_1.3.0-3build2_armhf.deb ... 105s Unpacking libnsl2:armhf (1.3.0-3build2) over (1.3.0-3) ... 105s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78673 files and directories currently installed.) 105s Removing libtirpc3:armhf (1.3.4+ds-1build1) ... 105s Selecting previously unselected package libtirpc3t64:armhf. 105s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78667 files and directories currently installed.) 105s Preparing to unpack .../00-libtirpc3t64_1.3.4+ds-1.1_armhf.deb ... 105s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' 105s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 105s Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1) ... 105s Preparing to unpack .../01-libmbim-proxy_1.31.2-0ubuntu2_armhf.deb ... 105s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ... 105s Preparing to unpack .../02-libmbim-glib4_1.31.2-0ubuntu2_armhf.deb ... 105s Unpacking libmbim-glib4:armhf (1.31.2-0ubuntu2) over (1.30.0-1) ... 105s Preparing to unpack .../03-libjson-glib-1.0-common_1.8.0-2build1_all.deb ... 105s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ... 105s Preparing to unpack .../04-libjson-glib-1.0-0_1.8.0-2build1_armhf.deb ... 105s Unpacking libjson-glib-1.0-0:armhf (1.8.0-2build1) over (1.8.0-2) ... 105s Preparing to unpack .../05-libnghttp2-14_1.59.0-1build1_armhf.deb ... 105s Unpacking libnghttp2-14:armhf (1.59.0-1build1) over (1.59.0-1) ... 105s Preparing to unpack .../06-libssh-4_0.10.6-2build1_armhf.deb ... 105s Unpacking libssh-4:armhf (0.10.6-2build1) over (0.10.6-2) ... 105s Preparing to unpack .../07-libusb-1.0-0_2%3a1.0.27-1_armhf.deb ... 105s Unpacking libusb-1.0-0:armhf (2:1.0.27-1) over (2:1.0.26-1) ... 106s Preparing to unpack .../08-libgusb2_0.4.8-1build1_armhf.deb ... 106s Unpacking libgusb2:armhf (0.4.8-1build1) over (0.4.8-1) ... 106s Preparing to unpack .../09-libmm-glib0_1.23.4-0ubuntu1_armhf.deb ... 106s Unpacking libmm-glib0:armhf (1.23.4-0ubuntu1) over (1.22.0-3) ... 106s Preparing to unpack .../10-libprotobuf-c1_1.4.1-1ubuntu3_armhf.deb ... 106s Unpacking libprotobuf-c1:armhf (1.4.1-1ubuntu3) over (1.4.1-1ubuntu2) ... 106s Preparing to unpack .../11-libsasl2-2_2.1.28+dfsg1-5ubuntu1_armhf.deb ... 106s Unpacking libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 106s Preparing to unpack .../12-libibverbs1_50.0-2build1_armhf.deb ... 106s Unpacking libibverbs1:armhf (50.0-2build1) over (50.0-2) ... 106s Preparing to unpack .../13-libfido2-1_1.14.0-1build1_armhf.deb ... 106s Unpacking libfido2-1:armhf (1.14.0-1build1) over (1.14.0-1) ... 106s Preparing to unpack .../14-coreutils_9.4-3ubuntu3_armhf.deb ... 106s Unpacking coreutils (9.4-3ubuntu3) over (9.4-2ubuntu4) ... 106s Setting up coreutils (9.4-3ubuntu3) ... 106s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78678 files and directories currently installed.) 106s Preparing to unpack .../util-linux_2.39.3-9ubuntu2_armhf.deb ... 106s Unpacking util-linux (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 106s Setting up util-linux (2.39.3-9ubuntu2) ... 107s fstrim.service is a disabled or a static unit not running, not starting it. 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78678 files and directories currently installed.) 107s Preparing to unpack .../libc-bin_2.39-0ubuntu6_armhf.deb ... 107s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 107s Setting up libc-bin (2.39-0ubuntu6) ... 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78678 files and directories currently installed.) 107s Removing libatm1:armhf (1:2.5.1-5) ... 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78673 files and directories currently installed.) 107s Preparing to unpack .../file_1%3a5.45-3_armhf.deb ... 107s Unpacking file (1:5.45-3) over (1:5.45-2) ... 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78673 files and directories currently installed.) 107s Removing libmagic1:armhf (1:5.45-2) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78663 files and directories currently installed.) 108s Preparing to unpack .../libmagic-mgc_1%3a5.45-3_armhf.deb ... 108s Unpacking libmagic-mgc (1:5.45-3) over (1:5.45-2) ... 108s Selecting previously unselected package libmagic1t64:armhf. 108s Preparing to unpack .../libmagic1t64_1%3a5.45-3_armhf.deb ... 108s Unpacking libmagic1t64:armhf (1:5.45-3) ... 108s Preparing to unpack .../libplymouth5_24.004.60-1ubuntu6_armhf.deb ... 108s Unpacking libplymouth5:armhf (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78674 files and directories currently installed.) 108s Removing libpng16-16:armhf (1.6.43-1) ... 108s Selecting previously unselected package libpng16-16t64:armhf. 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78664 files and directories currently installed.) 108s Preparing to unpack .../libpng16-16t64_1.6.43-3_armhf.deb ... 108s Unpacking libpng16-16t64:armhf (1.6.43-3) ... 108s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_armhf.deb ... 108s Unpacking bind9-host (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 108s Preparing to unpack .../bind9-dnsutils_1%3a9.18.24-0ubuntu3_armhf.deb ... 108s Unpacking bind9-dnsutils (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 108s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_armhf.deb ... 108s Unpacking bind9-libs:armhf (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78675 files and directories currently installed.) 108s Removing libuv1:armhf (1.48.0-1) ... 108s Selecting previously unselected package libuv1t64:armhf. 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78670 files and directories currently installed.) 108s Preparing to unpack .../libuv1t64_1.48.0-1.1_armhf.deb ... 108s Unpacking libuv1t64:armhf (1.48.0-1.1) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78676 files and directories currently installed.) 108s Removing python3-distutils (3.11.5-1) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 108s Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu2_armhf.deb ... 108s Unpacking uuid-runtime (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 108s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_armhf.deb ... 108s Unpacking libdebconfclient0:armhf (0.271ubuntu2) over (0.271ubuntu1) ... 108s Setting up libdebconfclient0:armhf (0.271ubuntu2) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 108s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ... 108s Unpacking libsemanage-common (3.5-1build4) over (3.5-1build2) ... 108s Setting up libsemanage-common (3.5-1build4) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 108s Preparing to unpack .../libsemanage2_3.5-1build4_armhf.deb ... 108s Unpacking libsemanage2:armhf (3.5-1build4) over (3.5-1build2) ... 109s Setting up libsemanage2:armhf (3.5-1build4) ... 109s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 109s Preparing to unpack .../install-info_7.1-3build1_armhf.deb ... 109s Unpacking install-info (7.1-3build1) over (7.1-3) ... 109s Setting up install-info (7.1-3build1) ... 109s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 109s Preparing to unpack .../00-gcc-13-base_13.2.0-19ubuntu1_armhf.deb ... 109s Unpacking gcc-13-base:armhf (13.2.0-19ubuntu1) over (13.2.0-17ubuntu2) ... 109s Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 109s Unpacking libss2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 109s Preparing to unpack .../02-dmsetup_2%3a1.02.185-3ubuntu2_armhf.deb ... 109s Unpacking dmsetup (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 109s Preparing to unpack .../03-eject_2.39.3-9ubuntu2_armhf.deb ... 109s Unpacking eject (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 109s Preparing to unpack .../04-krb5-locales_1.20.1-5.1ubuntu1_all.deb ... 109s Unpacking krb5-locales (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 109s Preparing to unpack .../05-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 109s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 109s Preparing to unpack .../06-libslang2_2.3.3-3build1_armhf.deb ... 109s Unpacking libslang2:armhf (2.3.3-3build1) over (2.3.3-3) ... 109s Preparing to unpack .../07-locales_2.39-0ubuntu6_all.deb ... 109s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 109s Preparing to unpack .../08-vim-tiny_2%3a9.1.0016-1ubuntu5_armhf.deb ... 109s Unpacking vim-tiny (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 109s Preparing to unpack .../09-vim-common_2%3a9.1.0016-1ubuntu5_all.deb ... 109s Unpacking vim-common (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 109s Selecting previously unselected package xdg-user-dirs. 109s Preparing to unpack .../10-xdg-user-dirs_0.18-1_armhf.deb ... 109s Unpacking xdg-user-dirs (0.18-1) ... 110s Preparing to unpack .../11-xxd_2%3a9.1.0016-1ubuntu5_armhf.deb ... 110s Unpacking xxd (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 110s Preparing to unpack .../12-apparmor_4.0.0-beta3-0ubuntu2_armhf.deb ... 110s Unpacking apparmor (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 111s Preparing to unpack .../13-ftp_20230507-2build1_all.deb ... 111s Unpacking ftp (20230507-2build1) over (20230507-2) ... 111s Preparing to unpack .../14-inetutils-telnet_2%3a2.5-3ubuntu3_armhf.deb ... 111s Unpacking inetutils-telnet (2:2.5-3ubuntu3) over (2:2.5-3ubuntu1) ... 111s Preparing to unpack .../15-info_7.1-3build1_armhf.deb ... 111s Unpacking info (7.1-3build1) over (7.1-3) ... 111s Preparing to unpack .../16-libxmuu1_2%3a1.1.3-3build1_armhf.deb ... 111s Unpacking libxmuu1:armhf (2:1.1.3-3build1) over (2:1.1.3-3) ... 111s Preparing to unpack .../17-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_armhf.deb ... 111s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ... 111s Preparing to unpack .../18-mtr-tiny_0.95-1.1build1_armhf.deb ... 111s Unpacking mtr-tiny (0.95-1.1build1) over (0.95-1.1) ... 112s Preparing to unpack .../19-plymouth-theme-ubuntu-text_24.004.60-1ubuntu6_armhf.deb ... 112s Unpacking plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 112s Preparing to unpack .../20-plymouth_24.004.60-1ubuntu6_armhf.deb ... 112s Unpacking plymouth (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 112s Preparing to unpack .../21-psmisc_23.7-1_armhf.deb ... 112s Unpacking psmisc (23.7-1) over (23.6-2) ... 112s Preparing to unpack .../22-telnet_0.17+2.5-3ubuntu3_all.deb ... 112s Unpacking telnet (0.17+2.5-3ubuntu3) over (0.17+2.5-3ubuntu1) ... 112s Preparing to unpack .../23-usb.ids_2024.03.18-1_all.deb ... 112s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ... 112s Preparing to unpack .../24-xz-utils_5.6.0-0.2_armhf.deb ... 112s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ... 112s Preparing to unpack .../25-libctf0_2.42-4ubuntu1_armhf.deb ... 112s Unpacking libctf0:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 112s Preparing to unpack .../26-libctf-nobfd0_2.42-4ubuntu1_armhf.deb ... 112s Unpacking libctf-nobfd0:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 112s Preparing to unpack .../27-binutils-arm-linux-gnueabihf_2.42-4ubuntu1_armhf.deb ... 112s Unpacking binutils-arm-linux-gnueabihf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 112s Preparing to unpack .../28-libbinutils_2.42-4ubuntu1_armhf.deb ... 112s Unpacking libbinutils:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 113s Preparing to unpack .../29-binutils_2.42-4ubuntu1_armhf.deb ... 113s Unpacking binutils (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 113s Preparing to unpack .../30-binutils-common_2.42-4ubuntu1_armhf.deb ... 113s Unpacking binutils-common:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 113s Preparing to unpack .../31-libsframe1_2.42-4ubuntu1_armhf.deb ... 113s Unpacking libsframe1:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 113s Preparing to unpack .../32-bolt_0.9.6-2build1_armhf.deb ... 113s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ... 113s Preparing to unpack .../33-cryptsetup-bin_2%3a2.7.0-1ubuntu2_armhf.deb ... 113s Unpacking cryptsetup-bin (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 113s Preparing to unpack .../34-dpkg-dev_1.22.6ubuntu4_all.deb ... 113s Unpacking dpkg-dev (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 113s Preparing to unpack .../35-libdpkg-perl_1.22.6ubuntu4_all.deb ... 113s Unpacking libdpkg-perl (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 113s Preparing to unpack .../36-gnupg-l10n_2.4.4-2ubuntu15_all.deb ... 113s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 113s Preparing to unpack .../37-ibverbs-providers_50.0-2build1_armhf.deb ... 113s Unpacking ibverbs-providers:armhf (50.0-2build1) over (50.0-2) ... 113s Preparing to unpack .../38-jq_1.7.1-3_armhf.deb ... 113s Unpacking jq (1.7.1-3) over (1.7.1-2) ... 113s Preparing to unpack .../39-libjq1_1.7.1-3_armhf.deb ... 113s Unpacking libjq1:armhf (1.7.1-3) over (1.7.1-2) ... 113s Selecting previously unselected package libatm1t64:armhf. 113s Preparing to unpack .../40-libatm1t64_1%3a2.5.1-5.1_armhf.deb ... 113s Unpacking libatm1t64:armhf (1:2.5.1-5.1) ... 113s Preparing to unpack .../41-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ... 113s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 113s Preparing to unpack .../42-libftdi1-2_1.5-6build4_armhf.deb ... 113s Unpacking libftdi1-2:armhf (1.5-6build4) over (1.5-6build3) ... 113s Preparing to unpack .../43-libldap-common_2.6.7+dfsg-1~exp1ubuntu6_all.deb ... 113s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 114s Preparing to unpack .../44-libsasl2-modules_2.1.28+dfsg1-5ubuntu1_armhf.deb ... 114s Unpacking libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 114s Preparing to unpack .../45-python3-lib2to3_3.12.2-3ubuntu2_all.deb ... 114s Unpacking python3-lib2to3 (3.12.2-3ubuntu2) over (3.11.5-1) ... 114s Preparing to unpack .../46-python3-pyrsistent_0.20.0-1build1_armhf.deb ... 114s Unpacking python3-pyrsistent:armhf (0.20.0-1build1) over (0.20.0-1) ... 114s Preparing to unpack .../47-python3-typing-extensions_4.10.0-1_all.deb ... 114s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ... 114s Preparing to unpack .../48-kpartx_0.9.4-5ubuntu6_armhf.deb ... 114s Unpacking kpartx (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ... 114s Setting up pinentry-curses (1.2.1-3ubuntu4) ... 114s Setting up libtext-iconv-perl:armhf (1.7-8build2) ... 114s Setting up libtext-charwidth-perl:armhf (0.04-11build2) ... 114s Setting up libibverbs1:armhf (50.0-2build1) ... 114s Setting up systemd-sysv (255.4-1ubuntu5) ... 114s Setting up libapparmor1:armhf (4.0.0-beta3-0ubuntu2) ... 114s Setting up libatm1t64:armhf (1:2.5.1-5.1) ... 114s Setting up libgdbm6t64:armhf (1.23-5.1) ... 114s Setting up bsdextrautils (2.39.3-9ubuntu2) ... 114s Setting up libgdbm-compat4t64:armhf (1.23-5.1) ... 114s Setting up xdg-user-dirs (0.18-1) ... 114s Setting up ibverbs-providers:armhf (50.0-2build1) ... 114s Setting up linux-headers-6.8.0-20 (6.8.0-20.20) ... 114s Setting up libmagic-mgc (1:5.45-3) ... 114s Setting up gawk (1:5.2.1-2build2) ... 114s Setting up psmisc (23.7-1) ... 114s Setting up libjq1:armhf (1.7.1-3) ... 114s Setting up libtirpc-common (1.3.4+ds-1.1) ... 114s Setting up libbrotli1:armhf (1.1.0-2build1) ... 114s Setting up libsqlite3-0:armhf (3.45.1-1ubuntu1) ... 114s Setting up libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) ... 114s Setting up libuv1t64:armhf (1.48.0-1.1) ... 114s Setting up libmagic1t64:armhf (1:5.45-3) ... 114s Setting up binutils-common:armhf (2.42-4ubuntu1) ... 114s Setting up libpsl5t64:armhf (0.21.2-1.1) ... 114s Setting up libnghttp2-14:armhf (1.59.0-1build1) ... 114s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ... 114s Setting up libctf-nobfd0:armhf (2.42-4ubuntu1) ... 114s Setting up libnss-systemd:armhf (255.4-1ubuntu5) ... 114s Setting up krb5-locales (1.20.1-5.1ubuntu1) ... 114s Setting up file (1:5.45-3) ... 114s Setting up kmod (31+20240202-2ubuntu4) ... 114s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ... 114s Setting up locales (2.39-0ubuntu6) ... 115s Generating locales (this might take a while)... 117s en_US.UTF-8... done 117s Generation complete. 117s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ... 117s Setting up libprotobuf-c1:armhf (1.4.1-1ubuntu3) ... 117s Setting up xxd (2:9.1.0016-1ubuntu5) ... 117s Setting up libsframe1:armhf (2.42-4ubuntu1) ... 117s Setting up libelf1t64:armhf (0.190-1.1build2) ... 117s Setting up libkrb5support0:armhf (1.20.1-5.1ubuntu1) ... 117s Setting up linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 117s Setting up eject (2.39.3-9ubuntu2) ... 117s Setting up apparmor (4.0.0-beta3-0ubuntu2) ... 117s Installing new version of config file /etc/apparmor.d/abstractions/authentication ... 117s Installing new version of config file /etc/apparmor.d/abstractions/crypto ... 117s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ... 117s Installing new version of config file /etc/apparmor.d/abstractions/openssl ... 117s Installing new version of config file /etc/apparmor.d/code ... 117s Installing new version of config file /etc/apparmor.d/firefox ... 118s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 118s 118s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 118s 118s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 118s 119s sysctl: cannot stat /proc/sys/kernel/apparmor_restrict_unprivileged_userns: No such file or directory 119s Reloading AppArmor profiles 119s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "busybox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "nautilus". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "toybox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 119s 119s Error: At least one profile failed to load 119s Setting up libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ... 119s No schema files found: doing nothing. 119s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 119s Setting up vim-common (2:9.1.0016-1ubuntu5) ... 119s Setting up gcc-13-base:armhf (13.2.0-19ubuntu1) ... 119s Setting up libqrtr-glib0:armhf (1.2.2-1ubuntu3) ... 119s Setting up libslang2:armhf (2.3.3-3build1) ... 119s Setting up libnvme1t64 (1.8-3) ... 119s Setting up mtr-tiny (0.95-1.1build1) ... 119s Setting up gnupg-l10n (2.4.4-2ubuntu15) ... 119s Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) ... 119s Setting up libdbus-1-3:armhf (1.14.10-4ubuntu2) ... 119s Setting up xz-utils (5.6.0-0.2) ... 119s Setting up perl-modules-5.38 (5.38.2-3.2) ... 119s Setting up libblockdev-utils3:armhf (3.1.0-1build1) ... 119s Setting up libpng16-16t64:armhf (1.6.43-3) ... 119s Setting up systemd-timesyncd (255.4-1ubuntu5) ... 119s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ... 119s Setting up udev (255.4-1ubuntu5) ... 120s Setting up libss2:armhf (1.47.0-2.4~exp1ubuntu2) ... 120s Setting up usb.ids (2024.03.18-1) ... 120s Setting up sudo (1.9.15p5-3ubuntu3) ... 120s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ... 120s Setting up gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) ... 120s Setting up libk5crypto3:armhf (1.20.1-5.1ubuntu1) ... 120s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ... 120s Setting up libfdisk1:armhf (2.39.3-9ubuntu2) ... 120s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-6) ... 120s Setting up libblockdev-nvme3:armhf (3.1.0-1build1) ... 120s Setting up libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) ... 120s Setting up libblockdev-fs3:armhf (3.1.0-1build1) ... 120s Setting up python-apt-common (2.7.6build1) ... 120s Setting up mount (2.39.3-9ubuntu2) ... 120s Setting up dmsetup (2:1.02.185-3ubuntu2) ... 120s Setting up uuid-runtime (2.39.3-9ubuntu2) ... 121s uuidd.service is a disabled or a static unit not running, not starting it. 121s Setting up libmm-glib0:armhf (1.23.4-0ubuntu1) ... 121s Setting up groff-base (1.23.0-3build1) ... 121s Setting up libplymouth5:armhf (24.004.60-1ubuntu6) ... 121s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ... 121s Setting up kpartx (0.9.4-5ubuntu6) ... 121s Setting up jq (1.7.1-3) ... 121s Setting up gpgconf (2.4.4-2ubuntu15) ... 121s Setting up libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ... 121s Setting up libcryptsetup12:armhf (2:2.7.0-1ubuntu2) ... 121s Setting up libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) ... 121s Setting up libjson-glib-1.0-common (1.8.0-2build1) ... 121s Setting up libkrb5-3:armhf (1.20.1-5.1ubuntu1) ... 121s Setting up libpython3.11-minimal:armhf (3.11.8-1build4) ... 121s Setting up libusb-1.0-0:armhf (2:1.0.27-1) ... 121s Setting up libperl5.38t64:armhf (5.38.2-3.2) ... 121s Setting up tnftp (20230507-2build1) ... 121s Setting up libbinutils:armhf (2.42-4ubuntu1) ... 121s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ... 121s Setting up libfido2-1:armhf (1.14.0-1build1) ... 121s Setting up openssl (3.0.13-0ubuntu2) ... 121s Setting up readline-common (8.2-3.1build1) ... 121s Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) ... 121s Setting up libxmuu1:armhf (2:1.1.3-3build1) ... 121s Setting up dbus-bin (1.14.10-4ubuntu2) ... 121s Setting up info (7.1-3build1) ... 121s Setting up liblocale-gettext-perl (1.07-6ubuntu4) ... 121s Setting up gpg (2.4.4-2ubuntu15) ... 121s Setting up libgudev-1.0-0:armhf (1:238-3ubuntu2) ... 121s Setting up libpolkit-gobject-1-0:armhf (124-1ubuntu1) ... 121s Setting up libbpf1:armhf (1:1.3.0-2build1) ... 121s Setting up libmbim-glib4:armhf (1.31.2-0ubuntu2) ... 121s Setting up rsync (3.2.7-1build1) ... 122s rsync.service is a disabled or a static unit not running, not starting it. 122s Setting up libudisks2-0:armhf (2.10.1-6) ... 122s Setting up bolt (0.9.6-2build1) ... 122s bolt.service is a disabled or a static unit not running, not starting it. 122s Setting up gnupg-utils (2.4.4-2ubuntu15) ... 122s Setting up initramfs-tools-bin (0.142ubuntu23) ... 122s Setting up libctf0:armhf (2.42-4ubuntu1) ... 122s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ... 122s Setting up python3.11-minimal (3.11.8-1build4) ... 123s Setting up tcpdump (4.99.4-3ubuntu2) ... 123s apparmor_parser: Unable to replace "tcpdump". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 123s 123s Setting up apt-utils (2.7.14) ... 123s Setting up gpg-agent (2.4.4-2ubuntu15) ... 124s Setting up libpython3.12-stdlib:armhf (3.12.2-4build3) ... 124s Setting up libblockdev-mdraid3:armhf (3.1.0-1build1) ... 124s Setting up wget (1.21.4-1ubuntu2) ... 124s Setting up libblockdev-swap3:armhf (3.1.0-1build1) ... 124s Setting up plymouth (24.004.60-1ubuntu6) ... 124s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 124s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 124s Setting up libxmlb2:armhf (0.3.15-1build1) ... 124s Setting up btrfs-progs (6.6.3-1.1build1) ... 124s Setting up libpython3.11-stdlib:armhf (3.11.8-1build4) ... 124s Setting up python3.12 (3.12.2-4build3) ... 126s Setting up libblockdev-loop3:armhf (3.1.0-1build1) ... 126s Setting up gpgsm (2.4.4-2ubuntu15) ... 126s Setting up inetutils-telnet (2:2.5-3ubuntu3) ... 126s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ... 126s update-initramfs: deferring update (trigger activated) 126s e2scrub_all.service is a disabled or a static unit not running, not starting it. 126s Setting up libparted2t64:armhf (3.6-3.1build2) ... 126s Setting up linux-headers-generic (6.8.0-20.20+1) ... 126s Setting up dbus-daemon (1.14.10-4ubuntu2) ... 126s Setting up libmbim-proxy (1.31.2-0ubuntu2) ... 126s Setting up vim-tiny (2:9.1.0016-1ubuntu5) ... 126s Setting up libnetplan1:armhf (1.0-1) ... 126s Setting up man-db (2.12.0-3build4) ... 127s Updating database of manual pages ... 128s apparmor_parser: Unable to replace "/usr/bin/man". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s man-db.service is a disabled or a static unit not running, not starting it. 128s Setting up libblockdev3:armhf (3.1.0-1build1) ... 128s Setting up fdisk (2.39.3-9ubuntu2) ... 128s Setting up libjson-glib-1.0-0:armhf (1.8.0-2build1) ... 128s Setting up libblockdev-part3:armhf (3.1.0-1build1) ... 128s Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) ... 128s Setting up libftdi1-2:armhf (1.5-6build4) ... 128s Setting up perl (5.38.2-3.2) ... 128s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) ... 128s update-initramfs: deferring update (trigger activated) 128s Setting up gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) ... 128s Setting up dbus (1.14.10-4ubuntu2) ... 128s A reboot is required to replace the running dbus-daemon. 128s Please reboot the system when convenient. 129s Setting up shared-mime-info (2.4-1build1) ... 129s Setting up libgssapi-krb5-2:armhf (1.20.1-5.1ubuntu1) ... 129s Setting up ftp (20230507-2build1) ... 129s Setting up keyboxd (2.4.4-2ubuntu15) ... 129s Setting up libdpkg-perl (1.22.6ubuntu4) ... 129s Setting up libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) ... 129s Setting up libssh-4:armhf (0.10.6-2build1) ... 129s Setting up libpam-systemd:armhf (255.4-1ubuntu5) ... 130s Setting up libpolkit-agent-1-0:armhf (124-1ubuntu1) ... 130s Setting up libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ... 130s Setting up netplan-generator (1.0-1) ... 130s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 130s Setting up initramfs-tools-core (0.142ubuntu23) ... 130s Setting up binutils-arm-linux-gnueabihf (2.42-4ubuntu1) ... 130s Setting up libarchive13t64:armhf (3.7.2-1.1ubuntu2) ... 130s Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) ... 130s Setting up libpython3-stdlib:armhf (3.12.2-0ubuntu1) ... 130s Setting up systemd-resolved (255.4-1ubuntu5) ... 130s Setting up python3.11 (3.11.8-1build4) ... 131s Setting up telnet (0.17+2.5-3ubuntu3) ... 131s Setting up initramfs-tools (0.142ubuntu23) ... 131s update-initramfs: deferring update (trigger activated) 131s Setting up libcurl4t64:armhf (8.5.0-2ubuntu7) ... 131s Setting up bind9-libs:armhf (1:9.18.24-0ubuntu3) ... 131s Setting up libtirpc3t64:armhf (1.3.4+ds-1.1) ... 131s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ... 131s Setting up iproute2 (6.1.0-1ubuntu5) ... 131s Setting up openssh-client (1:9.6p1-3ubuntu11) ... 131s Setting up libgusb2:armhf (0.4.8-1build1) ... 131s Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ... 131s Setting up parted (3.6-3.1build2) ... 131s Setting up libqmi-glib5:armhf (1.35.2-0ubuntu1) ... 131s Setting up python3 (3.12.2-0ubuntu1) ... 132s Setting up binutils (2.42-4ubuntu1) ... 132s Setting up libjcat1:armhf (0.2.0-2build2) ... 132s Setting up dpkg-dev (1.22.6ubuntu4) ... 132s Setting up dirmngr (2.4.4-2ubuntu15) ... 132s Setting up dbus-user-session (1.14.10-4ubuntu2) ... 132s Setting up python3-cryptography (41.0.7-4build2) ... 132s Setting up python3-gi (3.47.0-3build1) ... 132s Setting up python3-typing-extensions (4.10.0-1) ... 133s Setting up lsof (4.95.0-1build2) ... 133s Setting up python3-pyrsistent:armhf (0.20.0-1build1) ... 133s Setting up libnsl2:armhf (1.3.0-3build2) ... 133s Setting up gnupg (2.4.4-2ubuntu15) ... 133s Setting up python3-netplan (1.0-1) ... 133s Setting up curl (8.5.0-2ubuntu7) ... 133s Setting up libvolume-key1:armhf (0.3.12-7build1) ... 133s Setting up bind9-host (1:9.18.24-0ubuntu3) ... 133s Setting up python3-lib2to3 (3.12.2-3ubuntu2) ... 133s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... 133s Setting up openssh-sftp-server (1:9.6p1-3ubuntu11) ... 133s Setting up python3-dbus (1.3.2-5build2) ... 133s Setting up python3-setuptools (68.1.2-2ubuntu1) ... 134s Setting up gpg-wks-client (2.4.4-2ubuntu15) ... 134s Setting up openssh-server (1:9.6p1-3ubuntu11) ... 134s Replacing config file /etc/ssh/sshd_config with new version 136s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket. 137s Setting up libblockdev-crypto3:armhf (3.1.0-1build1) ... 137s Setting up python3-gdbm:armhf (3.12.2-3ubuntu2) ... 137s Setting up python3-apt (2.7.6build1) ... 137s Setting up libfwupd2:armhf (1.9.15-1) ... 137s Setting up python3-yaml (6.0.1-2build1) ... 137s Setting up libqmi-proxy (1.35.2-0ubuntu1) ... 137s Setting up netplan.io (1.0-1) ... 137s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ... 137s Setting up ubuntu-pro-client (31.2.1) ... 137s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 137s 139s Setting up fwupd (1.9.15-1) ... 139s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 139s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 139s fwupd.service is a disabled or a static unit not running, not starting it. 139s Setting up ubuntu-pro-client-l10n (31.2.1) ... 139s Setting up udisks2 (2.10.1-6) ... 139s vda: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/uevent': Permission denied 139s vda1: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda1/uevent': Permission denied 139s vda15: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda15/uevent': Permission denied 139s vda2: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda2/uevent': Permission denied 139s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied 139s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied 139s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 139s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 139s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 139s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 139s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 139s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 140s Processing triggers for ufw (0.36.2-5) ... 140s Processing triggers for systemd (255.4-1ubuntu5) ... 140s Processing triggers for install-info (7.1-3build1) ... 140s Processing triggers for libc-bin (2.39-0ubuntu6) ... 140s Processing triggers for initramfs-tools (0.142ubuntu23) ... 141s Reading package lists... 142s Building dependency tree... 142s Reading state information... 143s The following packages will be REMOVED: 143s linux-headers-6.8.0-11* python3-lib2to3* 143s 0 upgraded, 0 newly installed, 2 to remove and 1 not upgraded. 143s After this operation, 85.8 MB disk space will be freed. 143s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78592 files and directories currently installed.) 143s Removing linux-headers-6.8.0-11 (6.8.0-11.11) ... 144s Removing python3-lib2to3 (3.12.2-3ubuntu2) ... 146s autopkgtest [01:47:42]: rebooting testbed after setup commands that affected boot 183s autopkgtest [01:48:19]: testbed running kernel: Linux 5.15.0-101-generic #111-Ubuntu SMP Wed Mar 6 18:01:01 UTC 2024 207s autopkgtest [01:48:43]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-pscbs 217s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-pscbs 0.66.0-2 (dsc) [2361 B] 217s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-pscbs 0.66.0-2 (tar) [3692 kB] 217s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-pscbs 0.66.0-2 (diff) [3744 B] 218s gpgv: Signature made Mon Nov 1 20:33:04 2021 UTC 218s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 218s gpgv: issuer "nilesh@debian.org" 218s gpgv: Can't check signature: No public key 218s dpkg-source: warning: cannot verify inline signature for ./r-cran-pscbs_0.66.0-2.dsc: no acceptable signature found 218s autopkgtest [01:48:54]: testing package r-cran-pscbs version 0.66.0-2 220s autopkgtest [01:48:56]: build not needed 222s autopkgtest [01:48:58]: test run-unit-test: preparing testbed 231s Reading package lists... 231s Building dependency tree... 231s Reading state information... 232s Starting pkgProblemResolver with broken count: 0 232s Starting 2 pkgProblemResolver with broken count: 0 232s Done 232s The following additional packages will be installed: 232s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 232s fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax 232s javascript-common libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 232s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 232s libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3 232s libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables 232s libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax 232s libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify 232s libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 liblerc4 232s liblua5.4-0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 232s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 232s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 232s libxft2 libxrender1 libxss1 libxt6t64 littler node-bootstrap-sass 232s node-html5shiv node-normalize.css pandoc pandoc-data r-base-core 232s r-bioc-aroma.light r-bioc-biocgenerics r-bioc-dnacopy r-cran-acepack 232s r-cran-backports r-cran-base64enc r-cran-bslib r-cran-cachem 232s r-cran-checkmate r-cran-chron r-cran-cli r-cran-cluster r-cran-codetools 232s r-cran-colorspace r-cran-commonmark r-cran-cpp11 r-cran-crayon 232s r-cran-data.table r-cran-deldir r-cran-digest r-cran-dplyr r-cran-ellipsis 232s r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-fontawesome 232s r-cran-foreign r-cran-formula r-cran-fs r-cran-future r-cran-generics 232s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gridextra r-cran-gtable 232s r-cran-highr r-cran-hmisc r-cran-htmltable r-cran-htmltools 232s r-cran-htmlwidgets r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg 232s r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later 232s r-cran-lattice r-cran-latticeextra r-cran-lifecycle r-cran-listenv 232s r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats 232s r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme 232s r-cran-nnet r-cran-parallelly r-cran-pillar r-cran-pkgconfig 232s r-cran-pkgkitten r-cran-png r-cran-promises r-cran-pscbs r-cran-purrr 232s r-cran-r.cache r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 232s r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen 232s r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass 232s r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr 232s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex 232s r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr 232s r-cran-xfun r-cran-xtable r-cran-yaml unzip x11-common xdg-utils zip 232s Suggested packages: 232s apache2 | lighttpd | httpd libjs-jquery-ui-docs fonts-mathjax-extras 232s fonts-stix libjs-mathjax-doc tcl8.6 tk8.6 nodejs texlive-latex-recommended 232s texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context 232s wkhtmltopdf librsvg2-bin groff ghc php python ruby libjs-katex 232s citation-style-language-styles elpa-ess r-doc-info | r-doc-pdf r-mathlib 232s r-base-html r-cran-princurve r-bioc-biobase r-bioc-s4vectors r-bioc-iranges 232s r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools 232s r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-runit 232s r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shinyjs 232s r-cran-polyclip r-cran-covr r-cran-markdown r-cran-sp r-cran-scatterplot3d 232s r-cran-magick r-cran-sf r-cran-testthat r-cran-getopt r-cran-httr 232s r-cran-bit64 r-cran-dbi r-cran-formattable r-cran-nanotime 232s r-cran-palmerpenguins r-cran-units r-cran-vdiffr r-cran-roxygen2 232s r-cran-inline r-cran-bench r-cran-blob r-cran-brio r-cran-callr r-cran-here 232s r-cran-hms r-cran-pkgbuild r-cran-pkgload r-cran-plm r-cran-zoo 232s Recommended packages: 232s node-jquery r-recommended r-base-dev r-doc-html r-cran-curl r-cran-testthat 232s r-cran-thematic r-cran-fastmatch r-cran-devtools r-cran-tinytest 232s r-cran-callr r-cran-covr r-cran-mockery r-cran-processx r-cran-ps 232s r-cran-rprojroot r-cran-whoami r-cran-xml2 r-cran-bench r-cran-brio 232s r-cran-decor r-cran-desc r-cran-lobstr r-cran-progress r-cran-bit64 232s r-cran-bit r-cran-xts r-cran-nanotime r-cran-zoo r-cran-broom r-cran-dbi 232s r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite 232s r-cran-unitizer r-cran-rsvg r-cran-spelling r-cran-rhpcblasctl r-cran-r.rsp 232s r-cran-markdown r-cran-pkgload r-cran-hexbin r-cran-mapproj r-cran-maps 232s r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-sf 232s r-cran-svglite r-cran-vdiffr r-cran-waldo r-cran-testit r-cran-cairo 232s r-cran-httr r-cran-formatr r-cran-gridsvg r-cran-magick r-cran-reticulate 232s r-cran-rgl r-cran-tikzdevice r-cran-webshot node-highlight.js r-cran-lintr 232s r-cran-tidyverse r-cran-r.devices r-cran-lubridate r-cran-usethis 232s r-cran-dygraphs r-cran-rsconnect r-cran-downlit r-cran-dichromat r-cran-hms 232s r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot 232s r-cran-remotes r-cran-renv r-cran-runit libfile-mimeinfo-perl 232s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 233s The following NEW packages will be installed: 233s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 233s fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings 233s fonts-mathjax javascript-common libblas3 libcairo2 libdatrie1 libdeflate0 233s libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 233s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 233s libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery 233s libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json 233s libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js 233s libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 233s liblerc4 liblua5.4-0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 233s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 233s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 233s libxft2 libxrender1 libxss1 libxt6t64 littler node-bootstrap-sass 233s node-html5shiv node-normalize.css pandoc pandoc-data r-base-core 233s r-bioc-aroma.light r-bioc-biocgenerics r-bioc-dnacopy r-cran-acepack 233s r-cran-backports r-cran-base64enc r-cran-bslib r-cran-cachem 233s r-cran-checkmate r-cran-chron r-cran-cli r-cran-cluster r-cran-codetools 233s r-cran-colorspace r-cran-commonmark r-cran-cpp11 r-cran-crayon 233s r-cran-data.table r-cran-deldir r-cran-digest r-cran-dplyr r-cran-ellipsis 233s r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-fontawesome 233s r-cran-foreign r-cran-formula r-cran-fs r-cran-future r-cran-generics 233s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gridextra r-cran-gtable 233s r-cran-highr r-cran-hmisc r-cran-htmltable r-cran-htmltools 233s r-cran-htmlwidgets r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg 233s r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later 233s r-cran-lattice r-cran-latticeextra r-cran-lifecycle r-cran-listenv 233s r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats 233s r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme 233s r-cran-nnet r-cran-parallelly r-cran-pillar r-cran-pkgconfig 233s r-cran-pkgkitten r-cran-png r-cran-promises r-cran-pscbs r-cran-purrr 233s r-cran-r.cache r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 233s r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen 233s r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass 233s r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr 233s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex 233s r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr 233s r-cran-xfun r-cran-xtable r-cran-yaml unzip x11-common xdg-utils zip 233s 0 upgraded, 180 newly installed, 0 to remove and 1 not upgraded. 233s Need to get 165 MB/165 MB of archives. 233s After this operation, 499 MB of additional disk space will be used. 233s Get:1 /tmp/autopkgtest.0xi9ix/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [744 B] 233s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfreetype6 armhf 2.13.2+dfsg-1build2 [331 kB] 233s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 233s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 233s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu1 [37.4 kB] 233s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu1 [113 kB] 233s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fontconfig armhf 2.15.0-1.1ubuntu1 [189 kB] 233s Get:8 http://ftpmaster.internal/ubuntu noble/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 233s Get:9 http://ftpmaster.internal/ubuntu noble/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 233s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 233s Get:11 http://ftpmaster.internal/ubuntu noble/main armhf javascript-common all 11+nmu1 [5936 B] 233s Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libblas3 armhf 3.12.0-3 [123 kB] 233s Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libpixman-1-0 armhf 0.42.2-1 [184 kB] 233s Get:14 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-render0 armhf 1.15-1 [15.2 kB] 233s Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-shm0 armhf 1.15-1 [5852 B] 233s Get:16 http://ftpmaster.internal/ubuntu noble/main armhf libxrender1 armhf 1:0.9.10-1.1 [16.5 kB] 233s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcairo2 armhf 1.18.0-1ubuntu1 [482 kB] 233s Get:18 http://ftpmaster.internal/ubuntu noble/main armhf libdatrie1 armhf 0.2.13-3 [16.9 kB] 233s Get:19 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB] 233s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgfortran5 armhf 14-20240315-1ubuntu1 [312 kB] 233s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgomp1 armhf 14-20240315-1ubuntu1 [125 kB] 234s Get:22 http://ftpmaster.internal/ubuntu noble/main armhf libgraphite2-3 armhf 1.3.14-2 [72.7 kB] 234s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libharfbuzz0b armhf 8.3.0-2build1 [446 kB] 234s Get:24 http://ftpmaster.internal/ubuntu noble/main armhf x11-common all 1:7.7+23ubuntu2 [23.4 kB] 234s Get:25 http://ftpmaster.internal/ubuntu noble/main armhf libice6 armhf 2:1.0.10-1build2 [36.4 kB] 234s Get:26 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu1 [123 kB] 234s Get:27 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 234s Get:28 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 234s Get:29 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-popper.js all 1.16.1+ds-6 [54.1 kB] 234s Get:30 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB] 234s Get:31 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-d3 all 3.5.17-4 [132 kB] 234s Get:32 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-es5-shim all 4.6.7-2 [39.8 kB] 234s Get:33 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 234s Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 234s Get:35 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 234s Get:36 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 234s Get:37 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B] 234s Get:38 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 234s Get:39 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 234s Get:40 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-json all 0~20221030+~1.0.8-1 [20.6 kB] 234s Get:41 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB] 234s Get:42 http://ftpmaster.internal/ubuntu noble/main armhf liblapack3 armhf 3.12.0-3 [2085 kB] 234s Get:43 http://ftpmaster.internal/ubuntu noble/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu1 [152 kB] 234s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblua5.4-0 armhf 5.4.6-3build1 [133 kB] 234s Get:45 http://ftpmaster.internal/ubuntu noble/main armhf libthai-data all 0.1.29-2 [158 kB] 234s Get:46 http://ftpmaster.internal/ubuntu noble/main armhf libthai0 armhf 0.1.29-2 [15.1 kB] 234s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpango-1.0-0 armhf 1.52.1+ds-1 [206 kB] 234s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpangoft2-1.0-0 armhf 1.52.1+ds-1 [36.4 kB] 234s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpangocairo-1.0-0 armhf 1.52.1+ds-1 [24.9 kB] 234s Get:50 http://ftpmaster.internal/ubuntu noble/main armhf libpaper1 armhf 1.1.29 [12.5 kB] 234s Get:51 http://ftpmaster.internal/ubuntu noble/main armhf libpaper-utils armhf 1.1.29 [8170 B] 234s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsharpyuv0 armhf 1.3.2-0.4build2 [13.6 kB] 234s Get:53 http://ftpmaster.internal/ubuntu noble/main armhf libsm6 armhf 2:1.2.3-1build2 [15.1 kB] 234s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtcl8.6 armhf 8.6.14+dfsg-1 [903 kB] 234s Get:55 http://ftpmaster.internal/ubuntu noble/main armhf libjbig0 armhf 2.1-6.1ubuntu1 [24.9 kB] 234s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libwebp7 armhf 1.3.2-0.4build2 [183 kB] 234s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu1 [178 kB] 234s Get:58 http://ftpmaster.internal/ubuntu noble/main armhf libxft2 armhf 2.3.6-1 [36.8 kB] 234s Get:59 http://ftpmaster.internal/ubuntu noble/main armhf libxss1 armhf 1:1.2.3-1build2 [7580 B] 234s Get:60 http://ftpmaster.internal/ubuntu noble/main armhf libtk8.6 armhf 8.6.13-2 [680 kB] 234s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxt6t64 armhf 1:1.2.1-1.2 [145 kB] 234s Get:62 http://ftpmaster.internal/ubuntu noble/main armhf zip armhf 3.0-13 [162 kB] 234s Get:63 http://ftpmaster.internal/ubuntu noble/main armhf unzip armhf 6.0-28ubuntu3 [163 kB] 234s Get:64 http://ftpmaster.internal/ubuntu noble/main armhf xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 234s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf r-base-core armhf 4.3.3-2build1 [26.6 MB] 235s Get:66 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-littler armhf 0.3.19-1 [80.8 kB] 235s Get:67 http://ftpmaster.internal/ubuntu noble/universe armhf littler all 0.3.19-1 [2472 B] 235s Get:68 http://ftpmaster.internal/ubuntu noble/universe armhf node-bootstrap-sass all 3.4.3-2 [187 kB] 235s Get:69 http://ftpmaster.internal/ubuntu noble/universe armhf node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 235s Get:70 http://ftpmaster.internal/ubuntu noble/universe armhf node-normalize.css all 8.0.1-5 [10.8 kB] 235s Get:71 http://ftpmaster.internal/ubuntu noble/universe armhf pandoc-data all 3.1.3-1 [92.4 kB] 235s Get:72 http://ftpmaster.internal/ubuntu noble/universe armhf pandoc armhf 3.1.3+ds-2 [31.9 MB] 236s Get:73 http://ftpmaster.internal/ubuntu noble/universe armhf r-bioc-biocgenerics all 0.48.1-2 [595 kB] 236s Get:74 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 236s Get:75 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-r.oo all 1.26.0-1 [955 kB] 236s Get:76 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-r.utils all 2.12.3-1 [1386 kB] 236s Get:77 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-matrixstats armhf 1.2.0-1 [478 kB] 236s Get:78 http://ftpmaster.internal/ubuntu noble/universe armhf r-bioc-aroma.light all 3.32.0-1 [576 kB] 236s Get:79 http://ftpmaster.internal/ubuntu noble/universe armhf r-bioc-dnacopy armhf 1.76.0-1 [377 kB] 236s Get:80 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-acepack armhf 1.4.2-1 [58.4 kB] 236s Get:81 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-backports armhf 1.4.1-1 [101 kB] 236s Get:82 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-base64enc armhf 0.1-3-3 [27.3 kB] 236s Get:83 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-rlang armhf 1.1.3-1 [1658 kB] 236s Get:84 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-fastmap armhf 1.1.1-1 [68.1 kB] 236s Get:85 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-cachem armhf 1.0.8-1 [72.0 kB] 236s Get:86 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-digest armhf 0.6.34-1 [180 kB] 236s Get:87 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-ellipsis armhf 0.3.2-2 [35.0 kB] 236s Get:88 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-htmltools armhf 0.5.7-1 [368 kB] 236s Get:89 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB] 236s Get:90 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-jsonlite armhf 1.8.8+dfsg-1 [438 kB] 236s Get:91 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-cli armhf 3.6.2-1 [1363 kB] 236s Get:92 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-glue armhf 1.7.0-1 [153 kB] 236s Get:93 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 236s Get:94 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-memoise all 2.0.1-1 [53.9 kB] 236s Get:95 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-mime armhf 0.12-1 [35.5 kB] 236s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf r-cran-fs armhf 1.6.3+dfsg-1build1 [226 kB] 236s Get:97 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-r6 all 2.5.1-1 [99.0 kB] 236s Get:98 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-rappdirs armhf 0.3.3-1 [47.4 kB] 236s Get:99 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-sass armhf 0.4.8+dfsg-1 [921 kB] 236s Get:100 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-bslib all 0.6.1+dfsg-1 [5138 kB] 236s Get:101 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-checkmate armhf 2.3.1-1 [708 kB] 236s Get:102 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-chron armhf 2.3-61-2 [186 kB] 236s Get:103 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-cluster armhf 2.1.6-1 [548 kB] 237s Get:104 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-codetools all 0.2-19-1 [90.5 kB] 237s Get:105 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-colorspace armhf 2.1-0+dfsg-1 [1538 kB] 237s Get:106 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-commonmark armhf 1.9.1-1 [110 kB] 237s Get:107 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-cpp11 all 0.4.7-1 [266 kB] 237s Get:108 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-crayon all 1.5.2-1 [164 kB] 237s Get:109 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-data.table armhf 1.14.10+dfsg-1 [1816 kB] 237s Get:110 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-deldir armhf 2.0-4-1 [268 kB] 237s Get:111 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-generics all 0.1.3-1 [81.3 kB] 237s Get:112 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 237s Get:113 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-fansi armhf 1.0.5-1 [611 kB] 237s Get:114 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 237s Get:115 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 237s Get:116 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 237s Get:117 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 237s Get:118 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-tibble armhf 3.2.1+dfsg-2 [415 kB] 237s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf r-cran-withr all 3.0.0+dfsg-1 [228 kB] 237s Get:120 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-tidyselect armhf 1.2.0+dfsg-1 [218 kB] 237s Get:121 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-dplyr armhf 1.1.4-1 [1510 kB] 237s Get:122 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-evaluate all 0.23-1 [90.2 kB] 237s Get:123 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-farver armhf 2.1.1-1 [1346 kB] 237s Get:124 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-fontawesome all 0.5.2-1 [1300 kB] 237s Get:125 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-foreign armhf 0.8.86-1 [237 kB] 237s Get:126 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-formula all 1.2-5-1 [158 kB] 237s Get:127 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-globals all 0.16.2-1 [117 kB] 237s Get:128 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 237s Get:129 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-parallelly armhf 1.37.1-1 [364 kB] 237s Get:130 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-future all 1.33.1+dfsg-1 [634 kB] 237s Get:131 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 237s Get:132 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 237s Get:133 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-mass armhf 7.3-60.0.1-1 [1118 kB] 237s Get:134 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-lattice armhf 0.22-5-1 [1341 kB] 237s Get:135 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-nlme armhf 3.1.164-1 [2252 kB] 237s Get:136 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-matrix armhf 1.6-5-1 [3762 kB] 237s Get:137 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 237s Get:138 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 237s Get:139 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-munsell all 0.5.0-2build1 [208 kB] 237s Get:140 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 237s Get:141 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-viridislite all 0.4.2-2 [1088 kB] 237s Get:142 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-scales all 1.3.0-1 [603 kB] 237s Get:143 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 238s Get:144 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-gridextra all 2.3-3build1 [1024 kB] 238s Get:145 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-xfun armhf 0.41+dfsg-1 [415 kB] 238s Get:146 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-highr all 0.10+dfsg-1 [38.3 kB] 238s Get:147 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-survival armhf 3.5-8-1 [6104 kB] 238s Get:148 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-rpart armhf 4.1.23-1 [657 kB] 238s Get:149 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-nnet armhf 7.3-19-2 [110 kB] 238s Get:150 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-stringi armhf 1.8.3-1 [859 kB] 238s Get:151 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 238s Get:152 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-yaml armhf 2.3.8-1 [99.0 kB] 238s Get:153 http://ftpmaster.internal/ubuntu noble/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 238s Get:154 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-knitr all 1.45+dfsg-1 [917 kB] 238s Get:155 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-tinytex all 0.49-1 [141 kB] 238s Get:156 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-modernizr all 2.6.2+ds1-5 [48.3 kB] 238s Get:157 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 238s Get:158 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-rcpp armhf 1.0.12-1 [1968 kB] 238s Get:159 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-later armhf 1.3.2+dfsg-1 [118 kB] 238s Get:160 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-promises armhf 1.2.1+dfsg-1 [281 kB] 238s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf r-cran-httpuv armhf 1.6.14+dfsg-1build1 [489 kB] 238s Get:162 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-xtable all 1:1.8-4-2 [689 kB] 238s Get:163 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-sourcetools armhf 0.1.7-1-1 [45.7 kB] 238s Get:164 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 238s Get:165 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-shiny all 1.8.0+dfsg-1 [2762 kB] 238s Get:166 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-rmarkdown all 2.25+dfsg-3 [1481 kB] 238s Get:167 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] 238s Get:168 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-rstudioapi all 0.15.0-1 [277 kB] 238s Get:169 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-purrr armhf 1.0.2-1 [499 kB] 238s Get:170 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 238s Get:171 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-htmltable all 2.4.2-1 [381 kB] 238s Get:172 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-viridis all 0.6.5-1 [2770 kB] 238s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf r-cran-png armhf 0.1-8-1build1 [39.9 kB] 238s Get:174 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-jpeg armhf 0.1-10-1 [30.4 kB] 238s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf r-cran-rcppeigen armhf 0.3.4.0.0-1 [1401 kB] 238s Get:176 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-interp armhf 1.1-6-1 [1414 kB] 238s Get:177 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-latticeextra all 0.6-30-1 [2198 kB] 238s Get:178 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-hmisc armhf 5.1-1-1 [3489 kB] 239s Get:179 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-r.cache all 0.16.0-1 [113 kB] 239s Get:180 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-pscbs all 0.66.0-2 [4345 kB] 239s Preconfiguring packages ... 239s Fetched 165 MB in 6s (27.4 MB/s) 239s Selecting previously unselected package libfreetype6:armhf. 239s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58435 files and directories currently installed.) 239s Preparing to unpack .../000-libfreetype6_2.13.2+dfsg-1build2_armhf.deb ... 239s Unpacking libfreetype6:armhf (2.13.2+dfsg-1build2) ... 239s Selecting previously unselected package fonts-dejavu-mono. 239s Preparing to unpack .../001-fonts-dejavu-mono_2.37-8_all.deb ... 239s Unpacking fonts-dejavu-mono (2.37-8) ... 239s Selecting previously unselected package fonts-dejavu-core. 239s Preparing to unpack .../002-fonts-dejavu-core_2.37-8_all.deb ... 239s Unpacking fonts-dejavu-core (2.37-8) ... 240s Selecting previously unselected package fontconfig-config. 240s Preparing to unpack .../003-fontconfig-config_2.15.0-1.1ubuntu1_armhf.deb ... 240s Unpacking fontconfig-config (2.15.0-1.1ubuntu1) ... 240s Selecting previously unselected package libfontconfig1:armhf. 240s Preparing to unpack .../004-libfontconfig1_2.15.0-1.1ubuntu1_armhf.deb ... 240s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu1) ... 240s Selecting previously unselected package fontconfig. 240s Preparing to unpack .../005-fontconfig_2.15.0-1.1ubuntu1_armhf.deb ... 240s Unpacking fontconfig (2.15.0-1.1ubuntu1) ... 240s Selecting previously unselected package fonts-font-awesome. 240s Preparing to unpack .../006-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 240s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 240s Selecting previously unselected package fonts-glyphicons-halflings. 240s Preparing to unpack .../007-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 240s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 240s Selecting previously unselected package fonts-mathjax. 240s Preparing to unpack .../008-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 240s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 240s Selecting previously unselected package javascript-common. 240s Preparing to unpack .../009-javascript-common_11+nmu1_all.deb ... 240s Unpacking javascript-common (11+nmu1) ... 240s Selecting previously unselected package libblas3:armhf. 240s Preparing to unpack .../010-libblas3_3.12.0-3_armhf.deb ... 240s Unpacking libblas3:armhf (3.12.0-3) ... 240s Selecting previously unselected package libpixman-1-0:armhf. 240s Preparing to unpack .../011-libpixman-1-0_0.42.2-1_armhf.deb ... 240s Unpacking libpixman-1-0:armhf (0.42.2-1) ... 240s Selecting previously unselected package libxcb-render0:armhf. 240s Preparing to unpack .../012-libxcb-render0_1.15-1_armhf.deb ... 240s Unpacking libxcb-render0:armhf (1.15-1) ... 240s Selecting previously unselected package libxcb-shm0:armhf. 240s Preparing to unpack .../013-libxcb-shm0_1.15-1_armhf.deb ... 240s Unpacking libxcb-shm0:armhf (1.15-1) ... 240s Selecting previously unselected package libxrender1:armhf. 240s Preparing to unpack .../014-libxrender1_1%3a0.9.10-1.1_armhf.deb ... 240s Unpacking libxrender1:armhf (1:0.9.10-1.1) ... 240s Selecting previously unselected package libcairo2:armhf. 240s Preparing to unpack .../015-libcairo2_1.18.0-1ubuntu1_armhf.deb ... 240s Unpacking libcairo2:armhf (1.18.0-1ubuntu1) ... 240s Selecting previously unselected package libdatrie1:armhf. 241s Preparing to unpack .../016-libdatrie1_0.2.13-3_armhf.deb ... 241s Unpacking libdatrie1:armhf (0.2.13-3) ... 241s Selecting previously unselected package libdeflate0:armhf. 241s Preparing to unpack .../017-libdeflate0_1.19-1_armhf.deb ... 241s Unpacking libdeflate0:armhf (1.19-1) ... 241s Selecting previously unselected package libgfortran5:armhf. 241s Preparing to unpack .../018-libgfortran5_14-20240315-1ubuntu1_armhf.deb ... 241s Unpacking libgfortran5:armhf (14-20240315-1ubuntu1) ... 241s Selecting previously unselected package libgomp1:armhf. 241s Preparing to unpack .../019-libgomp1_14-20240315-1ubuntu1_armhf.deb ... 241s Unpacking libgomp1:armhf (14-20240315-1ubuntu1) ... 241s Selecting previously unselected package libgraphite2-3:armhf. 241s Preparing to unpack .../020-libgraphite2-3_1.3.14-2_armhf.deb ... 241s Unpacking libgraphite2-3:armhf (1.3.14-2) ... 241s Selecting previously unselected package libharfbuzz0b:armhf. 241s Preparing to unpack .../021-libharfbuzz0b_8.3.0-2build1_armhf.deb ... 241s Unpacking libharfbuzz0b:armhf (8.3.0-2build1) ... 241s Selecting previously unselected package x11-common. 241s Preparing to unpack .../022-x11-common_1%3a7.7+23ubuntu2_all.deb ... 241s Unpacking x11-common (1:7.7+23ubuntu2) ... 241s Selecting previously unselected package libice6:armhf. 241s Preparing to unpack .../023-libice6_2%3a1.0.10-1build2_armhf.deb ... 241s Unpacking libice6:armhf (2:1.0.10-1build2) ... 241s Selecting previously unselected package libjpeg-turbo8:armhf. 241s Preparing to unpack .../024-libjpeg-turbo8_2.1.5-2ubuntu1_armhf.deb ... 241s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu1) ... 241s Selecting previously unselected package libjpeg8:armhf. 241s Preparing to unpack .../025-libjpeg8_8c-2ubuntu11_armhf.deb ... 241s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 241s Selecting previously unselected package libjs-bootstrap. 241s Preparing to unpack .../026-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 241s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 241s Selecting previously unselected package libjs-popper.js. 241s Preparing to unpack .../027-libjs-popper.js_1.16.1+ds-6_all.deb ... 241s Unpacking libjs-popper.js (1.16.1+ds-6) ... 241s Selecting previously unselected package libjs-bootstrap4. 241s Preparing to unpack .../028-libjs-bootstrap4_4.6.1+dfsg1-4_all.deb ... 241s Unpacking libjs-bootstrap4 (4.6.1+dfsg1-4) ... 241s Selecting previously unselected package libjs-d3. 241s Preparing to unpack .../029-libjs-d3_3.5.17-4_all.deb ... 241s Unpacking libjs-d3 (3.5.17-4) ... 241s Selecting previously unselected package libjs-es5-shim. 241s Preparing to unpack .../030-libjs-es5-shim_4.6.7-2_all.deb ... 241s Unpacking libjs-es5-shim (4.6.7-2) ... 241s Selecting previously unselected package libjs-highlight.js. 241s Preparing to unpack .../031-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 241s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 241s Selecting previously unselected package libjs-jquery. 241s Preparing to unpack .../032-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 241s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 241s Selecting previously unselected package libjs-jquery-datatables. 241s Preparing to unpack .../033-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 241s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 241s Selecting previously unselected package libjs-sifter.js. 241s Preparing to unpack .../034-libjs-sifter.js_0.6.0+dfsg-3_all.deb ... 241s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ... 241s Selecting previously unselected package libjs-microplugin.js. 241s Preparing to unpack .../035-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ... 241s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ... 241s Selecting previously unselected package libjs-jquery-selectize.js. 241s Preparing to unpack .../036-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ... 241s Unpacking libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 241s Selecting previously unselected package libjs-jquery-ui. 241s Preparing to unpack .../037-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 241s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 241s Selecting previously unselected package libjs-json. 241s Preparing to unpack .../038-libjs-json_0~20221030+~1.0.8-1_all.deb ... 241s Unpacking libjs-json (0~20221030+~1.0.8-1) ... 241s Selecting previously unselected package libjs-prettify. 242s Preparing to unpack .../039-libjs-prettify_2015.12.04+dfsg-1.1_all.deb ... 242s Unpacking libjs-prettify (2015.12.04+dfsg-1.1) ... 242s Selecting previously unselected package liblapack3:armhf. 242s Preparing to unpack .../040-liblapack3_3.12.0-3_armhf.deb ... 242s Unpacking liblapack3:armhf (3.12.0-3) ... 242s Selecting previously unselected package liblerc4:armhf. 242s Preparing to unpack .../041-liblerc4_4.0.0+ds-4ubuntu1_armhf.deb ... 242s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu1) ... 242s Selecting previously unselected package liblua5.4-0:armhf. 242s Preparing to unpack .../042-liblua5.4-0_5.4.6-3build1_armhf.deb ... 242s Unpacking liblua5.4-0:armhf (5.4.6-3build1) ... 242s Selecting previously unselected package libthai-data. 242s Preparing to unpack .../043-libthai-data_0.1.29-2_all.deb ... 242s Unpacking libthai-data (0.1.29-2) ... 242s Selecting previously unselected package libthai0:armhf. 242s Preparing to unpack .../044-libthai0_0.1.29-2_armhf.deb ... 242s Unpacking libthai0:armhf (0.1.29-2) ... 242s Selecting previously unselected package libpango-1.0-0:armhf. 242s Preparing to unpack .../045-libpango-1.0-0_1.52.1+ds-1_armhf.deb ... 242s Unpacking libpango-1.0-0:armhf (1.52.1+ds-1) ... 242s Selecting previously unselected package libpangoft2-1.0-0:armhf. 242s Preparing to unpack .../046-libpangoft2-1.0-0_1.52.1+ds-1_armhf.deb ... 242s Unpacking libpangoft2-1.0-0:armhf (1.52.1+ds-1) ... 242s Selecting previously unselected package libpangocairo-1.0-0:armhf. 242s Preparing to unpack .../047-libpangocairo-1.0-0_1.52.1+ds-1_armhf.deb ... 242s Unpacking libpangocairo-1.0-0:armhf (1.52.1+ds-1) ... 242s Selecting previously unselected package libpaper1:armhf. 242s Preparing to unpack .../048-libpaper1_1.1.29_armhf.deb ... 242s Unpacking libpaper1:armhf (1.1.29) ... 242s Selecting previously unselected package libpaper-utils. 242s Preparing to unpack .../049-libpaper-utils_1.1.29_armhf.deb ... 242s Unpacking libpaper-utils (1.1.29) ... 242s Selecting previously unselected package libsharpyuv0:armhf. 242s Preparing to unpack .../050-libsharpyuv0_1.3.2-0.4build2_armhf.deb ... 242s Unpacking libsharpyuv0:armhf (1.3.2-0.4build2) ... 242s Selecting previously unselected package libsm6:armhf. 242s Preparing to unpack .../051-libsm6_2%3a1.2.3-1build2_armhf.deb ... 242s Unpacking libsm6:armhf (2:1.2.3-1build2) ... 242s Selecting previously unselected package libtcl8.6:armhf. 242s Preparing to unpack .../052-libtcl8.6_8.6.14+dfsg-1_armhf.deb ... 242s Unpacking libtcl8.6:armhf (8.6.14+dfsg-1) ... 242s Selecting previously unselected package libjbig0:armhf. 242s Preparing to unpack .../053-libjbig0_2.1-6.1ubuntu1_armhf.deb ... 242s Unpacking libjbig0:armhf (2.1-6.1ubuntu1) ... 242s Selecting previously unselected package libwebp7:armhf. 242s Preparing to unpack .../054-libwebp7_1.3.2-0.4build2_armhf.deb ... 242s Unpacking libwebp7:armhf (1.3.2-0.4build2) ... 242s Selecting previously unselected package libtiff6:armhf. 242s Preparing to unpack .../055-libtiff6_4.5.1+git230720-4ubuntu1_armhf.deb ... 242s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu1) ... 242s Selecting previously unselected package libxft2:armhf. 242s Preparing to unpack .../056-libxft2_2.3.6-1_armhf.deb ... 242s Unpacking libxft2:armhf (2.3.6-1) ... 242s Selecting previously unselected package libxss1:armhf. 242s Preparing to unpack .../057-libxss1_1%3a1.2.3-1build2_armhf.deb ... 242s Unpacking libxss1:armhf (1:1.2.3-1build2) ... 242s Selecting previously unselected package libtk8.6:armhf. 242s Preparing to unpack .../058-libtk8.6_8.6.13-2_armhf.deb ... 242s Unpacking libtk8.6:armhf (8.6.13-2) ... 242s Selecting previously unselected package libxt6t64:armhf. 242s Preparing to unpack .../059-libxt6t64_1%3a1.2.1-1.2_armhf.deb ... 242s Unpacking libxt6t64:armhf (1:1.2.1-1.2) ... 242s Selecting previously unselected package zip. 243s Preparing to unpack .../060-zip_3.0-13_armhf.deb ... 243s Unpacking zip (3.0-13) ... 243s Selecting previously unselected package unzip. 243s Preparing to unpack .../061-unzip_6.0-28ubuntu3_armhf.deb ... 243s Unpacking unzip (6.0-28ubuntu3) ... 243s Selecting previously unselected package xdg-utils. 243s Preparing to unpack .../062-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 243s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 243s Selecting previously unselected package r-base-core. 243s Preparing to unpack .../063-r-base-core_4.3.3-2build1_armhf.deb ... 243s Unpacking r-base-core (4.3.3-2build1) ... 243s Selecting previously unselected package r-cran-littler. 243s Preparing to unpack .../064-r-cran-littler_0.3.19-1_armhf.deb ... 243s Unpacking r-cran-littler (0.3.19-1) ... 243s Selecting previously unselected package littler. 243s Preparing to unpack .../065-littler_0.3.19-1_all.deb ... 243s Unpacking littler (0.3.19-1) ... 243s Selecting previously unselected package node-bootstrap-sass. 243s Preparing to unpack .../066-node-bootstrap-sass_3.4.3-2_all.deb ... 243s Unpacking node-bootstrap-sass (3.4.3-2) ... 243s Selecting previously unselected package node-html5shiv. 243s Preparing to unpack .../067-node-html5shiv_3.7.3+dfsg-5_all.deb ... 243s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 243s Selecting previously unselected package node-normalize.css. 243s Preparing to unpack .../068-node-normalize.css_8.0.1-5_all.deb ... 243s Unpacking node-normalize.css (8.0.1-5) ... 243s Selecting previously unselected package pandoc-data. 243s Preparing to unpack .../069-pandoc-data_3.1.3-1_all.deb ... 243s Unpacking pandoc-data (3.1.3-1) ... 243s Selecting previously unselected package pandoc. 243s Preparing to unpack .../070-pandoc_3.1.3+ds-2_armhf.deb ... 243s Unpacking pandoc (3.1.3+ds-2) ... 244s Selecting previously unselected package r-bioc-biocgenerics. 244s Preparing to unpack .../071-r-bioc-biocgenerics_0.48.1-2_all.deb ... 244s Unpacking r-bioc-biocgenerics (0.48.1-2) ... 244s Selecting previously unselected package r-cran-r.methodss3. 244s Preparing to unpack .../072-r-cran-r.methodss3_1.8.2-1_all.deb ... 244s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 244s Selecting previously unselected package r-cran-r.oo. 244s Preparing to unpack .../073-r-cran-r.oo_1.26.0-1_all.deb ... 244s Unpacking r-cran-r.oo (1.26.0-1) ... 244s Selecting previously unselected package r-cran-r.utils. 245s Preparing to unpack .../074-r-cran-r.utils_2.12.3-1_all.deb ... 245s Unpacking r-cran-r.utils (2.12.3-1) ... 245s Selecting previously unselected package r-cran-matrixstats. 245s Preparing to unpack .../075-r-cran-matrixstats_1.2.0-1_armhf.deb ... 245s Unpacking r-cran-matrixstats (1.2.0-1) ... 245s Selecting previously unselected package r-bioc-aroma.light. 245s Preparing to unpack .../076-r-bioc-aroma.light_3.32.0-1_all.deb ... 245s Unpacking r-bioc-aroma.light (3.32.0-1) ... 245s Selecting previously unselected package r-bioc-dnacopy. 245s Preparing to unpack .../077-r-bioc-dnacopy_1.76.0-1_armhf.deb ... 245s Unpacking r-bioc-dnacopy (1.76.0-1) ... 245s Selecting previously unselected package r-cran-acepack. 245s Preparing to unpack .../078-r-cran-acepack_1.4.2-1_armhf.deb ... 245s Unpacking r-cran-acepack (1.4.2-1) ... 245s Selecting previously unselected package r-cran-backports. 245s Preparing to unpack .../079-r-cran-backports_1.4.1-1_armhf.deb ... 245s Unpacking r-cran-backports (1.4.1-1) ... 245s Selecting previously unselected package r-cran-base64enc. 245s Preparing to unpack .../080-r-cran-base64enc_0.1-3-3_armhf.deb ... 245s Unpacking r-cran-base64enc (0.1-3-3) ... 245s Selecting previously unselected package r-cran-rlang. 245s Preparing to unpack .../081-r-cran-rlang_1.1.3-1_armhf.deb ... 245s Unpacking r-cran-rlang (1.1.3-1) ... 245s Selecting previously unselected package r-cran-fastmap. 245s Preparing to unpack .../082-r-cran-fastmap_1.1.1-1_armhf.deb ... 245s Unpacking r-cran-fastmap (1.1.1-1) ... 245s Selecting previously unselected package r-cran-cachem. 245s Preparing to unpack .../083-r-cran-cachem_1.0.8-1_armhf.deb ... 245s Unpacking r-cran-cachem (1.0.8-1) ... 245s Selecting previously unselected package r-cran-digest. 245s Preparing to unpack .../084-r-cran-digest_0.6.34-1_armhf.deb ... 245s Unpacking r-cran-digest (0.6.34-1) ... 245s Selecting previously unselected package r-cran-ellipsis. 245s Preparing to unpack .../085-r-cran-ellipsis_0.3.2-2_armhf.deb ... 245s Unpacking r-cran-ellipsis (0.3.2-2) ... 245s Selecting previously unselected package r-cran-htmltools. 245s Preparing to unpack .../086-r-cran-htmltools_0.5.7-1_armhf.deb ... 245s Unpacking r-cran-htmltools (0.5.7-1) ... 245s Selecting previously unselected package r-cran-jquerylib. 245s Preparing to unpack .../087-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ... 245s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ... 245s Selecting previously unselected package r-cran-jsonlite. 245s Preparing to unpack .../088-r-cran-jsonlite_1.8.8+dfsg-1_armhf.deb ... 245s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 245s Selecting previously unselected package r-cran-cli. 245s Preparing to unpack .../089-r-cran-cli_3.6.2-1_armhf.deb ... 245s Unpacking r-cran-cli (3.6.2-1) ... 245s Selecting previously unselected package r-cran-glue. 245s Preparing to unpack .../090-r-cran-glue_1.7.0-1_armhf.deb ... 245s Unpacking r-cran-glue (1.7.0-1) ... 245s Selecting previously unselected package r-cran-lifecycle. 245s Preparing to unpack .../091-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 245s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 245s Selecting previously unselected package r-cran-memoise. 245s Preparing to unpack .../092-r-cran-memoise_2.0.1-1_all.deb ... 245s Unpacking r-cran-memoise (2.0.1-1) ... 245s Selecting previously unselected package r-cran-mime. 245s Preparing to unpack .../093-r-cran-mime_0.12-1_armhf.deb ... 245s Unpacking r-cran-mime (0.12-1) ... 245s Selecting previously unselected package r-cran-fs. 245s Preparing to unpack .../094-r-cran-fs_1.6.3+dfsg-1build1_armhf.deb ... 245s Unpacking r-cran-fs (1.6.3+dfsg-1build1) ... 245s Selecting previously unselected package r-cran-r6. 245s Preparing to unpack .../095-r-cran-r6_2.5.1-1_all.deb ... 245s Unpacking r-cran-r6 (2.5.1-1) ... 245s Selecting previously unselected package r-cran-rappdirs. 245s Preparing to unpack .../096-r-cran-rappdirs_0.3.3-1_armhf.deb ... 245s Unpacking r-cran-rappdirs (0.3.3-1) ... 246s Selecting previously unselected package r-cran-sass. 246s Preparing to unpack .../097-r-cran-sass_0.4.8+dfsg-1_armhf.deb ... 246s Unpacking r-cran-sass (0.4.8+dfsg-1) ... 246s Selecting previously unselected package r-cran-bslib. 246s Preparing to unpack .../098-r-cran-bslib_0.6.1+dfsg-1_all.deb ... 246s Unpacking r-cran-bslib (0.6.1+dfsg-1) ... 246s Selecting previously unselected package r-cran-checkmate. 246s Preparing to unpack .../099-r-cran-checkmate_2.3.1-1_armhf.deb ... 246s Unpacking r-cran-checkmate (2.3.1-1) ... 246s Selecting previously unselected package r-cran-chron. 246s Preparing to unpack .../100-r-cran-chron_2.3-61-2_armhf.deb ... 246s Unpacking r-cran-chron (2.3-61-2) ... 246s Selecting previously unselected package r-cran-cluster. 246s Preparing to unpack .../101-r-cran-cluster_2.1.6-1_armhf.deb ... 246s Unpacking r-cran-cluster (2.1.6-1) ... 246s Selecting previously unselected package r-cran-codetools. 246s Preparing to unpack .../102-r-cran-codetools_0.2-19-1_all.deb ... 246s Unpacking r-cran-codetools (0.2-19-1) ... 246s Selecting previously unselected package r-cran-colorspace. 246s Preparing to unpack .../103-r-cran-colorspace_2.1-0+dfsg-1_armhf.deb ... 246s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 246s Selecting previously unselected package r-cran-commonmark. 246s Preparing to unpack .../104-r-cran-commonmark_1.9.1-1_armhf.deb ... 246s Unpacking r-cran-commonmark (1.9.1-1) ... 246s Selecting previously unselected package r-cran-cpp11. 246s Preparing to unpack .../105-r-cran-cpp11_0.4.7-1_all.deb ... 246s Unpacking r-cran-cpp11 (0.4.7-1) ... 246s Selecting previously unselected package r-cran-crayon. 246s Preparing to unpack .../106-r-cran-crayon_1.5.2-1_all.deb ... 246s Unpacking r-cran-crayon (1.5.2-1) ... 246s Selecting previously unselected package r-cran-data.table. 246s Preparing to unpack .../107-r-cran-data.table_1.14.10+dfsg-1_armhf.deb ... 246s Unpacking r-cran-data.table (1.14.10+dfsg-1) ... 246s Selecting previously unselected package r-cran-deldir. 246s Preparing to unpack .../108-r-cran-deldir_2.0-4-1_armhf.deb ... 246s Unpacking r-cran-deldir (2.0-4-1) ... 246s Selecting previously unselected package r-cran-generics. 246s Preparing to unpack .../109-r-cran-generics_0.1.3-1_all.deb ... 246s Unpacking r-cran-generics (0.1.3-1) ... 246s Selecting previously unselected package r-cran-magrittr. 246s Preparing to unpack .../110-r-cran-magrittr_2.0.3-1_armhf.deb ... 246s Unpacking r-cran-magrittr (2.0.3-1) ... 246s Selecting previously unselected package r-cran-fansi. 247s Preparing to unpack .../111-r-cran-fansi_1.0.5-1_armhf.deb ... 247s Unpacking r-cran-fansi (1.0.5-1) ... 247s Selecting previously unselected package r-cran-utf8. 247s Preparing to unpack .../112-r-cran-utf8_1.2.4-1_armhf.deb ... 247s Unpacking r-cran-utf8 (1.2.4-1) ... 247s Selecting previously unselected package r-cran-vctrs. 247s Preparing to unpack .../113-r-cran-vctrs_0.6.5-1_armhf.deb ... 247s Unpacking r-cran-vctrs (0.6.5-1) ... 247s Selecting previously unselected package r-cran-pillar. 247s Preparing to unpack .../114-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 247s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 247s Selecting previously unselected package r-cran-pkgconfig. 247s Preparing to unpack .../115-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 247s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 247s Selecting previously unselected package r-cran-tibble. 247s Preparing to unpack .../116-r-cran-tibble_3.2.1+dfsg-2_armhf.deb ... 247s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 247s Selecting previously unselected package r-cran-withr. 247s Preparing to unpack .../117-r-cran-withr_3.0.0+dfsg-1_all.deb ... 247s Unpacking r-cran-withr (3.0.0+dfsg-1) ... 247s Selecting previously unselected package r-cran-tidyselect. 247s Preparing to unpack .../118-r-cran-tidyselect_1.2.0+dfsg-1_armhf.deb ... 247s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 247s Selecting previously unselected package r-cran-dplyr. 247s Preparing to unpack .../119-r-cran-dplyr_1.1.4-1_armhf.deb ... 247s Unpacking r-cran-dplyr (1.1.4-1) ... 247s Selecting previously unselected package r-cran-evaluate. 247s Preparing to unpack .../120-r-cran-evaluate_0.23-1_all.deb ... 247s Unpacking r-cran-evaluate (0.23-1) ... 247s Selecting previously unselected package r-cran-farver. 247s Preparing to unpack .../121-r-cran-farver_2.1.1-1_armhf.deb ... 247s Unpacking r-cran-farver (2.1.1-1) ... 247s Selecting previously unselected package r-cran-fontawesome. 247s Preparing to unpack .../122-r-cran-fontawesome_0.5.2-1_all.deb ... 247s Unpacking r-cran-fontawesome (0.5.2-1) ... 247s Selecting previously unselected package r-cran-foreign. 247s Preparing to unpack .../123-r-cran-foreign_0.8.86-1_armhf.deb ... 247s Unpacking r-cran-foreign (0.8.86-1) ... 247s Selecting previously unselected package r-cran-formula. 247s Preparing to unpack .../124-r-cran-formula_1.2-5-1_all.deb ... 247s Unpacking r-cran-formula (1.2-5-1) ... 247s Selecting previously unselected package r-cran-globals. 247s Preparing to unpack .../125-r-cran-globals_0.16.2-1_all.deb ... 247s Unpacking r-cran-globals (0.16.2-1) ... 247s Selecting previously unselected package r-cran-listenv. 247s Preparing to unpack .../126-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 247s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 247s Selecting previously unselected package r-cran-parallelly. 247s Preparing to unpack .../127-r-cran-parallelly_1.37.1-1_armhf.deb ... 247s Unpacking r-cran-parallelly (1.37.1-1) ... 248s Selecting previously unselected package r-cran-future. 248s Preparing to unpack .../128-r-cran-future_1.33.1+dfsg-1_all.deb ... 248s Unpacking r-cran-future (1.33.1+dfsg-1) ... 248s Selecting previously unselected package r-cran-gtable. 248s Preparing to unpack .../129-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 248s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 248s Selecting previously unselected package r-cran-isoband. 248s Preparing to unpack .../130-r-cran-isoband_0.2.7-1_armhf.deb ... 248s Unpacking r-cran-isoband (0.2.7-1) ... 248s Selecting previously unselected package r-cran-mass. 248s Preparing to unpack .../131-r-cran-mass_7.3-60.0.1-1_armhf.deb ... 248s Unpacking r-cran-mass (7.3-60.0.1-1) ... 248s Selecting previously unselected package r-cran-lattice. 248s Preparing to unpack .../132-r-cran-lattice_0.22-5-1_armhf.deb ... 248s Unpacking r-cran-lattice (0.22-5-1) ... 248s Selecting previously unselected package r-cran-nlme. 248s Preparing to unpack .../133-r-cran-nlme_3.1.164-1_armhf.deb ... 248s Unpacking r-cran-nlme (3.1.164-1) ... 248s Selecting previously unselected package r-cran-matrix. 248s Preparing to unpack .../134-r-cran-matrix_1.6-5-1_armhf.deb ... 248s Unpacking r-cran-matrix (1.6-5-1) ... 248s Selecting previously unselected package r-cran-mgcv. 248s Preparing to unpack .../135-r-cran-mgcv_1.9-1-1_armhf.deb ... 248s Unpacking r-cran-mgcv (1.9-1-1) ... 248s Selecting previously unselected package r-cran-labeling. 248s Preparing to unpack .../136-r-cran-labeling_0.4.3-1_all.deb ... 248s Unpacking r-cran-labeling (0.4.3-1) ... 248s Selecting previously unselected package r-cran-munsell. 248s Preparing to unpack .../137-r-cran-munsell_0.5.0-2build1_all.deb ... 248s Unpacking r-cran-munsell (0.5.0-2build1) ... 248s Selecting previously unselected package r-cran-rcolorbrewer. 248s Preparing to unpack .../138-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 248s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 248s Selecting previously unselected package r-cran-viridislite. 248s Preparing to unpack .../139-r-cran-viridislite_0.4.2-2_all.deb ... 248s Unpacking r-cran-viridislite (0.4.2-2) ... 248s Selecting previously unselected package r-cran-scales. 248s Preparing to unpack .../140-r-cran-scales_1.3.0-1_all.deb ... 248s Unpacking r-cran-scales (1.3.0-1) ... 248s Selecting previously unselected package r-cran-ggplot2. 248s Preparing to unpack .../141-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 248s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 248s Selecting previously unselected package r-cran-gridextra. 248s Preparing to unpack .../142-r-cran-gridextra_2.3-3build1_all.deb ... 248s Unpacking r-cran-gridextra (2.3-3build1) ... 248s Selecting previously unselected package r-cran-xfun. 248s Preparing to unpack .../143-r-cran-xfun_0.41+dfsg-1_armhf.deb ... 248s Unpacking r-cran-xfun (0.41+dfsg-1) ... 248s Selecting previously unselected package r-cran-highr. 248s Preparing to unpack .../144-r-cran-highr_0.10+dfsg-1_all.deb ... 248s Unpacking r-cran-highr (0.10+dfsg-1) ... 248s Selecting previously unselected package r-cran-survival. 248s Preparing to unpack .../145-r-cran-survival_3.5-8-1_armhf.deb ... 248s Unpacking r-cran-survival (3.5-8-1) ... 248s Selecting previously unselected package r-cran-rpart. 248s Preparing to unpack .../146-r-cran-rpart_4.1.23-1_armhf.deb ... 248s Unpacking r-cran-rpart (4.1.23-1) ... 249s Selecting previously unselected package r-cran-nnet. 249s Preparing to unpack .../147-r-cran-nnet_7.3-19-2_armhf.deb ... 249s Unpacking r-cran-nnet (7.3-19-2) ... 249s Selecting previously unselected package r-cran-stringi. 249s Preparing to unpack .../148-r-cran-stringi_1.8.3-1_armhf.deb ... 249s Unpacking r-cran-stringi (1.8.3-1) ... 249s Selecting previously unselected package r-cran-stringr. 249s Preparing to unpack .../149-r-cran-stringr_1.5.1-1_all.deb ... 249s Unpacking r-cran-stringr (1.5.1-1) ... 249s Selecting previously unselected package r-cran-yaml. 249s Preparing to unpack .../150-r-cran-yaml_2.3.8-1_armhf.deb ... 249s Unpacking r-cran-yaml (2.3.8-1) ... 249s Selecting previously unselected package libjs-mathjax. 249s Preparing to unpack .../151-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 249s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 249s Selecting previously unselected package r-cran-knitr. 249s Preparing to unpack .../152-r-cran-knitr_1.45+dfsg-1_all.deb ... 249s Unpacking r-cran-knitr (1.45+dfsg-1) ... 249s Selecting previously unselected package r-cran-tinytex. 249s Preparing to unpack .../153-r-cran-tinytex_0.49-1_all.deb ... 249s Unpacking r-cran-tinytex (0.49-1) ... 250s Selecting previously unselected package libjs-modernizr. 250s Preparing to unpack .../154-libjs-modernizr_2.6.2+ds1-5_all.deb ... 250s Unpacking libjs-modernizr (2.6.2+ds1-5) ... 250s Selecting previously unselected package r-cran-pkgkitten. 250s Preparing to unpack .../155-r-cran-pkgkitten_0.2.3-1_all.deb ... 250s Unpacking r-cran-pkgkitten (0.2.3-1) ... 250s Selecting previously unselected package r-cran-rcpp. 250s Preparing to unpack .../156-r-cran-rcpp_1.0.12-1_armhf.deb ... 250s Unpacking r-cran-rcpp (1.0.12-1) ... 250s Selecting previously unselected package r-cran-later. 250s Preparing to unpack .../157-r-cran-later_1.3.2+dfsg-1_armhf.deb ... 250s Unpacking r-cran-later (1.3.2+dfsg-1) ... 250s Selecting previously unselected package r-cran-promises. 250s Preparing to unpack .../158-r-cran-promises_1.2.1+dfsg-1_armhf.deb ... 250s Unpacking r-cran-promises (1.2.1+dfsg-1) ... 250s Selecting previously unselected package r-cran-httpuv. 250s Preparing to unpack .../159-r-cran-httpuv_1.6.14+dfsg-1build1_armhf.deb ... 250s Unpacking r-cran-httpuv (1.6.14+dfsg-1build1) ... 250s Selecting previously unselected package r-cran-xtable. 250s Preparing to unpack .../160-r-cran-xtable_1%3a1.8-4-2_all.deb ... 250s Unpacking r-cran-xtable (1:1.8-4-2) ... 250s Selecting previously unselected package r-cran-sourcetools. 250s Preparing to unpack .../161-r-cran-sourcetools_0.1.7-1-1_armhf.deb ... 250s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 250s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 250s Preparing to unpack .../162-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 250s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 250s Selecting previously unselected package r-cran-shiny. 250s Preparing to unpack .../163-r-cran-shiny_1.8.0+dfsg-1_all.deb ... 250s Unpacking r-cran-shiny (1.8.0+dfsg-1) ... 250s Selecting previously unselected package r-cran-rmarkdown. 250s Preparing to unpack .../164-r-cran-rmarkdown_2.25+dfsg-3_all.deb ... 250s Unpacking r-cran-rmarkdown (2.25+dfsg-3) ... 250s Selecting previously unselected package r-cran-htmlwidgets. 250s Preparing to unpack .../165-r-cran-htmlwidgets_1.6.4+dfsg-1_all.deb ... 250s Unpacking r-cran-htmlwidgets (1.6.4+dfsg-1) ... 250s Selecting previously unselected package r-cran-rstudioapi. 250s Preparing to unpack .../166-r-cran-rstudioapi_0.15.0-1_all.deb ... 250s Unpacking r-cran-rstudioapi (0.15.0-1) ... 250s Selecting previously unselected package r-cran-purrr. 250s Preparing to unpack .../167-r-cran-purrr_1.0.2-1_armhf.deb ... 250s Unpacking r-cran-purrr (1.0.2-1) ... 251s Selecting previously unselected package r-cran-tidyr. 251s Preparing to unpack .../168-r-cran-tidyr_1.3.1-1_armhf.deb ... 251s Unpacking r-cran-tidyr (1.3.1-1) ... 251s Selecting previously unselected package r-cran-htmltable. 251s Preparing to unpack .../169-r-cran-htmltable_2.4.2-1_all.deb ... 251s Unpacking r-cran-htmltable (2.4.2-1) ... 251s Selecting previously unselected package r-cran-viridis. 251s Preparing to unpack .../170-r-cran-viridis_0.6.5-1_all.deb ... 251s Unpacking r-cran-viridis (0.6.5-1) ... 251s Selecting previously unselected package r-cran-png. 251s Preparing to unpack .../171-r-cran-png_0.1-8-1build1_armhf.deb ... 251s Unpacking r-cran-png (0.1-8-1build1) ... 251s Selecting previously unselected package r-cran-jpeg. 251s Preparing to unpack .../172-r-cran-jpeg_0.1-10-1_armhf.deb ... 251s Unpacking r-cran-jpeg (0.1-10-1) ... 251s Selecting previously unselected package r-cran-rcppeigen. 251s Preparing to unpack .../173-r-cran-rcppeigen_0.3.4.0.0-1_armhf.deb ... 251s Unpacking r-cran-rcppeigen (0.3.4.0.0-1) ... 251s Selecting previously unselected package r-cran-interp. 251s Preparing to unpack .../174-r-cran-interp_1.1-6-1_armhf.deb ... 251s Unpacking r-cran-interp (1.1-6-1) ... 251s Selecting previously unselected package r-cran-latticeextra. 251s Preparing to unpack .../175-r-cran-latticeextra_0.6-30-1_all.deb ... 251s Unpacking r-cran-latticeextra (0.6-30-1) ... 251s Selecting previously unselected package r-cran-hmisc. 251s Preparing to unpack .../176-r-cran-hmisc_5.1-1-1_armhf.deb ... 251s Unpacking r-cran-hmisc (5.1-1-1) ... 251s Selecting previously unselected package r-cran-r.cache. 251s Preparing to unpack .../177-r-cran-r.cache_0.16.0-1_all.deb ... 251s Unpacking r-cran-r.cache (0.16.0-1) ... 251s Selecting previously unselected package r-cran-pscbs. 251s Preparing to unpack .../178-r-cran-pscbs_0.66.0-2_all.deb ... 251s Unpacking r-cran-pscbs (0.66.0-2) ... 251s Selecting previously unselected package autopkgtest-satdep. 251s Preparing to unpack .../179-1-autopkgtest-satdep.deb ... 251s Unpacking autopkgtest-satdep (0) ... 251s Setting up libjs-json (0~20221030+~1.0.8-1) ... 251s Setting up javascript-common (11+nmu1) ... 251s Setting up libgraphite2-3:armhf (1.3.14-2) ... 251s Setting up libpixman-1-0:armhf (0.42.2-1) ... 251s Setting up libsharpyuv0:armhf (1.3.2-0.4build2) ... 251s Setting up libpaper1:armhf (1.1.29) ... 251s 251s Creating config file /etc/papersize with new version 251s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 251s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu1) ... 251s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 251s Setting up libxrender1:armhf (1:0.9.10-1.1) ... 251s Setting up libdatrie1:armhf (0.2.13-3) ... 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libc-bin (2.39-0ubuntu6) ... 285s (Reading database ... 77539 files and directories currently installed.) 285s Removing autopkgtest-satdep (0) ... 290s autopkgtest [01:50:06]: test run-unit-test: [----------------------- 292s + pkg=r-cran-pscbs 292s + [ /tmp/autopkgtest.0xi9ix/autopkgtest_tmp = ] 292s + cd /tmp/autopkgtest.0xi9ix/autopkgtest_tmp 292s + cp -a /usr/share/doc/r-cran-pscbs/tests/PairedPSCBS,boot.R /usr/share/doc/r-cran-pscbs/tests/findLargeGaps.R /usr/share/doc/r-cran-pscbs/tests/randomSeed.R.gz /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,calls.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,futures.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,median.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,prune.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,report.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,shiftTCN.R /usr/share/doc/r-cran-pscbs/tests/segmentByCBS,weights.R.gz /usr/share/doc/r-cran-pscbs/tests/segmentByCBS.R.gz /usr/share/doc/r-cran-pscbs/tests/segmentByNonPairedPSCBS,medianDH.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,DH.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,calls.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,futures.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,noNormalBAFs.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,report.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R /usr/share/doc/r-cran-pscbs/tests/segmentByPairedPSCBS.R.gz /usr/share/doc/r-cran-pscbs/tests/weightedQuantile.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp 292s + find . -name *.gz -exec gunzip {} ; 292s + export LC_ALL=C 292s + dpkg-architecture -qDEB_HOST_ARCH 292s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 292s + hostarch=armhf 292s + [ armhf = armhf ] 292s + rm -f segmentByCBS,futures.R segmentByPairedPSCBS,futures.R 292s + ls PairedPSCBS,boot.R findLargeGaps.R+ randomSeed.R segmentByCBS,calls.R segmentByCBS,median.R segmentByCBS,prune.R segmentByCBS,report.R segmentByCBS,shiftTCN.R segmentByCBS,weights.R segmentByCBS.R segmentByNonPairedPSCBS,medianDH.R segmentByPairedPSCBS,DH.R segmentByPairedPSCBS,calls.R segmentByPairedPSCBS,noNormalBAFs.R segmentByPairedPSCBS,report.R segmentByPairedPSCBS,seqOfSegmentsByDP.R segmentByPairedPSCBS.R weightedQuantile.R 292s sed s/\.R$// 292s + echo Begin test PairedPSCBS,boot 292s + Begin test PairedPSCBS,boot 292s exitcode=0 292s + R CMD BATCH PairedPSCBS,boot.R 300s 300s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 300s Copyright (C) 2024 The R Foundation for Statistical Computing 300s Platform: arm-unknown-linux-gnueabihf (32-bit) 300s 300s R is free software and comes with ABSOLUTELY NO WARRANTY. 300s You are welcome to redistribute it under certain conditions. 300s Type 'license()' or 'licence()' for distribution details. 300s 300s R is a collaborative project with many contributors. 300s Type 'contributors()' for more information and 300s 'citation()' on how to cite R or R packages in publications. 300s 300s Type 'demo()' for some demos, 'help()' for on-line help, or 300s 'help.start()' for an HTML browser interface to help. 300s Type 'q()' to quit R. 300s 300s > ########################################################### 300s > # This tests: 300s > # - Bootstrapping for PairedPSCBS objects 300s > ########################################################### 300s > library("PSCBS") 300s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 300s 300s Attaching package: 'PSCBS' 300s 300s The following objects are masked from 'package:base': 300s 300s append, load 300s 300s > 300s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 300s > # Load SNP microarray data 300s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 300s > data <- PSCBS::exampleData("paired.chr01") 300s > 300s > 300s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 300s > # Paired PSCBS segmentation 300s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 300s > # Drop single-locus outliers 300s > dataS <- dropSegmentationOutliers(data) 300s > dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 300s > nSegs <- 4L 300s > str(dataS) 300s 'data.frame': 14670 obs. of 6 variables: 300s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 300s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 300s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 300s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 300s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 300s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 300s > # Segment known regions 300s > knownSegments <- data.frame( 300s + chromosome = c( 1, 1, 1), 300s + start = c( -Inf, NA, 141510003), 300s + end = c(120992603, NA, +Inf) 300s + ) 300s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, avgDH="median", seed=0xBEEF) 300s > print(fit) 300s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 300s 1 1 1 1 554484 120992603 7586 1.385258 2108 300s 2 NA 2 1 NA NA NA NA 0 300s 3 1 3 1 141510003 185449813 2681 2.068861 777 300s 4 1 4 1 185449813 247137334 4391 2.634110 1311 300s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 300s 1 2108 2108 0.54551245 0.3147912 1.070467 300s 2 0 0 NA NA NA 300s 3 777 777 0.07132277 0.9606521 1.108209 300s 4 1311 1311 0.21663871 1.0317300 1.602380 300s > 300s > 300s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 300s > # Bootstrap 300s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 300s > B <- 1L 300s > seed <- 0xBEEF 300s > probs <- c(0.025, 0.05, 0.95, 0.975) 300s > 300s > sets <- getBootstrapLocusSets(fit, B=B, seed=seed) 300s > 300s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 300s > # Subset by first segment 300s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 300s > ss <- 1L 300s > 300s > fitT <- extractSegment(fit, ss) 300s > dataT <- getLocusData(fitT) 300s > segsT <- getSegments(fitT) 300s > 300s > # Truth 300s > bootT <- bootstrapSegmentsAndChangepoints(fitT, B=B, seed=seed) 300s > bootT1 <- bootT$segments[1L,,,drop=FALSE] 300s > types <- dimnames(bootT1)[[3L]] 300s > dim(bootT1) <- dim(bootT1)[-1L] 300s > colnames(bootT1) <- types 300s > sumsT <- apply(bootT1, MARGIN=2L, FUN=quantile, probs=probs) 300s > print(sumsT) 300s tcn dh c1 c2 300s 2.5% 1.383213 0.5466788 0.3135198 1.069693 300s 5% 1.383213 0.5466788 0.3135198 1.069693 300s 95% 1.383213 0.5466788 0.3135198 1.069693 300s 97.5% 1.383213 0.5466788 0.3135198 1.069693 300s > 300s > fitTB <- bootstrapTCNandDHByRegion(fitT, B=B, seed=seed) 300s > segsTB <- getSegments(fitTB) 300s > segsTB <- unlist(segsTB[,grep("_", colnames(segsTB))]) 300s > dim(segsTB) <- dim(sumsT) 300s > dimnames(segsTB) <- dimnames(sumsT) 300s > print(segsTB) 300s tcn dh c1 c2 300s 2.5% 1.383213 0.5466788 0.3135198 1.069693 300s 5% 1.383213 0.5466788 0.3135198 1.069693 300s 95% 1.383213 0.5466788 0.3135198 1.069693 300s 97.5% 1.383213 0.5466788 0.3135198 1.069693 300s > 300s > # Sanity check 300s > stopifnot(all.equal(segsTB, sumsT)) 300s > 300s > # Calculate summaries using the existing bootstrap samples 300s > fitTBp <- bootstrapTCNandDHByRegion(fitT, .boot=bootT) 300s > # Sanity check 300s > all.equal(fitTBp, fitTB) 300s [1] "Component \"tcn_2.5%\": Mean relative difference: 0.003070405" 300s [2] "Component \"tcn_5%\": Mean relative difference: 0.002241362" 300s [3] "Component \"tcn_95%\": Mean relative difference: 0.005458479" 300s [4] "Component \"tcn_97.5%\": Mean relative difference: 0.006030363" 300s [5] "Component \"dh_2.5%\": Mean relative difference: 0.02683423" 300s [6] "Component \"dh_5%\": Mean relative difference: 0.02409533" 300s [7] "Component \"dh_95%\": Mean relative difference: 0.0150081" 300s [8] "Component \"dh_97.5%\": Mean relative difference: 0.01826461" 300s [9] "Component \"c1_2.5%\": Mean relative difference: 0.02397349" 300s [10] "Component \"c1_5%\": Mean relative difference: 0.01800948" 300s [11] "Component \"c1_95%\": Mean relative difference: 0.0303456" 300s [12] "Component \"c1_97.5%\": Mean relative difference: 0.03420614" 300s [13] "Component \"c2_2.5%\": Mean relative difference: 0.008723378" 300s [14] "Component \"c2_5%\": Mean relative difference: 0.006834962" 300s [15] "Component \"c2_95%\": Mean relative difference: 0.00741949" 300s [16] "Component \"c2_97.5%\": Mean relative difference: 0.008743911" 300s attr(,"what") 300s [1] "getSegments()" 300s > 300s > 300s > # Bootstrap from scratch 300s > setsT <- getBootstrapLocusSets(fitT, B=B, seed=seed) 300s > lociT <- setsT$locusSet[[1L]]$bootstrap$loci 300s > idxs <- lociT$tcn 300s > tcnT <- array(dataT$CT[idxs], dim=dim(idxs)) 300s > tcnT <- apply(tcnT, MARGIN=2L, FUN=mean, na.rm=TRUE) 300s > idxs <- lociT$dh 300s > dhT <- array(dataT$rho[idxs], dim=dim(idxs)) 300s > dhT <- apply(dhT, MARGIN=2L, FUN=median, na.rm=TRUE) 300s > c1T <- (1-dhT) * tcnT / 2 300s > c2T <- tcnT - c1T 300s > bootT2 <- array(c(tcnT, dhT, c1T, c2T), dim=c(1L, 4L)) 300s > colnames(bootT2) <- colnames(bootT1) 300s > print(bootT2) 300s tcn dh c1 c2 300s [1,] 1.383213 0.5466788 0.3135198 1.069693 300s > 300s > # This comparison is only valid if B == 1L 300s > if (B == 1L) { 300s + # Sanity check 300s + stopifnot(all.equal(bootT2, bootT1)) 300s + } 300s > 300s > proc.time() 300s user system elapsed 300s 7.283 0.076 7.345 300s Test PairedPSCBS,boot passed 300s 0 300s Begin test findLargeGaps 300s + cat PairedPSCBS,boot.Rout 300s + [ 0 != 0 ] 300s + echo Test PairedPSCBS,boot passed 300s + echo 0 300s + echo Begin test findLargeGaps 300s + exitcode=0 300s + R CMD BATCH findLargeGaps.R 301s + cat findLargeGaps.Rout 301s 301s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 301s Copyright (C) 2024 The R Foundation for Statistical Computing 301s Platform: arm-unknown-linux-gnueabihf (32-bit) 301s 301s R is free software and comes with ABSOLUTELY NO WARRANTY. 301s You are welcome to redistribute it under certain conditions. 301s Type 'license()' or 'licence()' for distribution details. 301s 301s R is a collaborative project with many contributors. 301s Type 'contributors()' for more information and 301s 'citation()' on how to cite R or R packages in publications. 301s 301s Type 'demo()' for some demos, 'help()' for on-line help, or 301s 'help.start()' for an HTML browser interface to help. 301s Type 'q()' to quit R. 301s 301s [Previously saved workspace restored] 301s 301s > library("PSCBS") 301s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 301s 301s Attaching package: 'PSCBS' 301s 301s The following objects are masked from 'package:base': 301s 301s append, load 301s 301s > 301s > # Simulating copy-number data 301s > set.seed(0xBEEF) 301s > 301s > # Simulate CN data 301s > J <- 1000 301s > mu <- double(J) 301s > mu[200:300] <- mu[200:300] + 1 301s > mu[350:400] <- NA # centromere 301s > mu[650:800] <- mu[650:800] - 1 301s > eps <- rnorm(J, sd=1/2) 301s > y <- mu + eps 301s > x <- seq(from=1, to=100e6, length.out=J) 301s > 301s > data <- data.frame(chromosome=0L, x=x) 301s > 301s > gaps <- findLargeGaps(x=x, minLength=1e6) 301s > print(gaps) 301s [1] start end length 301s <0 rows> (or 0-length row.names) 301s > stopifnot(is.data.frame(gaps)) 301s > stopifnot(nrow(gaps) == 0L) 301s > segs <- gapsToSegments(gaps) 301s > print(segs) 301s chromosome start end 301s 1 0 -Inf Inf 301s > stopifnot(is.data.frame(segs)) 301s > stopifnot(nrow(segs) == 1L) 301s > 301s > 301s > gaps <- findLargeGaps(data, minLength=1e6) 301s > print(gaps) 301s [1] chromosome start end 301s <0 rows> (or 0-length row.names) 301s > stopifnot(is.data.frame(gaps)) 301s > stopifnot(nrow(gaps) == 0L) 301s > segs <- gapsToSegments(gaps) 301s > print(segs) 301s chromosome start end 301s 1 0 -Inf Inf 301s > stopifnot(is.data.frame(segs)) 301s > stopifnot(nrow(segs) == 1L) 301s > 301s > 301s > ## Add missing values 301s > data2 <- data 301s > data$x[30e6 < x & x < 50e6] <- NA 301s > gaps <- findLargeGaps(data, minLength=1e6) 301s > print(gaps) 301s chromosome start end length 301s 1 0 29929932 50050050 20120118 301s > stopifnot(is.data.frame(gaps)) 301s > stopifnot(nrow(gaps) == 1L) 301s > segs <- gapsToSegments(gaps) 301s > print(segs) 301s chromosome start end length 301s 1 0 -Inf 29929931 Inf 301s 2 0 29929932 50050050 20120118 301s 3 0 50050051 Inf Inf 301s > stopifnot(is.data.frame(segs)) 301s > stopifnot(nrow(segs) == 3L) 301s > 301s > 301s > 301s > # BUG FIX: Issue #6 301s > gaps <- findLargeGaps(chromosome=rep(1,10), x=1:10, minLength=2) 301s > print(gaps) 301s [1] chromosome start end 301s <0 rows> (or 0-length row.names) 301s > stopifnot(is.data.frame(gaps)) 301s > stopifnot(nrow(gaps) == 0L) 301s > # BUG FIX: Issue #9 301s > segs <- gapsToSegments(gaps) 301s > print(segs) 301s chromosome start end 301s 1 0 -Inf Inf 301s > stopifnot(is.data.frame(segs)) 301s > stopifnot(nrow(segs) == 1L) 301s > 301s > 301s > # BUG FIX: PSCBS GitHub Issue #8 301s > gaps <- try({ 301s + findLargeGaps(chromosome=rep(1,3), x=as.numeric(1:3), minLength=1) 301s + }) 301s Error in findLargeGaps.default(chromosome = rep(1, 3), x = as.numeric(1:3), : 301s Cannot identify large gaps. Argument 'resolution' (=1) is not strictly smaller than 'minLength' (=1). 301s > stopifnot(inherits(gaps, "try-error")) 301s > 301s > proc.time() 301s user system elapsed 301s 0.488 0.052 0.535 301s Test findLargeGaps passed 301s 0 301s Begin test randomSeed 301s + [ 0 != 0 ] 301s + echo Test findLargeGaps passed 301s + echo 0 301s + echo Begin test randomSeed 301s + exitcode=0 301s + R CMD BATCH randomSeed.R 301s + cat randomSeed.Rout 301s 301s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 301s Copyright (C) 2024 The R Foundation for Statistical Computing 301s Platform: arm-unknown-linux-gnueabihf (32-bit) 301s 301s R is free software and comes with ABSOLUTELY NO WARRANTY. 301s You are welcome to redistribute it under certain conditions. 301s Type 'license()' or 'licence()' for distribution details. 301s 301s R is a collaborative project with many contributors. 301s Type 'contributors()' for more information and 301s 'citation()' on how to cite R or R packages in publications. 301s 301s Type 'demo()' for some demos, 'help()' for on-line help, or 301s 'help.start()' for an HTML browser interface to help. 301s Type 'q()' to quit R. 301s 301s [Previously saved workspace restored] 301s 301s > library("PSCBS") 301s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 301s 301s Attaching package: 'PSCBS' 301s 301s The following objects are masked from 'package:base': 301s 301s append, load 301s 301s > 301s > message("*** randomSeed() - setup ...") 301s *** randomSeed() - setup ... 301s > ovars <- ls(envir=globalenv()) 301s > genv <- globalenv() 301s > RNGkind("Mersenne-Twister") 301s > if (exists(".Random.seed", envir=genv, inherits=FALSE)) 301s + rm(list=".Random.seed", envir=genv, inherits=FALSE) 301s > seed0 <- genv$.Random.seed 301s > stopifnot(is.null(seed0)) 301s > okind0 <- RNGkind()[1L] 301s > 301s > sample1 <- function() { sample(0:9, size=1L) } 301s > message("*** randomSeed() - setup ... done") 301s *** randomSeed() - setup ... done 301s > 301s > 301s > message("*** randomSeed('get') ...") 301s *** randomSeed('get') ... 301s > ## Get random seed 301s > seed <- randomSeed("get") 301s > stopifnot(identical(seed, seed0)) 301s > 301s > ## Repeat after new sample 301s > y1 <- sample1() 301s > message(sprintf("Random number: %d", y1)) 301s Random number: 5 301s > seed1 <- randomSeed("get") 301s > stopifnot(!identical(seed1, seed0)) 301s > message("*** randomSeed('get') ... done") 301s *** randomSeed('get') ... done 301s > 301s > 301s > message("*** randomSeed('set', 42L) ...") 301s *** randomSeed('set', 42L) ... 301s > randomSeed("set", seed=42L) 301s > seed2 <- randomSeed("get") 301s > stopifnot(!identical(seed2, seed1)) 301s > 301s > y2 <- sample1() 301s > message(sprintf("Random number: %d (with random seed = 42L)", y2)) 301s Random number: 0 (with random seed = 42L) 301s > 301s > ## Reset to previous state 301s > randomSeed("reset") 301s > seed3 <- randomSeed("get") 301s > stopifnot(identical(seed3, seed1)) 301s > stopifnot(identical(RNGkind()[1L], okind0), 301s + identical(randomSeed("get"), seed1)) 301s > message("*** randomSeed('set', 42L) ... done") 301s *** randomSeed('set', 42L) ... done 301s > 301s > 301s > message("*** randomSeed('set', NULL) ...") 301s *** randomSeed('set', NULL) ... 301s > randomSeed("set", seed=NULL) 301s > seed4 <- randomSeed("get") 301s > stopifnot(is.null(seed4)) 301s > 301s > y3 <- sample1() 301s > message(sprintf("Random number: %d", y3)) 301s Random number: 5 301s > 301s > message("*** randomSeed('set', NULL) ... done") 301s *** randomSeed('set', NULL) ... done 301s > 301s > 301s > message("*** randomSeed('set', 42L) again ...") 301s *** randomSeed('set', 42L) again ... 301s > seed5 <- randomSeed("get") 301s > randomSeed("set", seed=42L) 301s > y4 <- sample1() 301s > message(sprintf("Random number: %d (with random seed = 42L)", y4)) 301s Random number: 0 (with random seed = 42L) 301s > stopifnot(identical(y4, y2)) 301s > 301s > randomSeed("reset") 301s > stopifnot(identical(RNGkind()[1L], okind0), 301s + identical(randomSeed("get"), seed5)) 301s > message("*** randomSeed('set', 42L) again ... done") 301s *** randomSeed('set', 42L) again ... done 301s > 301s > 301s > 301s > ## L'Ecuyer-CMRG: Random number generation for parallel processing 301s > message("*** randomSeed(): L'Ecuyer-CMRG stream ...") 301s *** randomSeed(): L'Ecuyer-CMRG stream ... 301s > 301s > okind <- RNGkind()[1L] 301s > stopifnot(identical(okind, okind0)) 301s > 301s > randomSeed("set", seed=NULL) 301s > oseed <- randomSeed("get") 301s > stopifnot(is.null(oseed)) 301s > 301s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 301s > oseed2 <- randomSeed("reset") 301s > str(oseed2) 301s NULL 301s > stopifnot(identical(oseed2, oseed)) 301s > stopifnot(identical(RNGkind()[1L], okind), 301s + identical(randomSeed("get"), oseed)) 301s > 301s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 301s > seed0 <- randomSeed("get") 301s > seeds0 <- lapply(1:10, FUN=function(i) randomSeed("advance")) 301s > oseed2 <- randomSeed("reset") 301s > stopifnot(identical(oseed2, oseed)) 301s > stopifnot(identical(RNGkind()[1L], okind), 301s + identical(randomSeed("get"), oseed)) 301s > 301s > 301s > ## Assert reproducible .Random.seed stream 301s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 301s > seed1 <- randomSeed("get") 301s > seeds1 <- lapply(1:10, FUN=function(i) randomSeed("advance")) 301s > stopifnot(identical(seed1, seed0)) 301s > stopifnot(identical(seeds1, seeds0)) 301s > 301s > randomSeed("reset") 301s > stopifnot(identical(RNGkind()[1L], okind), 301s + identical(randomSeed("get"), oseed)) 301s > 301s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 301s > seeds2 <- randomSeed("advance", n=10L) 301s > stopifnot(identical(seeds2, seeds0)) 301s > 301s > randomSeed("reset") 301s > stopifnot(identical(RNGkind()[1L], okind), 301s + identical(randomSeed("get"), oseed)) 301s > 301s > randomSeed("set", seed=seeds2[[1]], kind="L'Ecuyer-CMRG") 301s > randomSeed("reset") 301s > stopifnot(identical(RNGkind()[1L], okind), 301s + identical(randomSeed("get"), oseed)) 301s > 301s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 301s > y0 <- sapply(1:10, FUN=function(ii) { 301s + randomSeed("advance") 301s + sample1() 301s + }) 301s > print(y0) 301s [1] 6 9 6 9 9 9 0 7 6 5 301s > randomSeed("reset") 301s > 301s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 301s > y1 <- sapply(1:10, FUN=function(ii) { 301s + randomSeed("advance") 301s + sample1() 301s + }) 301s > print(y1) 301s [1] 6 9 6 9 9 9 0 7 6 5 301s > stopifnot(identical(y1, y0)) 301s > randomSeed("reset") 301s > 301s > stopifnot(identical(RNGkind()[1L], okind)) 301s > 301s > message("*** randomSeed(): L'Ecuyer-CMRG stream ... done") 301s *** randomSeed(): L'Ecuyer-CMRG stream ... done 301s > 301s > 301s > ## Cleanup 301s > message("*** randomSeed() - cleanup ...") 301s *** randomSeed() - cleanup ... 301s > genv <- globalenv() 301s > RNGkind("Mersenne-Twister") 301s > if (exists(".Random.seed", envir=genv, inherits=FALSE)) 301s + rm(list=".Random.seed", envir=genv, inherits=FALSE) 301s > rm(list=ovars, envir=globalenv()) 301s > message("*** randomSeed() - cleanup ... done") 301s *** randomSeed() - cleanup ... done 301s > 301s > proc.time() 301s user system elapsed 301s 0.457 0.037 0.478 301s Test randomSeed passed 301s 0 301s Begin test segmentByCBS,calls 301s + [ 0 != 0 ] 301s + echo Test randomSeed passed 301s + echo 0 301s + echo Begin test segmentByCBS,calls 301s + exitcode=0 301s + R CMD BATCH segmentByCBS,calls.R 302s + cat segmentByCBS,calls.Rout 302s + [ 0 != 0 ] 302s + echo Test segmentByCBS,calls passed 302s + echo 0 302s + echo Begin test segmentByCBS,median 302s + exitcode=0 302s + R CMD BATCH segmentByCBS,median.R 302s 302s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 302s Copyright (C) 2024 The R Foundation for Statistical Computing 302s Platform: arm-unknown-linux-gnueabihf (32-bit) 302s 302s R is free software and comes with ABSOLUTELY NO WARRANTY. 302s You are welcome to redistribute it under certain conditions. 302s Type 'license()' or 'licence()' for distribution details. 302s 302s R is a collaborative project with many contributors. 302s Type 'contributors()' for more information and 302s 'citation()' on how to cite R or R packages in publications. 302s 302s Type 'demo()' for some demos, 'help()' for on-line help, or 302s 'help.start()' for an HTML browser interface to help. 302s Type 'q()' to quit R. 302s 302s [Previously saved workspace restored] 302s 302s > # This test script calls a report generator which requires 302s > # the 'ggplot2' package, which in turn will require packages 302s > # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'. 302s > 302s > # Only run this test in full testing mode 302s > if (Sys.getenv("_R_CHECK_FULL_") != "") { 302s + library("PSCBS") 302s + stext <- R.utils::stext 302s + 302s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 302s + # Load SNP microarray data 302s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 302s + data <- PSCBS::exampleData("paired.chr01") 302s + str(data) 302s + 302s + data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT) 302s + 302s + 302s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 302s + # CBS segmentation 302s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 302s + # Drop single-locus outliers 302s + dataS <- dropSegmentationOutliers(data) 302s + 302s + # Speed up example by segmenting fewer loci 302s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 302s + 302s + str(dataS) 302s + 302s + gaps <- findLargeGaps(dataS, minLength=2e6) 302s + knownSegments <- gapsToSegments(gaps) 302s + 302s + # CBS segmentation 302s + fit <- segmentByCBS(dataS, knownSegments=knownSegments, 302s + seed=0xBEEF, verbose=-10) 302s + signalType(fit) <- "ratio" 302s + plotTracks(fit) 302s + 302s + 302s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 302s + # Call using the UCSF MAD caller (not recommended) 302s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 302s + fitC <- callGainsAndLosses(fit) 302s + plotTracks(fitC) 302s + pars <- fitC$params$callGainsAndLosses 302s + stext(side=3, pos=1/2, line=-1, substitute(sigma==x, list(x=sprintf("%.2f", pars$sigmaMAD)))) 302s + mu <- pars$muR 302s + tau <- unlist(pars[c("tauLoss", "tauGain")], use.names=FALSE) 302s + abline(h=mu, lty=2, lwd=2) 302s + abline(h=tau, lwd=2) 302s + mtext(side=4, at=tau[1], expression(Delta[LOSS]), adj=-0.2, cex=0.7, las=2, xpd=TRUE) 302s + mtext(side=4, at=tau[2], expression(Delta[GAIN]), adj=-0.2, cex=0.7, las=2, xpd=TRUE) 302s + title(main="CN caller: \"ucsf-mad\"") 302s + 302s + 302s + # Caller to be implemented 302s + deltaCN <- estimateDeltaCN(fit) 302s + tau <- mu + 1/2*c(-1,+1)*deltaCN 302s + abline(h=tau, lty=2, lwd=1, col="red") 302s + 302s + 302s + 302s + } # if (Sys.getenv("_R_CHECK_FULL_")) 302s > 302s > proc.time() 302s user system elapsed 302s 0.156 0.024 0.164 302s Test segmentByCBS,calls passed 302s 0 302s Begin test segmentByCBS,median 304s + cat segmentByCBS,median.Rout 304s + [ 0 != 0 ] 304s + echo Test segmentByCBS,median passed 304s + echo 0 304s + echo Begin test segmentByCBS,prune 304s + exitcode=0 304s + R CMD BATCH segmentByCBS,prune.R 304s 304s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 304s Copyright (C) 2024 The R Foundation for Statistical Computing 304s Platform: arm-unknown-linux-gnueabihf (32-bit) 304s 304s R is free software and comes with ABSOLUTELY NO WARRANTY. 304s You are welcome to redistribute it under certain conditions. 304s Type 'license()' or 'licence()' for distribution details. 304s 304s R is a collaborative project with many contributors. 304s Type 'contributors()' for more information and 304s 'citation()' on how to cite R or R packages in publications. 304s 304s Type 'demo()' for some demos, 'help()' for on-line help, or 304s 'help.start()' for an HTML browser interface to help. 304s Type 'q()' to quit R. 304s 304s [Previously saved workspace restored] 304s 304s > library("PSCBS") 304s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 304s 304s Attaching package: 'PSCBS' 304s 304s The following objects are masked from 'package:base': 304s 304s append, load 304s 304s > 304s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 304s > # Simulating copy-number data 304s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 304s > set.seed(0xBEEF) 304s > 304s > # Number of loci 304s > J <- 1000 304s > 304s > x <- sort(runif(J, max=J)) * 1e5 304s > 304s > mu <- double(J) 304s > mu[200:300] <- mu[200:300] + 1 304s > mu[350:400] <- NA # centromere 304s > mu[650:800] <- mu[650:800] - 1 304s > eps <- rnorm(J, sd=1/2) 304s > y <- mu + eps 304s > 304s > outliers <- seq(from=1L, to=J, length.out=0.2*J) 304s > y[outliers] <- y[outliers] + 1.5 304s > 304s > w <- rep(1.0, times=J) 304s > w[outliers] <- 0.01 304s > 304s > data <- data.frame(chromosome=1L, x=x, y=y) 304s > dataW <- cbind(data, w=w) 304s > 304s > 304s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 304s > # Single-chromosome segmentation 304s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 304s > par(mar=c(2,3,0.2,1)+0.1) 304s > # Segment without weights 304s > fit <- segmentByCBS(data) 304s > sampleName(fit) <- "CBS_Example" 304s > print(fit) 304s sampleName chromosome start end nbrOfLoci mean 304s 1 CBS_Example 1 136857.7 19138391 199 0.2712 304s 2 CBS_Example 1 19138391.4 28682180 101 1.2168 304s 3 CBS_Example 1 28682180.1 64690253 298 0.3027 304s 4 CBS_Example 1 64690253.3 80738828 151 -0.7101 304s 5 CBS_Example 1 80738828.3 99932904 200 0.3655 304s > plotTracks(fit) 304s Warning message: 304s In plotTracks.CBS(fit) : 304s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning. 304s > ## Highlight outliers (they pull up the mean levels) 304s > points(x[outliers]/1e6, y[outliers], col="purple") 304s > 304s > # Segment without weights but with median 304s > fitM <- segmentByCBS(data, avg="median") 304s > sampleName(fitM) <- "CBS_Example (median)" 304s > print(fitM) 304s sampleName chromosome start end nbrOfLoci mean 304s 1 CBS_Example (median) 1 136857.7 19138391 199 0.1203255 304s 2 CBS_Example (median) 1 19138391.4 28682180 101 0.9949202 304s 3 CBS_Example (median) 1 28682180.1 64690253 298 0.1471793 304s 4 CBS_Example (median) 1 64690253.3 80738828 151 -0.8770443 304s 5 CBS_Example (median) 1 80738828.3 99932904 200 0.2211061 304s > drawLevels(fitM, col="magenta", lty=3) 304s NULL 304s > 304s > # Segment with weights 304s > fitW <- segmentByCBS(dataW, avg="median") 304s > sampleName(fitW) <- "CBS_Example (weighted)" 304s > print(fitW) 304s sampleName chromosome start end nbrOfLoci mean 304s 1 CBS_Example (weighted) 1 136857.7 19138391 199 -0.02220950 304s 2 CBS_Example (weighted) 1 19138391.4 28682180 101 0.92421628 304s 3 CBS_Example (weighted) 1 28682180.1 64690253 298 -0.02364830 304s 4 CBS_Example (weighted) 1 64690253.3 80738828 151 -1.04750872 304s 5 CBS_Example (weighted) 1 80738828.3 99932904 200 0.08961195 304s > drawLevels(fitW, col="red") 304s NULL 304s > 304s > # Segment with weights and median 304s > fitWM <- segmentByCBS(dataW, avg="median") 304s > sampleName(fitWM) <- "CBS_Example (weighted median)" 304s > print(fitWM) 304s sampleName chromosome start end nbrOfLoci 304s 1 CBS_Example (weighted median) 1 136857.7 19138391 199 304s 2 CBS_Example (weighted median) 1 19138391.4 28682180 101 304s 3 CBS_Example (weighted median) 1 28682180.1 64690253 298 304s 4 CBS_Example (weighted median) 1 64690253.3 80738828 151 304s 5 CBS_Example (weighted median) 1 80738828.3 99932904 200 304s mean 304s 1 -0.02220950 304s 2 0.92421628 304s 3 -0.02364830 304s 4 -1.04750872 304s 5 0.08961195 304s > drawLevels(fitWM, col="orange", lty=3) 304s NULL 304s > 304s > legend("topright", bg="white", legend=c("outliers", "non-weighted CBS (mean)", "non-weighted CBS (median)", "weighted CBS (mean)", "weighted CBS (median)"), col=c("purple", "purple", "magenta", "red", "orange"), lwd=c(NA,3,3,3,3), lty=c(NA,1,3,1,3), pch=c(1,NA,NA,NA,NA)) 304s > 304s > ## Assert that weighted segment means are less biased 304s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 304s > cat("Segment mean differences:\n") 304s Segment mean differences: 304s > print(dmean) 304s [1] 0.2934095 0.2925837 0.3263483 0.3374087 0.2758881 304s > stopifnot(all(dmean > 0, na.rm=TRUE)) 304s > 304s > dmean <- getSegments(fitM)$mean - getSegments(fitWM)$mean 304s > cat("Segment median differences:\n") 304s Segment median differences: 304s > print(dmean) 304s [1] 0.14253502 0.07070392 0.17082758 0.17046439 0.13149418 304s > stopifnot(all(dmean > 0, na.rm=TRUE)) 304s > 304s > 304s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 304s > # Multi-chromosome segmentation 304s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 304s > data2 <- data 304s > data2$chromosome <- 2L 304s > data <- rbind(data, data2) 304s > dataW <- cbind(data, w=w) 304s > 304s > par(mar=c(2,3,0.2,1)+0.1) 304s > # Segment without weights 304s > fit <- segmentByCBS(data) 304s > sampleName(fit) <- "CBS_Example" 304s > print(fit) 304s sampleName chromosome start end nbrOfLoci mean 304s 1 CBS_Example 1 136857.7 19138391 199 0.2712 304s 2 CBS_Example 1 19138391.4 28682180 101 1.2168 304s 3 CBS_Example 1 28682180.1 64690253 298 0.3027 304s 4 CBS_Example 1 64690253.3 80738828 151 -0.7101 304s 5 CBS_Example 1 80738828.3 99932904 200 0.3655 304s 6 NA NA NA NA NA 304s 7 CBS_Example 2 136857.7 19138391 199 0.2712 304s 8 CBS_Example 2 19138391.4 28682180 101 1.2168 304s 9 CBS_Example 2 28682180.1 64690253 298 0.3027 304s 10 CBS_Example 2 64690253.3 80738828 151 -0.7101 304s 11 CBS_Example 2 80738828.3 99932904 200 0.3655 304s > plotTracks(fit, Clim=c(-3,3)) 304s > 304s > # Segment without weights but with median 304s > fitM <- segmentByCBS(data, avg="median") 304s > sampleName(fitM) <- "CBS_Example (median)" 304s > print(fitM) 304s sampleName chromosome start end nbrOfLoci mean 304s 1 CBS_Example (median) 1 136857.7 19138391 199 0.1203255 304s 2 CBS_Example (median) 1 19138391.4 28682180 101 0.9949202 304s 3 CBS_Example (median) 1 28682180.1 64690253 298 0.1471793 304s 4 CBS_Example (median) 1 64690253.3 80738828 151 -0.8770443 304s 5 CBS_Example (median) 1 80738828.3 99932904 200 0.2211061 304s 6 NA NA NA NA NA 304s 7 CBS_Example (median) 2 136857.7 19138391 199 0.1203255 304s 8 CBS_Example (median) 2 19138391.4 28682180 101 0.9949202 304s 9 CBS_Example (median) 2 28682180.1 64690253 298 0.1471793 304s 10 CBS_Example (median) 2 64690253.3 80738828 151 -0.8770443 304s 11 CBS_Example (median) 2 80738828.3 99932904 200 0.2211061 304s > drawLevels(fitM, col="magenta", lty=3) 304s NULL 304s > 304s > # Segment with weights 304s > fitW <- segmentByCBS(dataW, avg="median") 304s > sampleName(fitW) <- "CBS_Example (weighted)" 304s > print(fitW) 304s sampleName chromosome start end nbrOfLoci mean 304s 1 CBS_Example (weighted) 1 136857.7 19138391 199 -0.02220950 304s 2 CBS_Example (weighted) 1 19138391.4 28682180 101 0.92421628 304s 3 CBS_Example (weighted) 1 28682180.1 64690253 298 -0.02364830 304s 4 CBS_Example (weighted) 1 64690253.3 80738828 151 -1.04750872 304s 5 CBS_Example (weighted) 1 80738828.3 99932904 200 0.08961195 304s 6 NA NA NA NA NA 304s 7 CBS_Example (weighted) 2 136857.7 19138391 199 -0.02220950 304s 8 CBS_Example (weighted) 2 19138391.4 28682180 101 0.92421628 304s 9 CBS_Example (weighted) 2 28682180.1 64690253 298 -0.02364830 304s 10 CBS_Example (weighted) 2 64690253.3 80738828 151 -1.04750872 304s 11 CBS_Example (weighted) 2 80738828.3 99932904 200 0.08961195 304s > drawLevels(fitW, col="red") 304s NULL 304s > 304s > # Segment with weights and median 304s > fitWM <- segmentByCBS(dataW, avg="median") 304s > sampleName(fitWM) <- "CBS_Example (weighted median)" 304s > print(fitWM) 304s sampleName chromosome start end nbrOfLoci 304s 1 CBS_Example (weighted median) 1 136857.7 19138391 199 304s 2 CBS_Example (weighted median) 1 19138391.4 28682180 101 304s 3 CBS_Example (weighted median) 1 28682180.1 64690253 298 304s 4 CBS_Example (weighted median) 1 64690253.3 80738828 151 304s 5 CBS_Example (weighted median) 1 80738828.3 99932904 200 304s 6 NA NA NA NA 304s 7 CBS_Example (weighted median) 2 136857.7 19138391 199 304s 8 CBS_Example (weighted median) 2 19138391.4 28682180 101 304s 9 CBS_Example (weighted median) 2 28682180.1 64690253 298 304s 10 CBS_Example (weighted median) 2 64690253.3 80738828 151 304s 11 CBS_Example (weighted median) 2 80738828.3 99932904 200 304s mean 304s 1 -0.02220950 304s 2 0.92421628 304s 3 -0.02364830 304s 4 -1.04750872 304s 5 0.08961195 304s 6 NA 304s 7 -0.02220950 304s 8 0.92421628 304s 9 -0.02364830 304s 10 -1.04750872 304s 11 0.08961195 304s > drawLevels(fitWM, col="orange", lty=3) 304s NULL 304s > 304s > legend("topright", bg="white", legend=c("outliers", "non-weighted CBS (mean)", "non-weighted CBS (median)", "weighted CBS (mean)", "weighted CBS (median)"), col=c("purple", "purple", "magenta", "red", "orange"), lwd=c(NA,3,3,3,3), lty=c(NA,1,3,1,3), pch=c(1,NA,NA,NA,NA)) 304s > 304s > ## Assert that weighted segment means are less biased 304s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 304s > cat("Segment mean differences:\n") 304s Segment mean differences: 304s > print(dmean) 304s [1] 0.2934095 0.2925837 0.3263483 0.3374087 0.2758881 NA 0.2934095 304s [8] 0.2925837 0.3263483 0.3374087 0.2758881 304s > stopifnot(all(dmean > 0, na.rm=TRUE)) 304s > 304s > dmean <- getSegments(fitM)$mean - getSegments(fitWM)$mean 304s > cat("Segment median differences:\n") 304s Segment median differences: 304s > print(dmean) 304s [1] 0.14253502 0.07070392 0.17082758 0.17046439 0.13149418 NA 304s [7] 0.14253502 0.07070392 0.17082758 0.17046439 0.13149418 304s > stopifnot(all(dmean > 0, na.rm=TRUE)) 304s > 304s > proc.time() 304s user system elapsed 304s 1.739 0.066 1.813 304s Test segmentByCBS,median passed 304s 0 304s Begin test segmentByCBS,prune 305s + cat segmentByCBS,prune.Rout 305s + [ 0 != 0 ] 305s + echo Test segmentByCBS,prune passed 305s + echo 0 305s + echo Begin test segmentByCBS,report 305s + exitcode=0 305s + R CMD BATCH segmentByCBS,report.R 305s 305s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 305s Copyright (C) 2024 The R Foundation for Statistical Computing 305s Platform: arm-unknown-linux-gnueabihf (32-bit) 305s 305s R is free software and comes with ABSOLUTELY NO WARRANTY. 305s You are welcome to redistribute it under certain conditions. 305s Type 'license()' or 'licence()' for distribution details. 305s 305s R is a collaborative project with many contributors. 305s Type 'contributors()' for more information and 305s 'citation()' on how to cite R or R packages in publications. 305s 305s Type 'demo()' for some demos, 'help()' for on-line help, or 305s 'help.start()' for an HTML browser interface to help. 305s Type 'q()' to quit R. 305s 305s [Previously saved workspace restored] 305s 305s > library("PSCBS") 305s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 305s 305s Attaching package: 'PSCBS' 305s 305s The following objects are masked from 'package:base': 305s 305s append, load 305s 305s > 305s > ## Compare segments 305s > assertMatchingSegments <- function(fitM, fit) { 305s + chrs <- getChromosomes(fitM) 305s + segsM <- lapply(chrs, FUN=function(chr) { 305s + getSegments(extractChromosome(fitM, chr)) 305s + }) 305s + segs <- lapply(fit[chrs], FUN=getSegments) 305s + stopifnot(all.equal(segsM, segs, check.attributes=FALSE)) 305s + } 305s > 305s > ## Simulate data 305s > set.seed(0xBEEF) 305s > J <- 1000 305s > mu <- double(J) 305s > mu[200:300] <- mu[200:300] + 1 305s > mu[350:400] <- NA 305s > mu[650:800] <- mu[650:800] - 1 305s > eps <- rnorm(J, sd=1/2) 305s > y <- mu + eps 305s > x <- sort(runif(length(y), max=length(y))) * 1e5 305s > 305s > data <- list() 305s > for (chr in 1:2) { 305s + data[[chr]] <- data.frame(chromosome=chr, x=x, y=y) 305s + } 305s > data$M <- Reduce(rbind, data) 305s > 305s > ## Segment 305s > message("*** segmentByCBS()") 305s *** segmentByCBS() 305s > fit <- lapply(data, FUN=segmentByCBS) 305s > print(fit) 305s [[1]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 20774251 201 0.0164 305s 2 1 20774250.85 29320105 99 1.0474 305s 3 1 29320104.86 65874675 298 -0.0203 305s 4 1 65874675.06 81348129 151 -1.0813 305s 5 1 81348129.20 99910827 200 -0.0612 305s 305s [[2]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 2 55167.82 20774251 201 0.0164 305s 2 2 20774250.85 29320105 99 1.0474 305s 3 2 29320104.86 65874675 298 -0.0203 305s 4 2 65874675.06 81348129 151 -1.0813 305s 5 2 81348129.20 99910827 200 -0.0612 305s 305s $M 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 20774251 201 0.0164 305s 2 1 20774250.85 29320105 99 1.0474 305s 3 1 29320104.86 65874675 298 -0.0203 305s 4 1 65874675.06 81348129 151 -1.0813 305s 5 1 81348129.20 99910827 200 -0.0612 305s 6 NA NA NA NA NA 305s 7 2 55167.82 20774251 201 0.0164 305s 8 2 20774250.85 29320105 99 1.0474 305s 9 2 29320104.86 65874675 298 -0.0203 305s 10 2 65874675.06 81348129 151 -1.0813 305s 11 2 81348129.20 99910827 200 -0.0612 305s 305s > assertMatchingSegments(fit$M, fit) 305s > 305s > ## Join segments 305s > message("*** joinSegments()") 305s *** joinSegments() 305s > fitj <- lapply(fit, FUN=joinSegments) 305s > print(fitj) 305s [[1]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 20774251 201 0.0164 305s 2 1 20774250.85 29320105 99 1.0474 305s 3 1 29320104.86 65874675 298 -0.0203 305s 4 1 65874675.06 81348129 151 -1.0813 305s 5 1 81348129.20 99910827 200 -0.0612 305s 305s [[2]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 2 55167.82 20774251 201 0.0164 305s 2 2 20774250.85 29320105 99 1.0474 305s 3 2 29320104.86 65874675 298 -0.0203 305s 4 2 65874675.06 81348129 151 -1.0813 305s 5 2 81348129.20 99910827 200 -0.0612 305s 305s $M 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 20774251 201 0.0164 305s 2 1 20774250.85 29320105 99 1.0474 305s 3 1 29320104.86 65874675 298 -0.0203 305s 4 1 65874675.06 81348129 151 -1.0813 305s 5 1 81348129.20 99910827 200 -0.0612 305s 6 NA NA NA NA NA 305s 7 2 55167.82 20774251 201 0.0164 305s 8 2 20774250.85 29320105 99 1.0474 305s 9 2 29320104.86 65874675 298 -0.0203 305s 10 2 65874675.06 81348129 151 -1.0813 305s 11 2 81348129.20 99910827 200 -0.0612 305s 305s > assertMatchingSegments(fitj$M, fitj) 305s > 305s > ## Reset segments 305s > message("*** resetSegments()") 305s *** resetSegments() 305s > fitj <- lapply(fit, FUN=resetSegments) 305s > print(fitj) 305s [[1]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 20774251 201 0.0164 305s 2 1 20774250.85 29320105 99 1.0474 305s 3 1 29320104.86 65874675 298 -0.0203 305s 4 1 65874675.06 81348129 151 -1.0813 305s 5 1 81348129.20 99910827 200 -0.0612 305s 305s [[2]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 2 55167.82 20774251 201 0.0164 305s 2 2 20774250.85 29320105 99 1.0474 305s 3 2 29320104.86 65874675 298 -0.0203 305s 4 2 65874675.06 81348129 151 -1.0813 305s 5 2 81348129.20 99910827 200 -0.0612 305s 305s $M 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 20774251 201 0.0164 305s 2 1 20774250.85 29320105 99 1.0474 305s 3 1 29320104.86 65874675 298 -0.0203 305s 4 1 65874675.06 81348129 151 -1.0813 305s 5 1 81348129.20 99910827 200 -0.0612 305s 6 NA NA NA NA NA 305s 7 2 55167.82 20774251 201 0.0164 305s 8 2 20774250.85 29320105 99 1.0474 305s 9 2 29320104.86 65874675 298 -0.0203 305s 10 2 65874675.06 81348129 151 -1.0813 305s 11 2 81348129.20 99910827 200 -0.0612 305s 305s > assertMatchingSegments(fitj$M, fitj) 305s > 305s > ## Prune by SD undo 305s > message("*** pruneBySdUndo()") 305s *** pruneBySdUndo() 305s > fitp <- lapply(fit, FUN=pruneBySdUndo) 305s > print(fitp) 305s [[1]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 99910827 949 -0.07857059 305s 305s [[2]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 2 55167.82 99910827 949 -0.07857059 305s 305s $M 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 99910827 949 -0.07857059 305s 2 NA NA NA NA NA 305s 3 2 55167.82 99910827 949 -0.07857059 305s 305s > assertMatchingSegments(fitp$M, fitp) 305s > 305s > ## Prune by hierarchical clustering 305s > message("*** pruneByHClust()") 305s *** pruneByHClust() 305s > fitp <- lapply(fit, FUN=pruneByHClust, k=1L) 305s > print(fitp) 305s [[1]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 99910827 949 -0.07857059 305s 305s [[2]] 305s sampleName chromosome start end nbrOfLoci mean 305s 1 2 55167.82 99910827 949 -0.07857059 305s 305s $M 305s sampleName chromosome start end nbrOfLoci mean 305s 1 1 55167.82 99910827 949 -0.07857059 305s 6 NA NA NA NA NA 305s 7 2 55167.82 99910827 949 -0.07857059 305s 305s > assertMatchingSegments(fitp$M, fitp) 305s > 305s > proc.time() 305s user system elapsed 305s 1.267 0.051 1.321 305s Test segmentByCBS,prune passed 305s 0 305s Begin test segmentByCBS,report 305s + cat segmentByCBS,report.Rout 305s + [ 0 != 0 ] 305s + echo Test segmentByCBS,report passed 305s + echo 0 305s + echo Begin test segmentByCBS,shiftTCN 305s + exitcode=0 305s + R CMD BATCH segmentByCBS,shiftTCN.R 305s 305s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 305s Copyright (C) 2024 The R Foundation for Statistical Computing 305s Platform: arm-unknown-linux-gnueabihf (32-bit) 305s 305s R is free software and comes with ABSOLUTELY NO WARRANTY. 305s You are welcome to redistribute it under certain conditions. 305s Type 'license()' or 'licence()' for distribution details. 305s 305s R is a collaborative project with many contributors. 305s Type 'contributors()' for more information and 305s 'citation()' on how to cite R or R packages in publications. 305s 305s Type 'demo()' for some demos, 'help()' for on-line help, or 305s 'help.start()' for an HTML browser interface to help. 305s Type 'q()' to quit R. 305s 305s [Previously saved workspace restored] 305s 305s > # This test script calls a report generator which requires 305s > # the 'ggplot2' package, which in turn will require packages 305s > # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'. 305s > 305s > # Only run this test in full testing mode 305s > if (Sys.getenv("_R_CHECK_FULL_") != "") { 305s + library("PSCBS") 305s + 305s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 305s + # Load SNP microarray data 305s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 305s + data <- PSCBS::exampleData("paired.chr01") 305s + str(data) 305s + 305s + data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT) 305s + 305s + 305s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 305s + # CBS segmentation 305s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 305s + # Drop single-locus outliers 305s + dataS <- dropSegmentationOutliers(data) 305s + 305s + # Speed up example by segmenting fewer loci 305s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 305s + 305s + str(dataS) 305s + 305s + gaps <- findLargeGaps(dataS, minLength=2e6) 305s + knownSegments <- gapsToSegments(gaps) 305s + 305s + # CBS segmentation 305s + fit <- segmentByCBS(dataS, knownSegments=knownSegments, 305s + seed=0xBEEF, verbose=-10) 305s + signalType(fit) <- "ratio" 305s + 305s + # Fake a multi-chromosome segmentation 305s + fit1 <- fit 305s + fit2 <- renameChromosomes(fit, from=1, to=2) 305s + fit <- c(fit1, fit2) 305s + 305s + report(fit, sampleName="CBS", studyName="CBS-Ex", verbose=-10) 305s + 305s + } # if (Sys.getenv("_R_CHECK_FULL_")) 305s > 305s > proc.time() 305s user system elapsed 305s 0.147 0.028 0.163 305s Test segmentByCBS,report passed 305s 0 305s Begin test segmentByCBS,shiftTCN 314s + cat segmentByCBS,shiftTCN.Rout 314s + [ 0 != 0 ] 314s + echo Test segmentByCBS,shiftTCN passed 314s + echo 0 314s + echo Begin test segmentByCBS,weights 314s + exitcode=0 314s + R CMD BATCH segmentByCBS,weights.R 314s 314s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 314s Copyright (C) 2024 The R Foundation for Statistical Computing 314s Platform: arm-unknown-linux-gnueabihf (32-bit) 314s 314s R is free software and comes with ABSOLUTELY NO WARRANTY. 314s You are welcome to redistribute it under certain conditions. 314s Type 'license()' or 'licence()' for distribution details. 314s 314s R is a collaborative project with many contributors. 314s Type 'contributors()' for more information and 314s 'citation()' on how to cite R or R packages in publications. 314s 314s Type 'demo()' for some demos, 'help()' for on-line help, or 314s 'help.start()' for an HTML browser interface to help. 314s Type 'q()' to quit R. 314s 314s [Previously saved workspace restored] 314s 314s > library("PSCBS") 314s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 314s 314s Attaching package: 'PSCBS' 314s 314s The following objects are masked from 'package:base': 314s 314s append, load 314s 314s > subplots <- R.utils::subplots 314s > 314s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 314s > # Simulating copy-number data 314s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 314s > set.seed(0xBEEF) 314s > 314s > # Number of loci 314s > J <- 1000 314s > 314s > mu <- double(J) 314s > eps <- rnorm(J, sd=1/2) 314s > y <- mu + eps 314s > x <- sort(runif(length(y), max=length(y))) 314s > 314s > idxs <- which(200 <= x & x < 300) 314s > y[idxs] <- y[idxs] + 1 314s > idxs <- which(350 <= x & x < 400) 314s > y[idxs] <- NA # centromere 314s > x[idxs] <- NA # centromere 314s > idxs <- which(650 <= x & x < 800) 314s > y[idxs] <- y[idxs] - 1 314s > x <- x*1e5 314s > 314s > keep <- is.finite(x) 314s > x <- x[keep] 314s > y <- y[keep] 314s > 314s > data <- list() 314s > for (chr in 1:2) { 314s + data[[chr]] <- data.frame(chromosome=chr, y=y, x=x) 314s + } 314s > data <- Reduce(rbind, data) 314s > 314s > 314s > subplots(7, ncol=1) 314s > par(mar=c(1.7,1,0.2,1)+0.1) 314s > 314s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 314s > # Segmentation 314s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 314s > fit <- segmentByCBS(data) 314s > print(fit) 314s sampleName chromosome start end nbrOfLoci mean 314s 1 1 55167.82 20341782 195 0.0145 314s 2 1 20341781.95 29617861 108 1.0437 314s 3 1 29617861.37 64995303 299 -0.0208 314s 4 1 64995302.97 80042680 151 -1.0700 314s 5 1 80042679.86 99910827 211 -0.0568 314s 6 NA NA NA NA NA 314s 7 2 55167.82 20341782 195 0.0145 314s 8 2 20341781.95 29617861 108 1.0437 314s 9 2 29617861.37 64995303 299 -0.0208 314s 10 2 64995302.97 80042680 151 -1.0700 314s 11 2 80042679.86 99910827 211 -0.0568 314s > 314s > Clim <- c(-3,3) + c(0,10) 314s > plotTracks(fit, Clim=Clim) 314s > 314s > 314s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 314s > # Shifting every other chromosome 314s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 314s > fitList <- list() 314s > chrs <- getChromosomes(fit) 314s > for (kk in seq_along(chrs)) { 314s + chr <- chrs[kk] 314s + fitKK <- extractChromosome(fit, chr) 314s + if (kk %% 2 == 0) { 314s + fitKK <- shiftTCN(fitKK, shift=+10) 314s + } 314s + fitList[[kk]] <- fitKK 314s + } # for (kk ...) 314s > fitT <- do.call(c, fitList) 314s > # Sanity check 314s > stopifnot(nbrOfSegments(fitT) == nbrOfSegments(fit)) 314s > 314s > plotTracks(fitT, Clim=Clim) 314s > 314s > 314s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 314s > # Shifting every other known segment 314s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 314s > gaps <- findLargeGaps(data, minLength=40e5) 314s > knownSegments <- gapsToSegments(gaps, dropGaps=TRUE) 314s > fit <- segmentByCBS(data, knownSegments=knownSegments) 314s > 314s > subplots(2, ncol=1) 314s > plotTracks(fit, Clim=Clim) 314s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 314s > 314s > fitList <- list() 314s > for (kk in seq_len(nrow(knownSegments))) { 314s + seg <- knownSegments[kk,] 314s + start <- seg$start 314s + end <- seg$end 314s + fitKK <- extractChromosome(fit, seg$chromosome) 314s + segsKK <- getSegments(fitKK) 314s + idxStart <- min(which(segsKK$start >= start)) 314s + idxEnd <- max(which(segsKK$end <= end)) 314s + idxs <- idxStart:idxEnd 314s + fitKK <- extractSegments(fitKK, idxs) 314s + if (kk %% 2 == 0) { 314s + fitKK <- shiftTCN(fitKK, shift=+10) 314s + } 314s + fitList[[kk]] <- fitKK 314s + } # for (kk ...) 314s > fitT <- do.call(c, fitList) 314s > # Sanity check 314s > stopifnot(nbrOfSegments(fitT) == nbrOfSegments(fit)) 314s > 314s > plotTracks(fitT, Clim=Clim) 314s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 314s > 314s > 314s > segList <- seqOfSegmentsByDP(fit) 314s > K <- length(segList) 314s > subplots(K, ncol=2, byrow=FALSE) 314s > par(mar=c(2,1,1,1)) 314s > for (kk in 1:K) { 314s + knownSegments <- segList[[kk]] 314s + fitKK <- resegment(fit, knownSegments=knownSegments, undo=+Inf) 314s + plotTracks(fitKK, Clim=c(-3,3)) 314s + } # for (kk ...) 314s > 314s > proc.time() 314s user system elapsed 314s 8.603 0.121 8.743 314s Test segmentByCBS,shiftTCN passed 314s 0 314s Begin test segmentByCBS,weights 318s + cat segmentByCBS,weights.Rout 318s 318s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 318s Copyright (C) 2024 The R Foundation for Statistical Computing 318s Platform: arm-unknown-linux-gnueabihf (32-bit) 318s 318s R is free software and comes with ABSOLUTELY NO WARRANTY. 318s You are welcome to redistribute it under certain conditions. 318s Type 'license()' or 'licence()' for distribution details. 318s 318s R is a collaborative project with many contributors. 318s Type 'contributors()' for more information and 318s 'citation()' on how to cite R or R packages in publications. 318s 318s Type 'demo()' for some demos, 'help()' for on-line help, or 318s 'help.start()' for an HTML browser interface to help. 318s Type 'q()' to quit R. 318s 318s [Previously saved workspace restored] 318s 318s > library("PSCBS") 318s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 318s 318s Attaching package: 'PSCBS' 318s 318s The following objects are masked from 'package:base': 318s 318s append, load 318s 318s > 318s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 318s > # Simulating copy-number data 318s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 318s > set.seed(0xBEEF) 318s > 318s > # Number of loci 318s > J <- 1000 318s > 318s > x <- sort(runif(J, max=J)) * 1e5 318s > 318s > mu <- double(J) 318s > mu[200:300] <- mu[200:300] + 1 318s > mu[350:400] <- NA # centromere 318s > mu[650:800] <- mu[650:800] - 1 318s > eps <- rnorm(J, sd=1/2) 318s > y <- mu + eps 318s > 318s > outliers <- seq(from=1L, to=J, length.out=0.2*J) 318s > y[outliers] <- y[outliers] + 1.5 318s > 318s > w <- rep(1.0, times=J) 318s > w[outliers] <- 0.01 318s > 318s > data <- data.frame(chromosome=1L, x=x, y=y) 318s > dataW <- cbind(data, w=w) 318s > 318s > 318s > par(mar=c(2,3,0.2,1)+0.1) 318s > 318s > 318s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 318s > # Single-chromosome segmentation 318s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 318s > # Segment without weights 318s > fit <- segmentByCBS(data) 318s > sampleName(fit) <- "CBS_Example" 318s > print(fit) 318s sampleName chromosome start end nbrOfLoci mean 318s 1 CBS_Example 1 136857.7 19138391 199 0.2712 318s 2 CBS_Example 1 19138391.4 28682180 101 1.2168 318s 3 CBS_Example 1 28682180.1 64690253 298 0.3027 318s 4 CBS_Example 1 64690253.3 80738828 151 -0.7101 318s 5 CBS_Example 1 80738828.3 99932904 200 0.3655 318s > plotTracks(fit) 318s Warning message: 318s In plotTracks.CBS(fit) : 318s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning. 318s > ## Highlight outliers (they pull up the mean levels) 318s > points(x[outliers]/1e6, y[outliers], col="purple") 318s > 318s > # Segment with weights 318s > fitW <- segmentByCBS(dataW) 318s > sampleName(fitW) <- "CBS_Example (weighted)" 318s > print(fitW) 318s sampleName chromosome start end nbrOfLoci mean 318s 1 CBS_Example (weighted) 1 136857.7 19138391 199 -0.0041 318s 2 CBS_Example (weighted) 1 19138391.4 28682180 101 0.8987 318s 3 CBS_Example (weighted) 1 28682180.1 64690253 298 0.0159 318s 4 CBS_Example (weighted) 1 64690253.3 80738828 151 -1.0215 318s 5 CBS_Example (weighted) 1 80738828.3 99932904 200 0.0653 318s > drawLevels(fitW, col="red") 318s NULL 318s > 318s > legend("topright", bg="white", legend=c("outliers", "non-weighted CBS", "weighted CBS"), col=c("purple", "purple", "red"), lwd=c(NA,3,3), pch=c(1,NA,NA)) 318s > 318s > ## Assert that weighted segment means are less biased 318s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 318s > cat("Segment mean differences:\n") 318s Segment mean differences: 318s > print(dmean) 318s [1] 0.2753 0.3181 0.2868 0.3114 0.3002 318s > stopifnot(all(dmean > 0, na.rm=TRUE)) 318s > 318s > 318s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 318s > # Segmentation with some known change points 318s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 318s > knownSegments <- data.frame( 318s + chromosome=c( 1, 1), 318s + start =x[c( 1, 401)], 318s + end =x[c(349, J)] 318s + ) 318s > fit2 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 318s Segmenting by CBS... 318s Chromosome: 1 318s Segmenting by CBS...done 318s > sampleName(fit2) <- "CBS_Example_2 (weighted)" 318s > print(fit2) 318s sampleName chromosom+ [ 0 != 0 ] 318s + echo Test segmentByCBS,weights passed 318s + echo 0 318s + echo Begin test segmentByCBS 318s + exitcode=0 318s + R CMD BATCH segmentByCBS.R 318s e start end nbrOfLoci mean 318s 1 CBS_Example_2 (weighted) 1 136857.7 19138391 199 -0.0041 318s 2 CBS_Example_2 (weighted) 1 19138391.4 28682180 101 0.8987 318s 3 CBS_Example_2 (weighted) 1 28682180.1 34062461 49 -0.0552 318s 4 CBS_Example_2 (weighted) 1 38343432.8 64690253 249 0.0298 318s 5 CBS_Example_2 (weighted) 1 64690253.3 80738828 151 -1.0215 318s 6 CBS_Example_2 (weighted) 1 80738828.3 99932904 200 0.0653 318s > plotTracks(fit2) 318s Warning message: 318s In plotTracks.CBS(fit2) : 318s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2) is unknown ('NA'). Use signalType(fit2) <- 'ratio' to avoid this warning. 318s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 318s > 318s > 318s > # Chromosome boundaries can be specified as -Inf and +Inf 318s > knownSegments <- data.frame( 318s + chromosome=c( 1, 1), 318s + start =c( -Inf, x[401]), 318s + end =c(x[349], +Inf) 318s + ) 318s > fit2b <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 318s Segmenting by CBS... 318s Chromosome: 1 318s Segmenting by CBS...done 318s > sampleName(fit2b) <- "CBS_Example_2b (weighted)" 318s > print(fit2b) 318s sampleName chromosome start end nbrOfLoci mean 318s 1 CBS_Example_2b (weighted) 1 136857.7 19138391 199 -0.0041 318s 2 CBS_Example_2b (weighted) 1 19138391.4 28682180 101 0.8987 318s 3 CBS_Example_2b (weighted) 1 28682180.1 34062461 49 -0.0552 318s 4 CBS_Example_2b (weighted) 1 38343432.8 64690253 249 0.0298 318s 5 CBS_Example_2b (weighted) 1 64690253.3 80738828 151 -1.0215 318s 6 CBS_Example_2b (weighted) 1 80738828.3 99932904 200 0.0653 318s > plotTracks(fit2b) 318s Warning message: 318s In plotTracks.CBS(fit2b) : 318s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2b) is unknown ('NA'). Use signalType(fit2b) <- 'ratio' to avoid this warning. 318s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 318s > 318s > 318s > # As a proof of concept, it is possible to segment just the centromere, 318s > # which contains no data. All statistics will be NAs. 318s > knownSegments <- data.frame( 318s + chromosome=c( 1), 318s + start =x[c(350)], 318s + end =x[c(400)] 318s + ) 318s > fit3 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 318s Segmenting by CBS... 318s Chromosome: 1 318s Segmenting by CBS...done 318s > sampleName(fit3) <- "CBS_Example_3" 318s > print(fit3) 318s sampleName chromosome start end nbrOfLoci mean 318s 1 CBS_Example_3 1 34108010 38257409 0 NA 318s > plotTracks(fit3, Clim=c(0,5), xlim=c(0,100)) 318s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 318s > 318s > 318s > # If one specify the (empty) centromere as a segment, then its 318s > # estimated statistics will be NAs, which becomes a natural 318s > # separator between the two "independent" arms. 318s > knownSegments <- data.frame( 318s + chromosome=c( 1, 1, 1), 318s + start =x[c( 1, 350, 401)], 318s + end =x[c(349, 400, J)] 318s + ) 318s > fit4 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 318s Segmenting by CBS... 318s Chromosome: 1 318s Segmenting by CBS...done 318s > sampleName(fit4) <- "CBS_Example_4" 318s > print(fit4) 318s sampleName chromosome start end nbrOfLoci mean 318s 1 CBS_Example_4 1 136857.7 19138391 199 -0.0041 318s 2 CBS_Example_4 1 19138391.4 28682180 101 0.8987 318s 3 CBS_Example_4 1 28682180.1 34062461 49 -0.0552 318s 4 CBS_Example_4 1 34108009.8 38257409 0 NA 318s 5 CBS_Example_4 1 38343432.8 64690253 249 0.0298 318s 6 CBS_Example_4 1 64690253.3 80738828 151 -1.0215 318s 7 CBS_Example_4 1 80738828.3 99932904 200 0.0653 318s > plotTracks(fit4) 318s Warning message: 318s In plotTracks.CBS(fit4) : 318s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit4) is unknown ('NA'). Use signalType(fit4) <- 'ratio' to avoid this warning. 318s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 318s > 318s > 318s > fit5 <- segmentByCBS(dataW, knownSegments=knownSegments, undo=Inf, verbose=TRUE) 318s Segmenting by CBS... 318s Chromosome: 1 318s Segmenting by CBS...done 318s > sampleName(fit5) <- "CBS_Example_5" 318s > print(fit5) 318s sampleName chromosome start end nbrOfLoci mean 318s 1 CBS_Example_5 1 136857.7 34062461 349 0.54781248 318s 2 CBS_Example_5 1 34108009.8 38257409 0 NA 318s 3 CBS_Example_5 1 38343432.8 99932904 600 0.06959745 318s > plotTracks(fit5) 318s Warning message: 318s In plotTracks.CBS(fit5) : 318s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit5) is unknown ('NA'). Use signalType(fit5) <- 'ratio' to avoid this warning. 318s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 318s > stopifnot(nbrOfSegments(fit5) == nrow(knownSegments)) 318s > 318s > 318s > # One can also force a separator between two segments by setting 318s > # 'start' and 'end' to NAs ('chromosome' has to be given) 318s > knownSegments <- data.frame( 318s + chromosome=c( 1, 1, 1), 318s + start =x[c( 1, NA, 401)], 318s + end =x[c(349, NA, J)] 318s + ) 318s > fit6 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 318s Segmenting by CBS... 318s Chromosome: 1 318s Segmenting by CBS...done 318s > sampleName(fit6) <- "CBS_Example_6" 318s > print(fit6) 318s sampleName chromosome start end nbrOfLoci mean 318s 1 CBS_Example_6 1 136857.7 19138391 199 -0.0041 318s 2 CBS_Example_6 1 19138391.4 28682180 101 0.8987 318s 3 CBS_Example_6 1 28682180.1 34062461 49 -0.0552 318s 4 NA NA NA NA NA 318s 5 CBS_Example_6 1 38343432.8 64690253 249 0.0298 318s 6 CBS_Example_6 1 64690253.3 80738828 151 -1.0215 318s 7 CBS_Example_6 1 80738828.3 99932904 200 0.0653 318s > plotTracks(fit6) 318s Warning message: 318s In plotTracks.CBS(fit6) : 318s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit6) is unknown ('NA'). Use signalType(fit6) <- 'ratio' to avoid this warning. 318s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 318s > 318s > 318s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 318s > # Multi-chromosome segmentation 318s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 318s > data2 <- data 318s > data2$chromosome <- 2L 318s > data <- rbind(data, data2) 318s > dataW <- cbind(data, w=w) 318s > 318s > par(mar=c(2,3,0.2,1)+0.1) 318s > # Segment without weights 318s > fit <- segmentByCBS(data) 318s > sampleName(fit) <- "CBS_Example" 318s > print(fit) 318s sampleName chromosome start end nbrOfLoci mean 318s 1 CBS_Example 1 136857.7 19138391 199 0.2712 318s 2 CBS_Example 1 19138391.4 28682180 101 1.2168 318s 3 CBS_Example 1 28682180.1 64690253 298 0.3027 318s 4 CBS_Example 1 64690253.3 80738828 151 -0.7101 318s 5 CBS_Example 1 80738828.3 99932904 200 0.3655 318s 6 NA NA NA NA NA 318s 7 CBS_Example 2 136857.7 19138391 199 0.2712 318s 8 CBS_Example 2 19138391.4 28682180 101 1.2168 318s 9 CBS_Example 2 28682180.1 64690253 298 0.3027 318s 10 CBS_Example 2 64690253.3 80738828 151 -0.7101 318s 11 CBS_Example 2 80738828.3 99932904 200 0.3655 318s > plotTracks(fit, Clim=c(-3,3)) 318s > 318s > # Segment with weights 318s > fitW <- segmentByCBS(dataW) 318s > sampleName(fitW) <- "CBS_Example (weighted)" 318s > print(fitW) 318s sampleName chromosome start end nbrOfLoci mean 318s 1 CBS_Example (weighted) 1 136857.7 19138391 199 -0.0041 318s 2 CBS_Example (weighted) 1 19138391.4 28682180 101 0.8987 318s 3 CBS_Example (weighted) 1 28682180.1 64690253 298 0.0159 318s 4 CBS_Example (weighted) 1 64690253.3 80738828 151 -1.0215 318s 5 CBS_Example (weighted) 1 80738828.3 99932904 200 0.0653 318s 6 NA NA NA NA NA 318s 7 CBS_Example (weighted) 2 136857.7 19138391 199 -0.0041 318s 8 CBS_Example (weighted) 2 19138391.4 28682180 101 0.8987 318s 9 CBS_Example (weighted) 2 28682180.1 64690253 298 0.0159 318s 10 CBS_Example (weighted) 2 64690253.3 80738828 151 -1.0215 318s 11 CBS_Example (weighted) 2 80738828.3 99932904 200 0.0653 318s > drawLevels(fitW, col="red") 318s NULL 318s > 318s > legend("topright", bg="white", legend=c("outliers", "non-weighted CBS", "weighted CBS"), col=c("purple", "purple", "red"), lwd=c(NA,3,3), pch=c(1,NA,NA)) 318s > 318s > ## Assert that weighted segment means are less biased 318s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 318s > cat("Segment mean differences:\n") 318s Segment mean differences: 318s > print(dmean) 318s [1] 0.2753 0.3181 0.2868 0.3114 0.3002 NA 0.2753 0.3181 0.2868 0.3114 318s [11] 0.3002 318s > stopifnot(all(dmean > 0, na.rm=TRUE)) 318s > 318s > proc.time() 318s user system elapsed 318s 2.999 0.089 3.075 318s Test segmentByCBS,weights passed 318s 0 318s Begin test segmentByCBS 322s + cat segmentByCBS.Rout 322s + [ 0 != 0 ] 322s + echo Test segmentByCBS passed 322s + echo 0 322s + echo Begin test segmentByNonPairedPSCBS,medianDH 322s + exitcode=0 322s + R CMD BATCH segmentByNonPairedPSCBS,medianDH.R 322s 322s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 322s Copyright (C) 2024 The R Foundation for Statistical Computing 322s Platform: arm-unknown-linux-gnueabihf (32-bit) 322s 322s R is free software and comes with ABSOLUTELY NO WARRANTY. 322s You are welcome to redistribute it under certain conditions. 322s Type 'license()' or 'licence()' for distribution details. 322s 322s R is a collaborative project with many contributors. 322s Type 'contributors()' for more information and 322s 'citation()' on how to cite R or R packages in publications. 322s 322s Type 'demo()' for some demos, 'help()' for on-line help, or 322s 'help.start()' for an HTML browser interface to help. 322s Type 'q()' to quit R. 322s 322s [Previously saved workspace restored] 322s 322s > ########################################################### 322s > # This tests: 322s > # - segmentByCBS(...) 322s > # - segmentByCBS(..., knownSegments) 322s > # - tileChromosomes() 322s > # - plotTracks() 322s > ########################################################### 322s > library("PSCBS") 322s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 322s 322s Attaching package: 'PSCBS' 322s 322s The following objects are masked from 'package:base': 322s 322s append, load 322s 322s > subplots <- R.utils::subplots 322s > 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > # Simulating copy-number data 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > set.seed(0xBEEF) 322s > 322s > # Number of loci 322s > J <- 1000 322s > 322s > mu <- double(J) 322s > mu[200:300] <- mu[200:300] + 1 322s > mu[350:400] <- NA # centromere 322s > mu[650:800] <- mu[650:800] - 1 322s > eps <- rnorm(J, sd=1/2) 322s > y <- mu + eps 322s > x <- sort(runif(length(y), max=length(y))) * 1e5 322s > w <- runif(J) 322s > w[650:800] <- 0.001 322s > 322s > 322s > subplots(8, ncol=1L) 322s > par(mar=c(1.7,1,0.2,1)+0.1) 322s > 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > # Segmentation 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > fit <- segmentByCBS(y, x=x) 322s > sampleName(fit) <- "CBS_Example" 322s > print(fit) 322s sampleName chromosome start end nbrOfLoci mean 322s 1 CBS_Example 0 55167.82 20774251 201 0.0164 322s 2 CBS_Example 0 20774250.85 29320105 99 1.0474 322s 3 CBS_Example 0 29320104.86 65874675 298 -0.0203 322s 4 CBS_Example 0 65874675.06 81348129 151 -1.0813 322s 5 CBS_Example 0 81348129.20 99910827 200 -0.0612 322s > plotTracks(fit) 322s Warning message: 322s In plotTracks.CBS(fit) : 322s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning. 322s > 322s > 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > # Segmentation with some known change points 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > knownSegments <- data.frame( 322s + chromosome=c( 0, 0), 322s + start =x[c( 1, 401)], 322s + end =x[c(349, J)] 322s + ) 322s > fit2 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 322s Segmenting by CBS... 322s Chromosome: 0 322s Segmenting by CBS...done 322s > sampleName(fit2) <- "CBS_Example_2" 322s > print(fit2) 322s sampleName chromosome start end nbrOfLoci mean 322s 1 CBS_Example_2 0 55167.82 20774251 201 0.0164 322s 2 CBS_Example_2 0 20774250.85 29320105 99 1.0474 322s 3 CBS_Example_2 0 29320104.86 34142178 49 -0.0193 322s 4 CBS_Example_2 0 41080532.92 65874675 249 -0.0205 322s 5 CBS_Example_2 0 65874675.06 81348129 151 -1.0813 322s 6 CBS_Example_2 0 81348129.20 99910827 200 -0.0612 322s > plotTracks(fit2) 322s Warning message: 322s In plotTracks.CBS(fit2) : 322s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2) is unknown ('NA'). Use signalType(fit2) <- 'ratio' to avoid this warning. 322s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 322s > 322s > 322s > # Chromosome boundaries can be specified as -Inf and +Inf 322s > knownSegments <- data.frame( 322s + chromosome=c( 0, 0), 322s + start =c( -Inf, x[401]), 322s + end =c(x[349], +Inf) 322s + ) 322s > fit2b <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 322s Segmenting by CBS... 322s Chromosome: 0 322s Segmenting by CBS...done 322s > sampleName(fit2b) <- "CBS_Example_2b" 322s > print(fit2b) 322s sampleName chromosome start end nbrOfLoci mean 322s 1 CBS_Example_2b 0 55167.82 20774251 201 0.0164 322s 2 CBS_Example_2b 0 20774250.85 29320105 99 1.0474 322s 3 CBS_Example_2b 0 29320104.86 34142178 49 -0.0193 322s 4 CBS_Example_2b 0 41080532.92 65874675 249 -0.0205 322s 5 CBS_Example_2b 0 65874675.06 81348129 151 -1.0813 322s 6 CBS_Example_2b 0 81348129.20 99910827 200 -0.0612 322s > plotTracks(fit2b) 322s Warning message: 322s In plotTracks.CBS(fit2b) : 322s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2b) is unknown ('NA'). Use signalType(fit2b) <- 'ratio' to avoid this warning. 322s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 322s > 322s > 322s > # As a proof of concept, it is possible to segment just the centromere, 322s > # which contains no data. All statistics will be NAs. 322s > knownSegments <- data.frame( 322s + chromosome=c( 0), 322s + start =x[c(350)], 322s + end =x[c(400)] 322s + ) 322s > fit3 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 322s Segmenting by CBS... 322s Chromosome: 0 322s Segmenting by CBS...done 322s > sampleName(fit3) <- "CBS_Example_3" 322s > print(fit3) 322s sampleName chromosome start end nbrOfLoci mean 322s 1 CBS_Example_3 0 34194740 41044125 0 NA 322s > plotTracks(fit3, Clim=c(0,5), xlim=c(0,100)) 322s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 322s > 322s > 322s > 322s > # If one specify the (empty) centromere as a segment, then its 322s > # estimated statistics will be NAs, which becomes a natural 322s > # separator between the two "independent" arms. 322s > knownSegments <- data.frame( 322s + chromosome=c( 0, 0, 0), 322s + start =x[c( 1, 350, 401)], 322s + end =x[c(349, 400, J)] 322s + ) 322s > fit4 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 322s Segmenting by CBS... 322s Chromosome: 0 322s Segmenting by CBS...done 322s > sampleName(fit4) <- "CBS_Example_4" 322s > print(fit4) 322s sampleName chromosome start end nbrOfLoci mean 322s 1 CBS_Example_4 0 55167.82 20774251 201 0.0164 322s 2 CBS_Example_4 0 20774250.85 29320105 99 1.0474 322s 3 CBS_Example_4 0 29320104.86 34142178 49 -0.0193 322s 4 CBS_Example_4 0 34194739.81 41044125 0 NA 322s 5 CBS_Example_4 0 41080532.92 65874675 249 -0.0205 322s 6 CBS_Example_4 0 65874675.06 81348129 151 -1.0813 322s 7 CBS_Example_4 0 81348129.20 99910827 200 -0.0612 322s > plotTracks(fit4) 322s Warning message: 322s In plotTracks.CBS(fit4) : 322s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit4) is unknown ('NA'). Use signalType(fit4) <- 'ratio' to avoid this warning. 322s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 322s > 322s > 322s > 322s > fit5 <- segmentByCBS(y, x=x, knownSegments=knownSegments, undo=Inf, verbose=TRUE) 322s Segmenting by CBS... 322s Chromosome: 0 322s Segmenting by CBS...done 322s > sampleName(fit5) <- "CBS_Example_5" 322s > print(fit5) 322s sampleName chromosome start end nbrOfLoci mean 322s 1 CBS_Example_5 0 55167.82 34142178 349 0.3038785 322s 2 CBS_Example_5 0 34194739.81 41044125 0 NA 322s 3 CBS_Example_5 0 41080532.92 99910827 600 -0.3010285 322s > plotTracks(fit5) 322s Warning message: 322s In plotTracks.CBS(fit5) : 322s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit5) is unknown ('NA'). Use signalType(fit5) <- 'ratio' to avoid this warning. 322s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 322s > stopifnot(nbrOfSegments(fit5) == nrow(knownSegments)) 322s > 322s > 322s > # One can also force a separator between two segments by setting 322s > # 'start' and 'end' to NAs ('chromosome' has to be given) 322s > knownSegments <- data.frame( 322s + chromosome=c( 0, 0, 0), 322s + start =x[c( 1, NA, 401)], 322s + end =x[c(349, NA, J)] 322s + ) 322s > fit6 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 322s Segmenting by CBS... 322s Chromosome: 0 322s Segmenting by CBS...done 322s > sampleName(fit6) <- "CBS_Example_6" 322s > print(fit6) 322s sampleName chromosome start end nbrOfLoci mean 322s 1 CBS_Example_6 0 55167.82 20774251 201 0.0164 322s 2 CBS_Example_6 0 20774250.85 29320105 99 1.0474 322s 3 CBS_Example_6 0 29320104.86 34142178 49 -0.0193 322s 4 NA NA NA NA NA 322s 5 CBS_Example_6 0 41080532.92 65874675 249 -0.0205 322s 6 CBS_Example_6 0 65874675.06 81348129 151 -1.0813 322s 7 CBS_Example_6 0 81348129.20 99910827 200 -0.0612 322s > plotTracks(fit6) 322s Warning message: 322s In plotTracks.CBS(fit6) : 322s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit6) is unknown ('NA'). Use signalType(fit6) <- 'ratio' to avoid this warning. 322s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 322s > 322s > 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > # Segment multiple chromosomes 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > # Simulate multiple chromosomes 322s > fit1 <- renameChromosomes(fit, from=0, to=1) 322s > fit2 <- renameChromosomes(fit, from=0, to=2) 322s > fitM <- c(fit1, fit2) 322s > fitM <- segmentByCBS(fitM) 322s > sampleName(fitM) <- "CBS_Example_M" 322s > print(fitM) 322s sampleName chromosome start end nbrOfLoci mean 322s 1 CBS_Example_M 1 55167.82 20774251 201 0.0164 322s 2 CBS_Example_M 1 20774250.85 29320105 99 1.0474 322s 3 CBS_Example_M 1 29320104.86 65874675 298 -0.0203 322s 4 CBS_Example_M 1 65874675.06 81348129 151 -1.0813 322s 5 CBS_Example_M 1 81348129.20 99910827 200 -0.0612 322s 6 NA NA NA NA NA 322s 7 CBS_Example_M 2 55167.82 20774251 201 0.0164 322s 8 CBS_Example_M 2 20774250.85 29320105 99 1.0474 322s 9 CBS_Example_M 2 29320104.86 65874675 298 -0.0203 322s 10 CBS_Example_M 2 65874675.06 81348129 151 -1.0813 322s 11 CBS_Example_M 2 81348129.20 99910827 200 -0.0612 322s > plotTracks(fitM, Clim=c(-3,3)) 322s > 322s > 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > # Tiling multiple chromosomes 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > # Tile chromosomes 322s > fitT <- tileChromosomes(fitM) 322s > fitTb <- tileChromosomes(fitT) 322s > stopifnot(identical(fitTb, fitT)) 322s > 322s > 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > # Write segmentation to file 322s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 322s > pathT <- tempdir() 322s > 322s > ## Tab-delimited file 322s > pathname <- writeSegments(fitM, path=pathT) 322s Warning message: 322s In write.table(file = pathnameT, data, append = TRUE, quote = FALSE, : 322s appending column names to file 322s > print(pathname) 322s [1] "/tmp/RtmpwdtbZG/CBS_Example_M.tsv" 322s > 322s > ## WIG file 322s > pathname <- writeWIG(fitM, path=pathT) 322s > print(pathname) 322s [1] "/tmp/RtmpwdtbZG/CBS_Example_M.wig" 322s > 322s > unlink(pathT, recursive=TRUE) 322s > 322s > proc.time() 322s user system elapsed 322s 3.100 0.556 3.303 322s Test segmentByCBS passed 322s 0 322s Begin test segmentByNonPairedPSCBS,medianDH 325s + cat segmentByNonPairedPSCBS,medianDH.Rout 325s 325s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 325s Copyright (C) 2024 The R Foundation for Statistical Computing 325s Platform: arm-unknown-linux-gnueabihf (32-bit) 325s 325s R is free software and comes with ABSOLUTELY NO WARRANTY. 325s You are welcome to redistribute it under certain conditions. 325s Type 'license()' or 'licence()' for distribution details. 325s 325s R is a collaborative project with many contributors. 325s Type 'contributors()' for more information and 325s 'citation()' on how to cite R or R packages in publications. 325s 325s Type 'demo()' for some demos, 'help()' for on-line help, or 325s 'help.start()' for an HTML browser interface to help. 325s Type 'q()' to quit R. 325s 325s [Previously saved workspace restored] 325s 325s > library("PSCBS") 325s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 325s 325s Attaching package: 'PSCBS' 325s 325s The following objects are masked from 'package:base': 325s 325s append, load 325s 325s > 325s > 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > # Load SNP microarray data 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > data <- PSCBS::exampleData("paired.chr01") 325s > str(data) 325s 'data.frame': 73346 obs. of 6 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 325s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 325s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 325s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 325s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 325s > 325s > # Non-paired / tumor-only data 325s > data <- data[,c("chromosome", "x", "CT", "betaT")] 325s > str(data) 325s 'data.frame': 73346 obs. of 4 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 325s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 325s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 325s > 325s > 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > # Paired PSCBS segmentation 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > # Drop single-locus outliers 325s > dataS <- dropSegmentationOutliers(data) 325s > 325s > # Speed up example by segmenting fewer loci 325s > dataS <- dataS[seq(from=1, to=nrow(data), by=20),] 325s > 325s > # Fake a second chromosome 325s > dataT <- dataS 325s > dataT$chromosome <- 2L 325s > dataS <- rbind(dataS, dataT) 325s > rm(dataT) 325s > str(dataS) 325s 'data.frame': 7336 obs. of 4 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : int 1145994 4276892 5034491 6266412 8418532 11211748 13928296 14370144 15014887 16589707 ... 325s $ CT : num 1.63 1.16 1.35 1.39 1.55 ... 325s $ betaT : num 0.7574 0.0576 0.8391 0.7917 0.8141 ... 325s > 325s > # Non-Paired PSCBS segmentation 325s > fit <- segmentByNonPairedPSCBS(dataS, avgDH="median", seed=0xBEEF, verbose=-10) 325s Segmenting non-paired tumor signals using Non-paired PSCBS... 325s Number of loci: 7336 325s Number of SNPs: 7336 325s Calling "genotypes" from tumor allele B fractions... 325s num [1:7336] 0.7574 0.0576 0.8391 0.7917 0.8141 ... 325s Upper quantile: 0.475631667925522 325s Symmetric lower quantile: 0.290517384533512 325s (tauA, tauB) estimates: (%g,%g)0.2094826154664880.790517384533512 325s Homozygous treshholds: 325s [1] 0.2094826 0.7905174 325s Inferred germline genotypes (via tumor): 325s num [1:7336] 0.5 0 1 1 1 0 0 0 0.5 1 ... 325s muNx 325s 0 0.5 1 325s 2230 2910 2196 325s Calling "genotypes" from tumor allele B fractions...done 325s Segmenting non-paired tumor signals using Non-paired PSCBS...done 325s Segment using Paired PSCBS... 325s Segmenting paired tumor-normal signals using Paired PSCBS... 325s Setup up data... 325s 'data.frame': 7336 obs. of 6 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : num 1145994 4276892 5034491 6266412 8418532 ... 325s $ CT : num 1.63 1.16 1.35 1.39 1.55 ... 325s $ betaT : num 0.7574 0.0576 0.8391 0.7917 0.8141 ... 325s $ betaTN : num 0.7574 0.0576 0.8391 0.7917 0.8141 ... 325s $ muN : num 0.5 0 1 1 1 0 0 0 0.5 1 ... 325s Setup up data...done 325s Dropping loci for which TCNs are missing... 325s Number of loci dropped: 12 325s Dropping loci for which TCN+ [ 0 != 0 ] 325s + echo Test segmentByNonPairedPSCBS,medianDH passed 325s + echo 0 325s + echo Begin test segmentByPairedPSCBS,DH 325s + exitcode=0 325s + R CMD BATCH segmentByPairedPSCBS,DH.R 325s s are missing...done 325s Ordering data along genome... 325s 'data.frame': 7324 obs. of 6 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : num 554484 1031563 1087198 1145994 1176365 ... 325s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 325s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s Ordering data along genome...done 325s Segmenting multiple chromosomes... 325s Number of chromosomes: 2 325s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 325s Produced 2 seeds from this stream for future usage 325s Chromosome #1 ('Chr01') of 2... 325s 'data.frame': 3662 obs. of 7 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : num 554484 1031563 1087198 1145994 1176365 ... 325s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 325s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 325s Known segments: 325s [1] chromosome start end 325s <0 rows> (or 0-length row.names) 325s Segmenting paired tumor-normal signals using Paired PSCBS... 325s Setup up data... 325s 'data.frame': 3662 obs. of 6 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : num 554484 1031563 1087198 1145994 1176365 ... 325s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 325s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s Setup up data...done 325s Ordering data along genome... 325s 'data.frame': 3662 obs. of 6 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : num 554484 1031563 1087198 1145994 1176365 ... 325s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 325s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s Ordering data along genome...done 325s Keeping only current chromosome for 'knownSegments'... 325s Chromosome: 1 325s Known segments for this chromosome: 325s [1] chromosome start end 325s <0 rows> (or 0-length row.names) 325s Keeping only current chromosome for 'knownSegments'...done 325s alphaTCN: 0.009 325s alphaDH: 0.001 325s Number of loci: 3662 325s Calculating DHs... 325s Number of SNPs: 3662 325s Number of heterozygous SNPs: 1451 (39.62%) 325s Normalized DHs: 325s num [1:3662] NA 0.216 0.198 0.515 0.29 ... 325s Calculating DHs...done 325s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 325s Produced 2 seeds from this stream for future usage 325s Identification of change points by total copy numbers... 325s Segmenting by CBS... 325s Chromosome: 1 325s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 325s Segmenting by CBS...done 325s List of 4 325s $ data :'data.frame': 3662 obs. of 4 variables: 325s ..$ chromosome: int [1:3662] 1 1 1 1 1 1 1 1 1 1 ... 325s ..$ x : num [1:3662] 554484 1031563 1087198 1145994 1176365 ... 325s ..$ y : num [1:3662] 1.88 1.64 1.77 1.63 1.59 ... 325s ..$ index : int [1:3662] 1 2 3 4 5 6 7 8 9 10 ... 325s $ output :'data.frame': 3 obs. of 6 variables: 325s ..$ sampleName: chr [1:3] NA NA NA 325s ..$ chromosome: int [1:3] 1 1 1 325s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 325s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 325s ..$ nbrOfLoci : int [1:3] 1880 671 1111 325s ..$ mean : num [1:3] 1.39 2.09 2.65 325s $ segRows:'data.frame': 3 obs. of 2 variables: 325s ..$ startRow: int [1:3] 1 1881 2552 325s ..$ endRow : int [1:3] 1880 2551 3662 325s $ params :List of 5 325s ..$ alpha : num 0.009 325s ..$ undo : num 0 325s ..$ joinSegments : logi TRUE 325s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 325s .. ..$ chromosome: int 1 325s .. ..$ start : num -Inf 325s .. ..$ end : num Inf 325s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 325s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 325s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.115 0 0.116 0 0 325s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 325s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 325s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 325s Identification of change points by total copy numbers...done 325s Restructure TCN segmentation results... 325s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 325s 1 1 554484 143663981 1880 1.3916 325s 2 1 143663981 185240536 671 2.0925 325s 3 1 185240536 246679946 1111 2.6545 325s Number of TCN segments: 3 325s Restructure TCN segmentation results...done 325s TCN-only segmentation... 325s Total CN segment #1 ([ 554484,1.43664e+08]) of 3... 325s Number of TCN loci in segment: 1880 325s Locus data for TCN segment: 325s 'data.frame': 1880 obs. of 8 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : num 554484 1031563 1087198 1145994 1176365 ... 325s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 325s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 325s $ rho : num NA 0.216 0.198 0.515 0.29 ... 325s Number of loci: 1880 325s Number of SNPs: 765 (40.69%) 325s Number of heterozygous SNPs: 765 (100.00%) 325s Total CN segment #1 ([ 554484,1.43664e+08]) of 3...done 325s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3... 325s Number of TCN loci in segment: 671 325s Locus data for TCN segment: 325s 'data.frame': 671 obs. of 8 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 325s $ CT : num 2.26 2.1 2.1 1.89 1.97 ... 325s $ betaT : num 0.958 0.19 0.909 0.13 0.141 ... 325s $ betaTN : num 0.958 0.19 0.909 0.13 0.141 ... 325s $ muN : num 1 0 1 0 0 0 0 0.5 0 1 ... 325s $ index : int 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 325s $ rho : num NA NA NA NA NA ... 325s Number of loci: 671 325s Number of SNPs: 272 (40.54%) 325s Number of heterozygous SNPs: 272 (100.00%) 325s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3...done 325s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3... 325s Number of TCN loci in segment: 1111 325s Locus data for TCN segment: 325s 'data.frame': 1111 obs. of 8 variables: 325s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 325s $ x : num 1.85e+08 1.86e+08 1.86e+08 1.86e+08 1.86e+08 ... 325s $ CT : num 2.44 3 2.32 2.76 2.48 ... 325s $ betaT : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 325s $ betaTN : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 325s $ muN : num 0 0.5 0.5 1 0 1 0 1 1 0.5 ... 325s $ index : int 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 325s $ rho : num NA 0.369 0.535 NA NA ... 325s Number of loci: 1111 325s Number of SNPs: 414 (37.26%) 325s Number of heterozygous SNPs: 414 (100.00%) 325s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3...done 325s TCN-only segmentation...done 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.3916 765 325s 2 1 2 1 143663981 185240536 671 2.0925 272 325s 3 1 3 1 185240536 246679946 1111 2.6545 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean 325s 1 765 765 554484 143663981 0.3979122 325s 2 272 272 143663981 185240536 0.2306116 325s 3 414 414 185240536 246679946 0.2798120 325s Calculating (C1,C2) per segment... 325s Calculating (C1,C2) per segment...done 325s Number of segments: 3 325s Segmenting paired tumor-normal signals using Paired PSCBS...done 325s Updating mean level using different estimator... 325s TCN estimator: mean 325s DH estimator: median 325s Updating mean level using different estimator...done 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s Chromosome #1 ('Chr01') of 2...done 325s Chromosome #2 ('Chr02') of 2... 325s 'data.frame': 3662 obs. of 7 variables: 325s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 325s $ x : num 554484 1031563 1087198 1145994 1176365 ... 325s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 325s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s $ index : int 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 325s Known segments: 325s [1] chromosome start end 325s <0 rows> (or 0-length row.names) 325s Segmenting paired tumor-normal signals using Paired PSCBS... 325s Setup up data... 325s 'data.frame': 3662 obs. of 6 variables: 325s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 325s $ x : num 554484 1031563 1087198 1145994 1176365 ... 325s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 325s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s Setup up data...done 325s Ordering data along genome... 325s 'data.frame': 3662 obs. of 6 variables: 325s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 325s $ x : num 554484 1031563 1087198 1145994 1176365 ... 325s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 325s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s Ordering data along genome...done 325s Keeping only current chromosome for 'knownSegments'... 325s Chromosome: 2 325s Known segments for this chromosome: 325s [1] chromosome start end 325s <0 rows> (or 0-length row.names) 325s Keeping only current chromosome for 'knownSegments'...done 325s alphaTCN: 0.009 325s alphaDH: 0.001 325s Number of loci: 3662 325s Calculating DHs... 325s Number of SNPs: 3662 325s Number of heterozygous SNPs: 1451 (39.62%) 325s Normalized DHs: 325s num [1:3662] NA 0.216 0.198 0.515 0.29 ... 325s Calculating DHs...done 325s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 325s Produced 2 seeds from this stream for future usage 325s Identification of change points by total copy numbers... 325s Segmenting by CBS... 325s Chromosome: 2 325s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 325s Segmenting by CBS...done 325s List of 4 325s $ data :'data.frame': 3662 obs. of 4 variables: 325s ..$ chromosome: int [1:3662] 2 2 2 2 2 2 2 2 2 2 ... 325s ..$ x : num [1:3662] 554484 1031563 1087198 1145994 1176365 ... 325s ..$ y : num [1:3662] 1.88 1.64 1.77 1.63 1.59 ... 325s ..$ index : int [1:3662] 1 2 3 4 5 6 7 8 9 10 ... 325s $ output :'data.frame': 3 obs. of 6 variables: 325s ..$ sampleName: chr [1:3] NA NA NA 325s ..$ chromosome: int [1:3] 2 2 2 325s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 325s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 325s ..$ nbrOfLoci : int [1:3] 1880 671 1111 325s ..$ mean : num [1:3] 1.39 2.09 2.65 325s $ segRows:'data.frame': 3 obs. of 2 variables: 325s ..$ startRow: int [1:3] 1 1881 2552 325s ..$ endRow : int [1:3] 1880 2551 3662 325s $ params :List of 5 325s ..$ alpha : num 0.009 325s ..$ undo : num 0 325s ..$ joinSegments : logi TRUE 325s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 325s .. ..$ chromosome: int 2 325s .. ..$ start : num -Inf 325s .. ..$ end : num Inf 325s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 325s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 325s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.107 0 0.106 0 0 325s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 325s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 325s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 325s Identification of change points by total copy numbers...done 325s Restructure TCN segmentation results... 325s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 325s 1 2 554484 143663981 1880 1.3916 325s 2 2 143663981 185240536 671 2.0925 325s 3 2 185240536 246679946 1111 2.6545 325s Number of TCN segments: 3 325s Restructure TCN segmentation results...done 325s TCN-only segmentation... 325s Total CN segment #1 ([ 554484,1.43664e+08]) of 3... 325s Number of TCN loci in segment: 1880 325s Locus data for TCN segment: 325s 'data.frame': 1880 obs. of 8 variables: 325s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 325s $ x : num 554484 1031563 1087198 1145994 1176365 ... 325s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 325s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 325s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 325s $ rho : num NA 0.216 0.198 0.515 0.29 ... 325s Number of loci: 1880 325s Number of SNPs: 765 (40.69%) 325s Number of heterozygous SNPs: 765 (100.00%) 325s Total CN segment #1 ([ 554484,1.43664e+08]) of 3...done 325s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3... 325s Number of TCN loci in segment: 671 325s Locus data for TCN segment: 325s 'data.frame': 671 obs. of 8 variables: 325s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 325s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 325s $ CT : num 2.26 2.1 2.1 1.89 1.97 ... 325s $ betaT : num 0.958 0.19 0.909 0.13 0.141 ... 325s $ betaTN : num 0.958 0.19 0.909 0.13 0.141 ... 325s $ muN : num 1 0 1 0 0 0 0 0.5 0 1 ... 325s $ index : int 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 325s $ rho : num NA NA NA NA NA ... 325s Number of loci: 671 325s Number of SNPs: 272 (40.54%) 325s Number of heterozygous SNPs: 272 (100.00%) 325s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3...done 325s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3... 325s Number of TCN loci in segment: 1111 325s Locus data for TCN segment: 325s 'data.frame': 1111 obs. of 8 variables: 325s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 325s $ x : num 1.85e+08 1.86e+08 1.86e+08 1.86e+08 1.86e+08 ... 325s $ CT : num 2.44 3 2.32 2.76 2.48 ... 325s $ betaT : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 325s $ betaTN : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 325s $ muN : num 0 0.5 0.5 1 0 1 0 1 1 0.5 ... 325s $ index : int 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 325s $ rho : num NA 0.369 0.535 NA NA ... 325s Number of loci: 1111 325s Number of SNPs: 414 (37.26%) 325s Number of heterozygous SNPs: 414 (100.00%) 325s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3...done 325s TCN-only segmentation...done 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 2 1 1 554484 143663981 1880 1.3916 765 325s 2 2 2 1 143663981 185240536 671 2.0925 272 325s 3 2 3 1 185240536 246679946 1111 2.6545 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean 325s 1 765 765 554484 143663981 0.3979122 325s 2 272 272 143663981 185240536 0.2306116 325s 3 414 414 185240536 246679946 0.2798120 325s Calculating (C1,C2) per segment... 325s Calculating (C1,C2) per segment...done 325s Number of segments: 3 325s Segmenting paired tumor-normal signals using Paired PSCBS...done 325s Updating mean level using different estimator... 325s TCN estimator: mean 325s DH estimator: median 325s Updating mean level using different estimator...done 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 2 1 1 554484 143663981 1880 1.391608 765 325s 2 2 2 1 143663981 185240536 671 2.092452 272 325s 3 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 2 1 1 554484 143663981 1880 1.391608 765 325s 2 2 2 1 143663981 185240536 671 2.092452 272 325s 3 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 2 1 1 554484 143663981 1880 1.391608 765 325s 2 2 2 1 143663981 185240536 671 2.092452 272 325s 3 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 2 1 1 554484 143663981 1880 1.391608 765 325s 2 2 2 1 143663981 185240536 671 2.092452 272 325s 3 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s Chromosome #2 ('Chr02') of 2...done 325s Merging (independently) segmented chromosome... 325s List of 5 325s $ data :Classes 'PairedPSCNData' and 'data.frame': 7324 obs. of 7 variables: 325s ..$ chromosome: int [1:7324] 1 1 1 1 1 1 1 1 1 1 ... 325s ..$ x : num [1:7324] 554484 1031563 1087198 1145994 1176365 ... 325s ..$ CT : num [1:7324] 1.88 1.64 1.77 1.63 1.59 ... 325s ..$ betaT : num [1:7324] 0.0646 0.6078 0.401 0.7574 0.645 ... 325s ..$ betaTN : num [1:7324] 0.0646 0.6078 0.401 0.7574 0.645 ... 325s ..$ muN : num [1:7324] 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 325s ..$ rho : num [1:7324] NA 0.216 0.198 0.515 0.29 ... 325s $ output :Classes 'PairedPSCNSegments' and 'data.frame': 7 obs. of 15 variables: 325s ..$ chromosome : int [1:7] 1 1 1 NA 2 2 2 325s ..$ tcnId : int [1:7] 1 2 3 NA 1 2 3 325s ..$ dhId : int [1:7] 1 1 1 NA 1 1 1 325s ..$ tcnStart : num [1:7] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 325s ..$ tcnEnd : num [1:7] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 325s ..$ tcnNbrOfLoci: int [1:7] 1880 671 1111 NA 1880 671 1111 325s ..$ tcnMean : num [1:7] 1.39 2.09 2.65 NA 1.39 ... 325s ..$ tcnNbrOfSNPs: int [1:7] 765 272 414 NA 765 272 414 325s ..$ tcnNbrOfHets: int [1:7] 765 272 414 NA 765 272 414 325s ..$ dhNbrOfLoci : int [1:7] 765 272 414 NA 765 272 414 325s ..$ dhStart : num [1:7] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 325s ..$ dhEnd : num [1:7] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 325s ..$ dhMean : num [1:7] 0.421 0.176 0.27 NA 0.421 ... 325s ..$ c1Mean : num [1:7] 0.403 0.862 0.969 NA 0.403 ... 325s ..$ c2Mean : num [1:7] 0.988 1.231 1.685 NA 0.988 ... 325s $ tcnSegRows:'data.frame': 7 obs. of 2 variables: 325s ..$ startRow: int [1:7] 1 1881 2552 NA 3663 5543 6214 325s ..$ endRow : int [1:7] 1880 2551 3662 NA 5542 6213 7324 325s $ dhSegRows :'data.frame': 7 obs. of 2 variables: 325s ..$ startRow: int [1:7] 2 1888 2553 NA 3664 5550 6215 325s ..$ endRow : int [1:7] 1876 2548 3659 NA 5538 6210 7321 325s $ params :List of 8 325s ..$ alphaTCN : num 0.009 325s ..$ alphaDH : num 0.001 325s ..$ flavor : chr "tcn" 325s ..$ tbn : logi FALSE 325s ..$ joinSegments : logi TRUE 325s ..$ knownSegments :'data.frame': 0 obs. of 3 variables: 325s .. ..$ chromosome: int(0) 325s .. ..$ start : int(0) 325s .. ..$ end : int(0) 325s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 325s ..$ meanEstimators:List of 2 325s .. ..$ tcn: chr "mean" 325s .. ..$ dh : chr "median" 325s - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" 325s Merging (independently) segmented chromosome...done 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s 4 NA NA NA NA NA NA NA NA 325s 5 2 1 1 554484 143663981 1880 1.391608 765 325s 6 2 2 1 143663981 185240536 671 2.092452 272 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s 4 NA NA NA NA NA NA NA 325s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s 4 NA NA NA NA NA NA NA NA 325s 5 2 1 1 554484 143663981 1880 1.391608 765 325s 6 2 2 1 143663981 185240536 671 2.092452 272 325s 7 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s 4 NA NA NA NA NA NA NA 325s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 7 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s Segmenting multiple chromosomes...done 325s Segmenting paired tumor-normal signals using Paired PSCBS...done 325s Segment using Paired PSCBS...done 325s Coercing to Non-Paired PSCBS results... 325s Coercing to Non-Paired PSCBS results...done 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s 4 NA NA NA NA NA NA NA NA 325s 5 2 1 1 554484 143663981 1880 1.391608 765 325s 6 2 2 1 143663981 185240536 671 2.092452 272 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s 4 NA NA NA NA NA NA NA 325s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s 4 NA NA NA NA NA NA NA NA 325s 5 2 1 1 554484 143663981 1880 1.391608 765 325s 6 2 2 1 143663981 185240536 671 2.092452 272 325s 7 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s 4 NA NA NA NA NA NA NA 325s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 325s 7 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 325s > print(fit) 325s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s 4 NA NA NA NA NA NA NA NA 325s 5 2 1 1 554484 143663981 1880 1.391608 765 325s 6 2 2 1 143663981 185240536 671 2.092452 272 325s 7 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 325s 1 765 765 0.4206323 0.4031263 0.9884817 325s 2 272 272 0.1762428 0.8618360 1.2306156 325s 3 414 414 0.2697420 0.9692395 1.6852728 325s 4 NA NA NA NA NA 325s 5 765 765 0.4206323 0.4031263 0.9884817 325s 6 272 272 0.1762428 0.8618360 1.2306156 325s 7 414 414 0.2697420 0.9692395 1.6852728 325s > 325s > 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > # Bootstrap segment level estimates 325s > # (used by the AB caller, which, if skipped here, 325s > # will do it automatically) 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > fit <- bootstrapTCNandDHByRegion(fit, B=100, verbose=-10) 325s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 325s Already done? 325s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 325s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 325s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 325s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 325s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 325s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 325s Number of loci: 7324 325s Number of SNPs: 2902 325s Number of non-SNPs: 4422 325s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 325s num [1:7, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : NULL 325s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 325s Segment #1 (chr 1, tcnId=1, dhId=1) of 7... 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s Number of TCNs: 1880 325s Number of DHs: 765 325s int [1:1880] 1 2 3 4 5 6 7 8 9 10 ... 325s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 325s int [1:1880] 1 2 3 4 5 6 7 8 9 10 ... 325s Identify loci used to bootstrap DH means... 325s Heterozygous SNPs to resample for DH: 325s int [1:765] 2 3 4 5 6 8 9 10 11 12 ... 325s Identify loci used to bootstrap DH means...done 325s Identify loci used to bootstrap TCN means... 325s SNPs: 325s int [1:765] 2 3 4 5 6 8 9 10 11 12 ... 325s Non-polymorphic loci: 325s int [1:1115] 1 7 15 28 30 32 34 35 36 37 ... 325s Heterozygous SNPs to resample for TCN: 325s int [1:765] 2 3 4 5 6 8 9 10 11 12 ... 325s Homozygous SNPs to resample for TCN: 325s int(0) 325s Non-polymorphic loci to resample for TCN: 325s int [1:1115] 1 7 15 28 30 32 34 35 36 37 ... 325s Heterozygous SNPs with non-DH to resample for TCN: 325s int(0) 325s Loci to resample for TCN: 325s int [1:1880] 1 2 3 4 5 6 7 8 9 10 ... 325s Identify loci used to bootstrap TCN means...done 325s Number of (#hets, #homs, #nonSNPs): (765,0,1115) 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 325s Number of bootstrap samples: 100 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 325s Segment #1 (chr 1, tcnId=1, dhId=1) of 7...done 325s Segment #2 (chr 1, tcnId=2, dhId=1) of 7... 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 2 272 272 143663981 185240536 0.1762428 0.861836 1.230616 325s Number of TCNs: 671 325s Number of DHs: 272 325s int [1:671] 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 325s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 325s int [1:671] 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 325s Identify loci used to bootstrap DH means... 325s Heterozygous SNPs to resample for DH: 325s int [1:272] 1888 1893 1894 1895 1896 1897 1901 1903 1907 1908 ... 325s Identify loci used to bootstrap DH means...done 325s Identify loci used to bootstrap TCN means... 325s SNPs: 325s int [1:272] 1888 1893 1894 1895 1896 1897 1901 1903 1907 1908 ... 325s Non-polymorphic loci: 325s int [1:399] 1881 1882 1883 1884 1885 1886 1887 1889 1890 1891 ... 325s Heterozygous SNPs to resample for TCN: 325s int [1:272] 1888 1893 1894 1895 1896 1897 1901 1903 1907 1908 ... 325s Homozygous SNPs to resample for TCN: 325s int(0) 325s Non-polymorphic loci to resample for TCN: 325s int [1:399] 1881 1882 1883 1884 1885 1886 1887 1889 1890 1891 ... 325s Heterozygous SNPs with non-DH to resample for TCN: 325s int(0) 325s Loci to resample for TCN: 325s int [1:671] 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 325s Identify loci used to bootstrap TCN means...done 325s Number of (#hets, #homs, #nonSNPs): (272,0,399) 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 325s Number of bootstrap samples: 100 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 325s Segment #2 (chr 1, tcnId=2, dhId=1) of 7...done 325s Segment #3 (chr 1, tcnId=3, dhId=1) of 7... 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 3 414 414 185240536 246679946 0.269742 0.9692395 1.685273 325s Number of TCNs: 1111 325s Number of DHs: 414 325s int [1:1111] 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 325s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 325s int [1:1111] 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 325s Identify loci used to bootstrap DH means... 325s Heterozygous SNPs to resample for DH: 325s int [1:414] 2553 2554 2561 2562 2563 2568 2569 2572 2573 2574 ... 325s Identify loci used to bootstrap DH means...done 325s Identify loci used to bootstrap TCN means... 325s SNPs: 325s int [1:414] 2553 2554 2561 2562 2563 2568 2569 2572 2573 2574 ... 325s Non-polymorphic loci: 325s int [1:697] 2552 2555 2556 2557 2558 2559 2560 2564 2565 2566 ... 325s Heterozygous SNPs to resample for TCN: 325s int [1:414] 2553 2554 2561 2562 2563 2568 2569 2572 2573 2574 ... 325s Homozygous SNPs to resample for TCN: 325s int(0) 325s Non-polymorphic loci to resample for TCN: 325s int [1:697] 2552 2555 2556 2557 2558 2559 2560 2564 2565 2566 ... 325s Heterozygous SNPs with non-DH to resample for TCN: 325s int(0) 325s Loci to resample for TCN: 325s int [1:1111] 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 325s Identify loci used to bootstrap TCN means...done 325s Number of (#hets, #homs, #nonSNPs): (414,0,697) 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 325s Number of bootstrap samples: 100 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 325s Segment #3 (chr 1, tcnId=3, dhId=1) of 7...done 325s Segment #5 (chr 2, tcnId=1, dhId=1) of 7... 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 5 2 1 1 554484 143663981 1880 1.391608 765 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 325s Number of TCNs: 1880 325s Number of DHs: 765 325s int [1:1880] 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 325s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 325s int [1:1880] 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 325s Identify loci used to bootstrap DH means... 325s Heterozygous SNPs to resample for DH: 325s int [1:765] 3664 3665 3666 3667 3668 3670 3671 3672 3673 3674 ... 325s Identify loci used to bootstrap DH means...done 325s Identify loci used to bootstrap TCN means... 325s SNPs: 325s int [1:765] 3664 3665 3666 3667 3668 3670 3671 3672 3673 3674 ... 325s Non-polymorphic loci: 325s int [1:1115] 3663 3669 3677 3690 3692 3694 3696 3697 3698 3699 ... 325s Heterozygous SNPs to resample for TCN: 325s int [1:765] 3664 3665 3666 3667 3668 3670 3671 3672 3673 3674 ... 325s Homozygous SNPs to resample for TCN: 325s int(0) 325s Non-polymorphic loci to resample for TCN: 325s int [1:1115] 3663 3669 3677 3690 3692 3694 3696 3697 3698 3699 ... 325s Heterozygous SNPs with non-DH to resample for TCN: 325s int(0) 325s Loci to resample for TCN: 325s int [1:1880] 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 325s Identify loci used to bootstrap TCN means...done 325s Number of (#hets, #homs, #nonSNPs): (765,0,1115) 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 325s Number of bootstrap samples: 100 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 325s Segment #5 (chr 2, tcnId=1, dhId=1) of 7...done 325s Segment #6 (chr 2, tcnId=2, dhId=1) of 7... 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 6 2 2 1 143663981 185240536 671 2.092452 272 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 6 272 272 143663981 185240536 0.1762428 0.861836 1.230616 325s Number of TCNs: 671 325s Number of DHs: 272 325s int [1:671] 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 ... 325s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 325s int [1:671] 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 ... 325s Identify loci used to bootstrap DH means... 325s Heterozygous SNPs to resample for DH: 325s int [1:272] 5550 5555 5556 5557 5558 5559 5563 5565 5569 5570 ... 325s Identify loci used to bootstrap DH means...done 325s Identify loci used to bootstrap TCN means... 325s SNPs: 325s int [1:272] 5550 5555 5556 5557 5558 5559 5563 5565 5569 5570 ... 325s Non-polymorphic loci: 325s int [1:399] 5543 5544 5545 5546 5547 5548 5549 5551 5552 5553 ... 325s Heterozygous SNPs to resample for TCN: 325s int [1:272] 5550 5555 5556 5557 5558 5559 5563 5565 5569 5570 ... 325s Homozygous SNPs to resample for TCN: 325s int(0) 325s Non-polymorphic loci to resample for TCN: 325s int [1:399] 5543 5544 5545 5546 5547 5548 5549 5551 5552 5553 ... 325s Heterozygous SNPs with non-DH to resample for TCN: 325s int(0) 325s Loci to resample for TCN: 325s int [1:671] 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 ... 325s Identify loci used to bootstrap TCN means...done 325s Number of (#hets, #homs, #nonSNPs): (272,0,399) 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 325s Number of bootstrap samples: 100 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 325s Segment #6 (chr 2, tcnId=2, dhId=1) of 7...done 325s Segment #7 (chr 2, tcnId=3, dhId=1) of 7... 325s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 7 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 325s 7 414 414 185240536 246679946 0.269742 0.9692395 1.685273 325s Number of TCNs: 1111 325s Number of DHs: 414 325s int [1:1111] 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 ... 325s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 325s int [1:1111] 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 ... 325s Identify loci used to bootstrap DH means... 325s Heterozygous SNPs to resample for DH: 325s int [1:414] 6215 6216 6223 6224 6225 6230 6231 6234 6235 6236 ... 325s Identify loci used to bootstrap DH means...done 325s Identify loci used to bootstrap TCN means... 325s SNPs: 325s int [1:414] 6215 6216 6223 6224 6225 6230 6231 6234 6235 6236 ... 325s Non-polymorphic loci: 325s int [1:697] 6214 6217 6218 6219 6220 6221 6222 6226 6227 6228 ... 325s Heterozygous SNPs to resample for TCN: 325s int [1:414] 6215 6216 6223 6224 6225 6230 6231 6234 6235 6236 ... 325s Homozygous SNPs to resample for TCN: 325s int(0) 325s Non-polymorphic loci to resample for TCN: 325s int [1:697] 6214 6217 6218 6219 6220 6221 6222 6226 6227 6228 ... 325s Heterozygous SNPs with non-DH to resample for TCN: 325s int(0) 325s Loci to resample for TCN: 325s int [1:1111] 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 ... 325s Identify loci used to bootstrap TCN means...done 325s Number of (#hets, #homs, #nonSNPs): (414,0,697) 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 325s Number of bootstrap samples: 100 325s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 325s Segment #7 (chr 2, tcnId=3, dhId=1) of 7...done 325s Bootstrapped segment mean levels 325s num [1:7, 1:100, 1:4] 1.4 2.09 2.64 NA 1.39 ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : NULL 325s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 325s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 325s num [1:7, 1:100, 1:4] 1.4 2.09 2.64 NA 1.39 ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : NULL 325s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 325s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 325s Calculating polar (alpha,radius,manhattan) for change points... 325s num [1:6, 1:100, 1:2] -0.448 -0.131 NA NA -0.477 ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : NULL 325s ..$ : chr [1:2] "c1" "c2" 325s Bootstrapped change points 325s num [1:6, 1:100, 1:5] -2.65 -1.87 NA NA -2.72 ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : NULL 325s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 325s Calculating polar (alpha,radius,manhattan) for change points...done 325s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 325s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 325s num [1:7, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 325s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 325s Field #1 ('tcn') of 4... 325s Segment #1 of 7... 325s Segment #1 of 7...done 325s Segment #2 of 7... 325s Segment #2 of 7...done 325s Segment #3 of 7... 325s Segment #3 of 7...done 325s Segment #4 of 7... 325s Segment #4 of 7...done 325s Segment #5 of 7... 325s Segment #5 of 7...done 325s Segment #6 of 7... 325s Segment #6 of 7...done 325s Segment #7 of 7... 325s Segment #7 of 7...done 325s Field #1 ('tcn') of 4...done 325s Field #2 ('dh') of 4... 325s Segment #1 of 7... 325s Segment #1 of 7...done 325s Segment #2 of 7... 325s Segment #2 of 7...done 325s Segment #3 of 7... 325s Segment #3 of 7...done 325s Segment #4 of 7... 325s Segment #4 of 7...done 325s Segment #5 of 7... 325s Segment #5 of 7...done 325s Segment #6 of 7... 325s Segment #6 of 7...done 325s Segment #7 of 7... 325s Segment #7 of 7...done 325s Field #2 ('dh') of 4...done 325s Field #3 ('c1') of 4... 325s Segment #1 of 7... 325s Segment #1 of 7...done 325s Segment #2 of 7... 325s Segment #2 of 7...done 325s Segment #3 of 7... 325s Segment #3 of 7...done 325s Segment #4 of 7... 325s Segment #4 of 7...done 325s Segment #5 of 7... 325s Segment #5 of 7...done 325s Segment #6 of 7... 325s Segment #6 of 7...done 325s Segment #7 of 7... 325s Segment #7 of 7...done 325s Field #3 ('c1') of 4...done 325s Field #4 ('c2') of 4... 325s Segment #1 of 7... 325s Segment #1 of 7...done 325s Segment #2 of 7... 325s Segment #2 of 7...done 325s Segment #3 of 7... 325s Segment #3 of 7...done 325s Segment #4 of 7... 325s Segment #4 of 7...done 325s Segment #5 of 7... 325s Segment #5 of 7...done 325s Segment #6 of 7... 325s Segment #6 of 7...done 325s Segment #7 of 7... 325s Segment #7 of 7...done 325s Field #4 ('c2') of 4...done 325s Bootstrap statistics 325s num [1:7, 1:4, 1:4] 1.38 2.07 2.63 NA 1.38 ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 325s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 325s Statistical sanity checks (iff B >= 100)... 325s Available summaries: 2.5%, 5%, 95%, 97.5% 325s Available quantiles: 0.025, 0.05, 0.95, 0.975 325s num [1:7, 1:4, 1:4] 1.38 2.07 2.63 NA 1.38 ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 325s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 325s Field #1 ('tcn') of 4... 325s Seg 1. mean=1.39161, range=[1.38025,1.40693], n=1880 325s Seg 2. mean=2.09245, range=[2.06856,2.1165], n=671 325s Seg 3. mean=2.65451, range=[2.62678,2.6834], n=1111 325s Seg 4. mean=NA, range=[NA,NA], n=NA 325s Seg 5. mean=1.39161, range=[1.37999,1.40474], n=1880 325s Seg 6. mean=2.09245, range=[2.06923,2.11747], n=671 325s Seg 7. mean=2.65451, range=[2.62867,2.68639], n=1111 325s Field #1 ('tcn') of 4...done 325s Field #2 ('dh') of 4... 325s Seg 1. mean=0.420632, range=[0.406983,0.437756], n=765 325s Seg 2. mean=0.176243, range=[0.141232,0.202975], n=272 325s Seg 3. mean=0.269742, range=[0.245337,0.292784], n=414 325s Seg 4. mean=NA, range=[NA,NA], n=NA 325s Seg 5. mean=0.420632, range=[0.406204,0.436189], n=765 325s Seg 6. mean=0.176243, range=[0.13696,0.212132], n=272 325s Seg 7. mean=0.269742, range=[0.230034,0.296763], n=414 325s Field #2 ('dh') of 4...done 325s Field #3 ('c1') of 4... 325s Seg 1. mean=0.403126, range=[0.391189,0.413437], n=765 325s Seg 2. mean=0.861836, range=[0.833296,0.900874], n=272 325s Seg 3. mean=0.969239, range=[0.937437,1.00659], n=414 325s Seg 4. mean=NA, range=[NA,NA], n=NA 325s Seg 5. mean=0.403126, range=[0.392112,0.414529], n=765 325s Seg 6. mean=0.861836, range=[0.823193,0.907577], n=272 325s Seg 7. mean=0.969239, range=[0.931951,1.01968], n=414 325s Field #3 ('c1') of 4...done 325s Field #4 ('c2') of 4... 325s Seg 1. mean=0.988482, range=[0.974501,1.00244], n=765 325s Seg 2. mean=1.23062, range=[1.18964,1.26157], n=272 325s Seg 3. mean=1.68527, range=[1.6481,1.72497], n=414 325s Seg 4. mean=NA, range=[NA,NA], n=NA 325s Seg 5. mean=0.988482, range=[0.9761,1.00076], n=765 325s Seg 6. mean=1.23062, range=[1.18936,1.26647], n=272 325s Seg 7. mean=1.68527, range=[1.63171,1.72526], n=414 325s Field #4 ('c2') of 4...done 325s Statistical sanity checks (iff B >= 100)...done 325s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 325s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 325s num [1:6, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 325s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 325s Field #1 ('alpha') of 5... 325s Changepoint #1 of 6... 325s Changepoint #1 of 6...done 325s Changepoint #2 of 6... 325s Changepoint #2 of 6...done 325s Changepoint #3 of 6... 325s Changepoint #3 of 6...done 325s Changepoint #4 of 6... 325s Changepoint #4 of 6...done 325s Changepoint #5 of 6... 325s Changepoint #5 of 6...done 325s Changepoint #6 of 6... 325s Changepoint #6 of 6...done 325s Field #1 ('alpha') of 5...done 325s Field #2 ('radius') of 5... 325s Changepoint #1 of 6... 325s Changepoint #1 of 6...done 325s Changepoint #2 of 6... 325s Changepoint #2 of 6...done 325s Changepoint #3 of 6... 325s Changepoint #3 of 6...done 325s Changepoint #4 of 6... 325s Changepoint #4 of 6...done 325s Changepoint #5 of 6... 325s Changepoint #5 of 6...done 325s Changepoint #6 of 6... 325s Changepoint #6 of 6...done 325s Field #2 ('radius') of 5...done 325s Field #3 ('manhattan') of 5... 325s Changepoint #1 of 6... 325s Changepoint #1 of 6...done 325s Changepoint #2 of 6... 325s Changepoint #2 of 6...done 325s Changepoint #3 of 6... 325s Changepoint #3 of 6...done 325s Changepoint #4 of 6... 325s Changepoint #4 of 6...done 325s Changepoint #5 of 6... 325s Changepoint #5 of 6...done 325s Changepoint #6 of 6... 325s Changepoint #6 of 6...done 325s Field #3 ('manhattan') of 5...done 325s Field #4 ('d1') of 5... 325s Changepoint #1 of 6... 325s Changepoint #1 of 6...done 325s Changepoint #2 of 6... 325s Changepoint #2 of 6...done 325s Changepoint #3 of 6... 325s Changepoint #3 of 6...done 325s Changepoint #4 of 6... 325s Changepoint #4 of 6...done 325s Changepoint #5 of 6... 325s Changepoint #5 of 6...done 325s Changepoint #6 of 6... 325s Changepoint #6 of 6...done 325s Field #4 ('d1') of 5...done 325s Field #5 ('d2') of 5... 325s Changepoint #1 of 6... 325s Changepoint #1 of 6...done 325s Changepoint #2 of 6... 325s Changepoint #2 of 6...done 325s Changepoint #3 of 6... 325s Changepoint #3 of 6...done 325s Changepoint #4 of 6... 325s Changepoint #4 of 6...done 325s Changepoint #5 of 6... 325s Changepoint #5 of 6...done 325s Changepoint #6 of 6... 325s Changepoint #6 of 6...done 325s Field #5 ('d2') of 5...done 325s Bootstrap statistics 325s num [1:6, 1:4, 1:5] -2.76 -1.91 NA NA -2.76 ... 325s - attr(*, "dimnames")=List of 3 325s ..$ : NULL 325s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 325s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 325s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 325s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 325s > print(fit) 325s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s 4 NA NA NA NA NA NA NA NA 325s 5 2 1 1 554484 143663981 1880 1.391608 765 325s 6 2 2 1 143663981 185240536 671 2.092452 272 325s 7 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 325s 1 765 765 0.4206323 0.4031263 0.9884817 325s 2 272 272 0.1762428 0.8618360 1.2306156 325s 3 414 414 0.2697420 0.9692395 1.6852728 325s 4 NA NA NA NA NA 325s 5 765 765 0.4206323 0.4031263 0.9884817 325s 6 272 272 0.1762428 0.8618360 1.2306156 325s 7 414 414 0.2697420 0.9692395 1.6852728 325s > 325s > 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > # Calling segments in allelic balance (AB) 325s > # NOTE: Ideally, this should be done on whole-genome data 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > # Explicitly estimate the threshold in DH for calling AB 325s > # (which be done by default by the caller, if skipped here) 325s > deltaAB <- estimateDeltaAB(fit, flavor="qq(DH)", verbose=-10) 325s Estimating DH threshold for calling allelic imbalances... 325s flavor: qq(DH) 325s scale: 1 325s Estimating DH threshold for AB caller... 325s quantile #1: 0.05 325s Symmetric quantile #2: 0.9 325s Number of segments: 6 325s Weighted 5% quantile of DH: 0.199618 325s Number of segments with small DH: 2 325s Number of data points: 1342 325s Number of finite data points: 544 325s Estimate of (1-0.9):th and 50% quantiles: (0.0289919,0.176243) 325s Estimate of 0.9:th "symmetric" quantile: 0.323494 325s Estimating DH threshold for AB caller...done 325s Estimated delta: 0.323 325s Estimating DH threshold for calling allelic imbalances...done 325s > print(deltaAB) 325s [1] 0.3234938 325s > 325s > fit <- callAB(fit, delta=deltaAB, verbose=-10) 325s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 325s delta (offset adjusting for bias in DH): 0.323493772175137 325s alpha (CI quantile; significance level): 0.05 325s Calling segments... 325s Number of segments called allelic balance (AB): 4 (57.14%) of 7 325s Calling segments...done 325s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 325s > print(fit) 325s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s 4 NA NA NA NA NA NA NA NA 325s 5 2 1 1 554484 143663981 1880 1.391608 765 325s 6 2 2 1 143663981 185240536 671 2.092452 272 325s 7 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall 325s 1 765 765 0.4206323 0.4031263 0.9884817 FALSE 325s 2 272 272 0.1762428 0.8618360 1.2306156 TRUE 325s 3 414 414 0.2697420 0.9692395 1.6852728 TRUE 325s 4 NA NA NA NA NA NA 325s 5 765 765 0.4206323 0.4031263 0.9884817 FALSE 325s 6 272 272 0.1762428 0.8618360 1.2306156 TRUE 325s 7 414 414 0.2697420 0.9692395 1.6852728 TRUE 325s > 325s > 325s > # Even if not explicitly specified, the estimated 325s > # threshold parameter is returned by the caller 325s > stopifnot(fit$params$deltaAB == deltaAB) 325s > 325s > 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > # Calling segments in loss-of-heterozygosity (LOH) 325s > # NOTE: Ideally, this should be done on whole-genome data 325s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 325s > # Explicitly estimate the threshold in C1 for calling LOH 325s > # (which be done by default by the caller, if skipped here) 325s > deltaLOH <- estimateDeltaLOH(fit, flavor="minC1|nonAB", verbose=-10) 325s Estimating DH threshold for calling LOH... 325s flavor: minC1|nonAB 325s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1... 325s Argument 'midpoint': 0.5 325s Number of segments: 6 325s Number of segments in allelic balance: 4 (66.7%) of 6 325s Number of segments not in allelic balance: 2 (33.3%) of 6 325s Number of segments in allelic balance and TCN <= 3.00: 4 (66.7%) of 6 325s C: 2.09, 2.65, 2.09, 2.65 325s Corrected C1 (=C/2): 1.05, 1.33, 1.05, 1.33 325s Number of DHs: 272, 414, 272, 414 325s Weights: 0.198, 0.302, 0.198, 0.302 325s Weighted median of (corrected) C1 in allelic balance: 1.274 325s Smallest C1 among segments not in allelic balance: 0.403 325s There are 2 segments with in total 765 heterozygous SNPs with this level. 325s There are 2 segments with in total 765 heterozygous SNPs with this level. 325s Midpoint between the two: 0.839 325s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1...done 325s delta: 0.839 325s Estimating DH threshold for calling LOH...done 325s > print(deltaLOH) 325s [1] 0.838563 325s > 325s > fit <- callLOH(fit, delta=deltaLOH, verbose=-10) 325s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 325s delta (offset adjusting for bias in C1): 0.838562992888546 325s alpha (CI quantile; significance level): 0.05 325s Calling segments... 325s Number of segments called low C1 (LowC1, "LOH_C1"): 3 (42.86%) of 7 325s Calling segments...done 325s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 325s > print(fit) 325s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 325s 1 1 1 1 554484 143663981 1880 1.391608 765 325s 2 1 2 1 143663981 185240536 671 2.092452 272 325s 3 1 3 1 185240536 246679946 1111 2.654512 414 325s 4 NA NA NA NA NA NA NA NA 325s 5 2 1 1 554484 143663981 1880 1.391608 765 325s 6 2 2 1 143663981 185240536 671 2.092452 272 325s 7 2 3 1 185240536 246679946 1111 2.654512 414 325s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall lohCall 325s 1 765 765 0.4206323 0.4031263 0.9884817 FALSE TRUE 325s 2 272 272 0.1762428 0.8618360 1.2306156 TRUE NA 325s 3 414 414 0.2697420 0.9692395 1.6852728 TRUE FALSE 325s 4 NA NA NA NA NA NA NA 325s 5 765 765 0.4206323 0.4031263 0.9884817 FALSE TRUE 325s 6 272 272 0.1762428 0.8618360 1.2306156 TRUE FALSE 325s 7 414 414 0.2697420 0.9692395 1.6852728 TRUE FALSE 325s > plotTracks(fit) 325s > 325s > # Even if not explicitly specified, the estimated 325s > # threshold parameter is returned by the caller 325s > stopifnot(fit$params$deltaLOH == deltaLOH) 325s > 325s > proc.time() 325s user system elapsed 325s 2.546 0.102 2.648 325s Test segmentByNonPairedPSCBS,medianDH passed 325s 0 325s Begin test segmentByPairedPSCBS,DH 330s + cat segmentByPairedPSCBS,DH.Rout 330s + [ 0 != 0 ] 330s + echo Test segmentByPairedPSCBS,DH passed 330s + echo 0 330s + echo Begin test segmentByPairedPSCBS,calls 330s + exitcode=0 330s + R CMD BATCH segmentByPairedPSCBS,calls.R 330s 330s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 330s Copyright (C) 2024 The R Foundation for Statistical Computing 330s Platform: arm-unknown-linux-gnueabihf (32-bit) 330s 330s R is free software and comes with ABSOLUTELY NO WARRANTY. 330s You are welcome to redistribute it under certain conditions. 330s Type 'license()' or 'licence()' for distribution details. 330s 330s R is a collaborative project with many contributors. 330s Type 'contributors()' for more information and 330s 'citation()' on how to cite R or R packages in publications. 330s 330s Type 'demo()' for some demos, 'help()' for on-line help, or 330s 'help.start()' for an HTML browser interface to help. 330s Type 'q()' to quit R. 330s 330s [Previously saved workspace restored] 330s 330s > library("PSCBS") 330s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 330s 330s Attaching package: 'PSCBS' 330s 330s The following objects are masked from 'package:base': 330s 330s append, load 330s 330s > 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > # Load SNP microarray data 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > data <- PSCBS::exampleData("paired.chr01") 330s > str(data) 330s 'data.frame': 73346 obs. of 6 variables: 330s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 330s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 330s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 330s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 330s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 330s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 330s > 330s > # Drop single-locus outliers 330s > dataS <- dropSegmentationOutliers(data) 330s > 330s > # Run light-weight tests 330s > # Use only every 5th data point 330s > dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 330s > # Number of segments (for assertion) 330s > nSegs <- 3L 330s > # Number of bootstrap samples (see below) 330s > B <- 100L 330s > 330s > str(dataS) 330s 'data.frame': 14670 obs. of 6 variables: 330s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 330s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 330s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 330s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 330s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 330s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 330s > R.oo::attachLocally(dataS) 330s > 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > # Calculate DH 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > muN <- aroma.light::callNaiveGenotypes(betaN, censorAt=c(0,1)) 330s > # SNPs are identifies as those loci that have non-missing 'betaT' & 'muN' 330s > isSnp <- (!is.na(betaT) & !is.na(muN)) 330s > isHet <- isSnp & (muN == 1/2) 330s > rho <- rep(NA_real_, length=length(muN)) 330s > rho[isHet] <- 2*abs(betaT[isHet]-1/2) 330s > 330s > 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > # Paired PSCBS segmentation using TCN and DH only 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > fit <- segmentByPairedPSCBS(CT, rho=rho, 330s + chromosome=chromosome, x=x, 330s + seed=0xBEEF, verbose=-10) 330s Segmenting paired tumor-normal signals using Paired PSCBS... 330s Setup up data... 330s 'data.frame': 14670 obs. of 4 variables: 330s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 330s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 330s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 330s $ rho : num NA 0.662 NA NA NA ... 330s Setup up data...done 330s Dropping loci for which TCNs are missing... 330s Number of loci dropped: 12 330s Dropping loci for which TCNs are missing...done 330s Ordering data along genome... 330s 'data.frame': 14658 obs. of 4 variables: 330s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 330s $ x : num 554484 730720 782343 878522 916294 ... 330s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 330s $ rho : num NA NA NA NA NA ... 330s Ordering data along genome...done 330s Keeping only current chromosome for 'knownSegments'... 330s Chromosome: 1 330s Known segments for this chromosome: 330s [1] chromosome start end 330s <0 rows> (or 0-length row.names) 330s Keeping only current chromosome for 'knownSegments'...done 330s alphaTCN: 0.009 330s alphaDH: 0.001 330s Number of loci: 14658 330s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 330s Produced 2 seeds from this stream for future usage 330s Identification of change points by total copy numbers... 330s Segmenting by CBS... 330s Chromosome: 1 330s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 330s Segmenting by CBS...done 330s List of 4 330s $ data :'data.frame': 14658 obs. of 4 variables: 330s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 330s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 330s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 330s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 330s $ output :'data.frame': 3 obs. of 6 variables: 330s ..$ sampleName: chr [1:3] NA NA NA 330s ..$ chromosome: int [1:3] 1 1 1 330s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 330s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 330s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 330s ..$ mean : num [1:3] 1.39 2.07 2.63 330s $ segRows:'data.frame': 3 obs. of 2 variables: 330s ..$ startRow: int [1:3] 1 7600 10268 330s ..$ endRow : int [1:3] 7599 10267 14658 330s $ params :List of 5 330s ..$ alpha : num 0.009 330s ..$ undo : num 0 330s ..$ joinSegments : logi TRUE 330s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 330s .. ..$ chromosome: int 1 330s .. ..$ start : num -Inf 330s .. ..$ end : num Inf 330s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 330s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 330s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.922 0.003 1.929 0 0 330s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 330s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 330s - attr(*, "randomSeed")= int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 330s Identification of change points by total copy numbers...done 330s Restructure TCN segmentation results... 330s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 330s 1 1 554484 143926517 7599 1.3859 330s 2 1 143926517 185449813 2668 2.0704 330s 3 1 185449813 247137334 4391 2.6341 330s Number of TCN segments: 3 330s Restructure TCN segmentation results...done 330s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 330s Number of TCN loci in segment: 7599 330s Locus data for TCN segment: 330s 'data.frame': 7599 obs. of 5 variables: 330s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 330s $ x : num 554484 730720 782343 878522 916294 ... 330s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 330s $ rho : num NA NA NA NA NA ... 330s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 330s Number of loci: 7599 330s Number of SNPs: 2111 (27.78%) 330s Number of heterozygous SNPs: 2111 (100.00%) 330s Chromosome: 1 330s Segmenting DH signals... 330s Segmenting by CBS... 330s Chromosome: 1 330s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 330s Segmenting by CBS...done 330s List of 4 330s $ data :'data.frame': 7599 obs. of 4 variables: 330s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 330s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 330s ..$ y : num [1:7599] NA NA NA NA NA ... 330s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 330s $ output :'data.frame': 1 obs. of 6 variables: 330s ..$ sampleName: chr NA 330s ..$ chromosome: int 1 330s ..$ start : num 554484 330s ..$ end : num 1.44e+08 330s ..$ nbrOfLoci : int 2111 330s ..$ mean : num 0.524 330s $ segRows:'data.frame': 1 obs. of 2 variables: 330s ..$ startRow: int 10 330s ..$ endRow : int 7594 330s $ params :List of 5 330s ..$ alpha : num 0.001 330s ..$ undo : num 0 330s ..$ joinSegments : logi TRUE 330s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 330s .. ..$ chromosome: int 1 330s .. ..$ start : num 554484 330s .. ..$ end : num 1.44e+08 330s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 330s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 330s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.03 0 0 330s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 330s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 330s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 330s DH segmentation (locally-indexed) rows: 330s startRow endRow 330s 1 10 7594 330s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 330s DH segmentation rows: 330s startRow endRow 330s 1 10 7594 330s Segmenting DH signals...done 330s DH segmentation table: 330s dhStart dhEnd dhNbrOfLoci dhMean 330s 1 554484 143926517 2111 0.5237 330s startRow endRow 330s 1 10 7594 330s Rows: 330s [1] 1 330s TCN segmentation rows: 330s startRow endRow 330s 1 1 7599 330s TCN and DH segmentation rows: 330s startRow endRow 330s 1 1 7599 330s startRow endRow 330s 1 10 7594 330s NULL 330s TCN segmentation (expanded) rows: 330s startRow endRow 330s 1 1 7599 330s TCN and DH segmentation rows: 330s startRow endRow 330s 1 1 7599 330s 2 7600 10267 330s 3 10268 14658 330s startRow endRow 330s 1 10 7594 330s startRow endRow 330s 1 1 7599 330s Total CN segmentation table (expanded): 330s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 330s 1 1 554484 143926517 7599 1.3859 2111 2111 330s (TCN,DH) segmentation for one total CN segment: 330s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 1 1 1 1 554484 143926517 7599 1.3859 2111 330s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 330s 1 2111 554484 143926517 2111 0.5237 330s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 330s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 330s Number of TCN loci in segment: 2668 330s Locus data for TCN segment: 330s 'data.frame': 2668 obs. of 5 variables: 330s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 330s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 330s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 330s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 330s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 330s Number of loci: 2668 330s Number of SNPs: 774 (29.01%) 330s Number of heterozygous SNPs: 774 (100.00%) 330s Chromosome: 1 330s Segmenting DH signals... 330s Segmenting by CBS... 330s Chromosome: 1 330s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 330s Segmenting by CBS...done 330s List of 4 330s $ data :'data.frame': 2668 obs. of 4 variables: 330s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 330s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 330s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 330s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 330s $ output :'data.frame': 1 obs. of 6 variables: 330s ..$ sampleName: chr NA 330s ..$ chromosome: int 1 330s ..$ start : num 1.44e+08 330s ..$ end : num 1.85e+08 330s ..$ nbrOfLoci : int 774 330s ..$ mean : num 0.154 330s $ segRows:'data.frame': 1 obs. of 2 variables: 330s ..$ startRow: int 15 330s ..$ endRow : int 2664 330s $ params :List of 5 330s ..$ alpha : num 0.001 330s ..$ undo : num 0 330s ..$ joinSegments : logi TRUE 330s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 330s .. ..$ chromosome: int 1 330s .. ..$ start : num 1.44e+08 330s .. ..$ end : num 1.85e+08 330s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 330s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 330s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.015 0 0.015 0 0 330s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 330s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 330s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 330s DH segmentation (locally-indexed) rows: 330s startRow endRow 330s 1 15 2664 330s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 330s DH segmentation rows: 330s startRow endRow 330s 1 7614 10263 330s Segmenting DH signals...done 330s DH segmentation table: 330s dhStart dhEnd dhNbrOfLoci dhMean 330s 1 143926517 185449813 774 0.1542 330s startRow endRow 330s 1 7614 10263 330s Rows: 330s [1] 2 330s TCN segmentation rows: 330s startRow endRow 330s 2 7600 10267 330s TCN and DH segmentation rows: 330s startRow endRow 330s 2 7600 10267 330s startRow endRow 330s 1 7614 10263 330s startRow endRow 330s 1 1 7599 330s TCN segmentation (expanded) rows: 330s startRow endRow 330s 1 1 7599 330s 2 7600 10267 330s TCN and DH segmentation rows: 330s startRow endRow 330s 1 1 7599 330s 2 7600 10267 330s 3 10268 14658 330s startRow endRow 330s 1 10 7594 330s 2 7614 10263 330s startRow endRow 330s 1 1 7599 330s 2 7600 10267 330s Total CN segmentation table (expanded): 330s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 330s 2 1 143926517 185449813 2668 2.0704 774 774 330s (TCN,DH) segmentation for one total CN segment: 330s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 2 2 1 1 143926517 185449813 2668 2.0704 774 330s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 330s 2 774 143926517 185449813 774 0.1542 330s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 330s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 330s Number of TCN loci in segment: 4391 330s Locus data for TCN segment: 330s 'data.frame': 4391 obs. of 5 variables: 330s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 330s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 330s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 330s $ rho : num NA 0.0308 NA 0.2533 NA ... 330s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 330s Number of loci: 4391 330s Number of SNPs: 1311 (29.86%) 330s Number of heterozygous SNPs: 1311 (100.00%) 330s Chromosome: 1 330s Segmenting DH signals... 330s Segmenting by CBS... 330s Chromosome: 1 330s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 330s Segmenting by CBS...done 330s List of 4 330s $ data :'data.frame': 4391 obs. of 4 variables: 330s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 330s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 330s ..$ y : num [1:4391] NA 0.0308 NA 0.2533 NA ... 330s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 330s $ output :'data.frame': 1 obs. of 6 variables: 330s ..$ sampleName: chr NA 330s ..$ chromosome: int 1 330s ..$ start : num 1.85e+08 330s ..$ end : num 2.47e+08 330s ..$ nbrOfLoci : int 1311 330s ..$ mean : num 0.251 330s $ segRows:'data.frame': 1 obs. of 2 variables: 330s ..$ startRow: int 2 330s ..$ endRow : int 4388 330s $ params :List of 5 330s ..$ alpha : num 0.001 330s ..$ undo : num 0 330s ..$ joinSegments : logi TRUE 330s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 330s .. ..$ chromosome: int 1 330s .. ..$ start : num 1.85e+08 330s .. ..$ end : num 2.47e+08 330s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 330s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 330s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.024 0 0.024 0 0 330s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 330s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 330s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 330s DH segmentation (locally-indexed) rows: 330s startRow endRow 330s 1 2 4388 330s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 330s DH segmentation rows: 330s startRow endRow 330s 1 10269 14655 330s Segmenting DH signals...done 330s DH segmentation table: 330s dhStart dhEnd dhNbrOfLoci dhMean 330s 1 185449813 247137334 1311 0.2512 330s startRow endRow 330s 1 10269 14655 330s Rows: 330s [1] 3 330s TCN segmentation rows: 330s startRow endRow 330s 3 10268 14658 330s TCN and DH segmentation rows: 330s startRow endRow 330s 3 10268 14658 330s startRow endRow 330s 1 10269 14655 330s startRow endRow 330s 1 1 7599 330s 2 7600 10267 330s TCN segmentation (expanded) rows: 330s startRow endRow 330s 1 1 7599 330s 2 7600 10267 330s 3 10268 14658 330s TCN and DH segmentation rows: 330s startRow endRow 330s 1 1 7599 330s 2 7600 10267 330s 3 10268 14658 330s startRow endRow 330s 1 10 7594 330s 2 7614 10263 330s 3 10269 14655 330s startRow endRow 330s 1 1 7599 330s 2 7600 10267 330s 3 10268 14658 330s Total CN segmentation table (expanded): 330s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 330s 3 1 185449813 247137334 4391 2.6341 1311 1311 330s (TCN,DH) segmentation for one total CN segment: 330s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 3 3 1 1 185449813 247137334 4391 2.6341 1311 330s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 330s 3 1311 185449813 247137334 1311 0.2512 330s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 330s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 1 1 1 1 554484 143926517 7599 1.3859 2111 330s 2 1 2 1 143926517 185449813 2668 2.0704 774 330s 3 1 3 1 185449813 247137334 4391 2.6341 1311 330s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 330s 1 2111 554484 143926517 2111 0.5237 330s 2 774 143926517 185449813 774 0.1542 330s 3 1311 185449813 247137334 1311 0.2512 330s Calculating (C1,C2) per segment... 330s Calculating (C1,C2) per segment...done 330s Number of segments: 3 330s Segmenting paired tumor-normal signals using Paired PSCBS...done 330s Post-segmenting TCNs... 330s Number of segments: 3 330s Number of chromosomes: 1 330s [1] 1 330s Chromosome 1 ('chr01') of 1... 330s Rows: 330s [1] 1 2 3 330s Number of segments: 3 330s TCN segment #1 ('1') of 3... 330s Nothing todo. Only one DH segmentation. Skipping. 330s TCN segment #1 ('1') of 3...done 330s TCN segment #2 ('2') of 3... 330s Nothing todo. Only one DH segmentation. Skipping. 330s TCN segment #2 ('2') of 3...done 330s TCN segment #3 ('3') of 3... 330s Nothing todo. Only one DH segmentation. Skipping. 330s TCN segment #3 ('3') of 3...done 330s Chromosome 1 ('chr01') of 1...done 330s Update (C1,C2) per segment... 330s Update (C1,C2) per segment...done 330s Post-segmenting TCNs...done 330s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 1 1 1 1 554484 143926517 7599 1.3859 2111 330s 2 1 2 1 143926517 185449813 2668 2.0704 774 330s 3 1 3 1 185449813 247137334 4391 2.6341 1311 330s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 330s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 330s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 330s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 330s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 1 1 1 1 554484 143926517 7599 1.3859 2111 330s 2 1 2 1 143926517 185449813 2668 2.0704 774 330s 3 1 3 1 185449813 247137334 4391 2.6341 1311 330s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 330s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 330s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 330s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 330s > print(fit) 330s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 1 1 1 1 554484 143926517 7599 1.3859 2111 330s 2 1 2 1 143926517 185449813 2668 2.0704 774 330s 3 1 3 1 185449813 247137334 4391 2.6341 1311 330s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 330s 1 2111 2111 0.5237 0.3300521 1.055848 330s 2 774 774 0.1542 0.8755722 1.194828 330s 3 1311 1311 0.2512 0.9862070 1.647893 330s > 330s > # Plot results 330s > plotTracks(fit) 330s > 330s > 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > # Bootstrap segment level estimates 330s > # (used by the AB caller, which, if skipped here, 330s > # will do it automatically) 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > fit <- bootstrapTCNandDHByRegion(fit, B=B, verbose=-10) 330s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 330s Already done? 330s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 330s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 330s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 330s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 330s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 330s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 330s Number of loci: 14658 330s Number of SNPs: 4196 330s Number of non-SNPs: 10462 330s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 330s num [1:3, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : NULL 330s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 330s Segment #1 (chr 1, tcnId=1, dhId=1) of 3... 330s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 1 1 1 1 554484 143926517 7599 1.3859 2111 330s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 330s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 330s Number of TCNs: 7599 330s Number of DHs: 2111 330s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 330s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 330s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 330s Identify loci used to bootstrap DH means... 330s Heterozygous SNPs to resample for DH: 330s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 330s Identify loci used to bootstrap DH means...done 330s Identify loci used to bootstrap TCN means... 330s SNPs: 330s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 330s Non-polymorphic loci: 330s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 330s Heterozygous SNPs to resample for TCN: 330s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 330s Homozygous SNPs to resample for TCN: 330s int(0) 330s Non-polymorphic loci to resample for TCN: 330s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 330s Heterozygous SNPs with non-DH to resample for TCN: 330s int(0) 330s Loci to resample for TCN: 330s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 330s Identify loci used to bootstrap TCN means...done 330s Number of (#hets, #homs, #nonSNPs): (2111,0,5488) 330s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 330s Number of bootstrap samples: 100 330s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 330s Segment #1 (chr 1, tcnId=1, dhId=1) of 3...done 330s Segment #2 (chr 1, tcnId=2, dhId=1) of 3... 330s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 2 1 2 1 143926517 185449813 2668 2.0704 774 330s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 330s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 330s Number of TCNs: 2668 330s Number of DHs: 774 330s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 330s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 330s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 330s Identify loci used to bootstrap DH means... 330s Heterozygous SNPs to resample for DH: 330s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 330s Identify loci used to bootstrap DH means...done 330s Identify loci used to bootstrap TCN means... 330s SNPs: 330s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 330s Non-polymorphic loci: 330s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 330s Heterozygous SNPs to resample for TCN: 330s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 330s Homozygous SNPs to resample for TCN: 330s int(0) 330s Non-polymorphic loci to resample for TCN: 330s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 330s Heterozygous SNPs with non-DH to resample for TCN: 330s int(0) 330s Loci to resample for TCN: 330s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 330s Identify loci used to bootstrap TCN means...done 330s Number of (#hets, #homs, #nonSNPs): (774,0,1894) 330s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 330s Number of bootstrap samples: 100 330s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 330s Segment #2 (chr 1, tcnId=2, dhId=1) of 3...done 330s Segment #3 (chr 1, tcnId=3, dhId=1) of 3... 330s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 3 1 3 1 185449813 247137334 4391 2.6341 1311 330s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 330s 3 1311 185449813 247137334 1311 0.2512 0.986207 1.647893 330s Number of TCNs: 4391 330s Number of DHs: 1311 330s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 330s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 330s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 330s Identify loci used to bootstrap DH means... 330s Heterozygous SNPs to resample for DH: 330s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 330s Identify loci used to bootstrap DH means...done 330s Identify loci used to bootstrap TCN means... 330s SNPs: 330s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 330s Non-polymorphic loci: 330s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 330s Heterozygous SNPs to resample for TCN: 330s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 330s Homozygous SNPs to resample for TCN: 330s int(0) 330s Non-polymorphic loci to resample for TCN: 330s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 330s Heterozygous SNPs with non-DH to resample for TCN: 330s int(0) 330s Loci to resample for TCN: 330s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 330s Identify loci used to bootstrap TCN means...done 330s Number of (#hets, #homs, #nonSNPs): (1311,0,3080) 330s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 330s Number of bootstrap samples: 100 330s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 330s Segment #3 (chr 1, tcnId=3, dhId=1) of 3...done 330s Bootstrapped segment mean levels 330s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : NULL 330s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 330s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 330s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : NULL 330s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 330s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 330s Calculating polar (alpha,radius,manhattan) for change points... 330s num [1:2, 1:100, 1:2] -0.5588 -0.0962 -0.5365 -0.1285 -0.5378 ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : NULL 330s ..$ : chr [1:2] "c1" "c2" 330s Bootstrapped change points 330s num [1:2, 1:100, 1:5] -2.89 -1.78 -2.87 -1.86 -2.88 ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : NULL 330s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 330s Calculating polar (alpha,radius,manhattan) for change points...done 330s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 330s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 330s num [1:3, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 330s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 330s Field #1 ('tcn') of 4... 330s Segment #1 of 3... 330s Segment #1 of 3...done 330s Segment #2 of 3... 330s Segment #2 of 3...done 330s Segment #3 of 3... 330s Segment #3 of 3...done 330s Field #1 ('tcn') of 4...done 330s Field #2 ('dh') of 4... 330s Segment #1 of 3... 330s Segment #1 of 3...done 330s Segment #2 of 3... 330s Segment #2 of 3...done 330s Segment #3 of 3... 330s Segment #3 of 3...done 330s Field #2 ('dh') of 4...done 330s Field #3 ('c1') of 4... 330s Segment #1 of 3... 330s Segment #1 of 3...done 330s Segment #2 of 3... 330s Segment #2 of 3...done 330s Segment #3 of 3... 330s Segment #3 of 3...done 330s Field #3 ('c1') of 4...done 330s Field #4 ('c2') of 4... 330s Segment #1 of 3... 330s Segment #1 of 3...done 330s Segment #2 of 3... 330s Segment #2 of 3...done 330s Segment #3 of 3... 330s Segment #3 of 3...done 330s Field #4 ('c2') of 4...done 330s Bootstrap statistics 330s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 330s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 330s Statistical sanity checks (iff B >= 100)... 330s Available summaries: 2.5%, 5%, 95%, 97.5% 330s Available quantiles: 0.025, 0.05, 0.95, 0.975 330s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 330s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 330s Field #1 ('tcn') of 4... 330s Seg 1. mean=1.3859, range=[1.38092,1.3949], n=7599 330s Seg 2. mean=2.0704, range=[2.05747,2.08326], n=2668 330s Seg 3. mean=2.6341, range=[2.62068,2.64694], n=4391 330s Field #1 ('tcn') of 4...done 330s Field #2 ('dh') of 4... 330s Seg 1. mean=0.5237, range=[0.51753,0.532002], n=2111 330s Seg 2. mean=0.1542, range=[0.144468,0.16453], n=774 330s Seg 3. mean=0.2512, range=[0.242575,0.258832], n=1311 330s Field #2 ('dh') of 4...done 330s Field #3 ('c1') of 4... 330s Seg 1. mean=0.330052, range=[0.323996,0.336038], n=2111 330s Seg 2. mean=0.875572, range=[0.86318,0.887699], n=774 330s Seg 3. mean=0.986207, range=[0.975123,0.998982], n=1311 330s Field #3 ('c1') of 4...done 330s Field #4 ('c2') of 4... 330s Seg 1. mean=1.05585, range=[1.05006,1.06231], n=2111 330s Seg 2. mean=1.19483, range=[1.18417,1.2081], n=774 330s Seg 3. mean=1.64789, range=[1.63403,1.66098], n=1311 330s Field #4 ('c2') of 4...done 330s Statistical sanity checks (iff B >= 100)...done 330s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 330s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 330s num [1:2, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 330s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 330s Field #1 ('alpha') of 5... 330s Changepoint #1 of 2... 330s Changepoint #1 of 2...done 330s Changepoint #2 of 2... 330s Changepoint #2 of 2...done 330s Field #1 ('alpha') of 5...done 330s Field #2 ('radius') of 5... 330s Changepoint #1 of 2... 330s Changepoint #1 of 2...done 330s Changepoint #2 of 2... 330s Changepoint #2 of 2...done 330s Field #2 ('radius') of 5...done 330s Field #3 ('manhattan') of 5... 330s Changepoint #1 of 2... 330s Changepoint #1 of 2...done 330s Changepoint #2 of 2... 330s Changepoint #2 of 2...done 330s Field #3 ('manhattan') of 5...done 330s Field #4 ('d1') of 5... 330s Changepoint #1 of 2... 330s Changepoint #1 of 2...done 330s Changepoint #2 of 2... 330s Changepoint #2 of 2...done 330s Field #4 ('d1') of 5...done 330s Field #5 ('d2') of 5... 330s Changepoint #1 of 2... 330s Changepoint #1 of 2...done 330s Changepoint #2 of 2... 330s Changepoint #2 of 2...done 330s Field #5 ('d2') of 5...done 330s Bootstrap statistics 330s num [1:2, 1:4, 1:5] -2.92 -1.86 -2.91 -1.85 -2.87 ... 330s - attr(*, "dimnames")=List of 3 330s ..$ : NULL 330s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 330s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 330s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 330s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 330s > print(fit) 330s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 1 1 1 1 554484 143926517 7599 1.3859 2111 330s 2 1 2 1 143926517 185449813 2668 2.0704 774 330s 3 1 3 1 185449813 247137334 4391 2.6341 1311 330s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 330s 1 2111 2111 0.5237 0.3300521 1.055848 330s 2 774 774 0.1542 0.8755722 1.194828 330s 3 1311 1311 0.2512 0.9862070 1.647893 330s > plotTracks(fit) 330s > 330s > 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > # Calling segments in allelic balance (AB) and 330s > # in loss-of-heterozygosity (LOH) 330s > # NOTE: Ideally, this should be done on whole-genome data 330s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 330s > fit <- callAB(fit, verbose=-10) 330s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 330s delta (offset adjusting for bias in DH): 0.3466649145302 330s alpha (CI quantile; significance level): 0.05 330s Calling segments... 330s Number of segments called allelic balance (AB): 2 (66.67%) of 3 330s Calling segments...done 330s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 330s > fit <- callLOH(fit, verbose=-10) 330s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 330s delta (offset adjusting for bias in C1): 0.771236438183453 330s alpha (CI quantile; significance level): 0.05 330s Calling segments... 330s Number of segments called low C1 (LowC1, "LOH_C1"): 1 (33.33%) of 3 330s Calling segments...done 330s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 330s > print(fit) 330s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 330s 1 1 1 1 554484 143926517 7599 1.3859 2111 330s 2 1 2 1 143926517 185449813 2668 2.0704 774 330s 3 1 3 1 185449813 247137334 4391 2.6341 1311 330s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall lohCall 330s 1 2111 2111 0.5237 0.3300521 1.055848 FALSE TRUE 330s 2 774 774 0.1542 0.8755722 1.194828 TRUE FALSE 330s 3 1311 1311 0.2512 0.9862070 1.647893 TRUE FALSE 330s > plotTracks(fit) 330s > 330s > proc.time() 330s user system elapsed 330s 4.645 0.129 4.772 330s Test segmentByPairedPSCBS,DH passed 330s 0 330s Begin test segmentByPairedPSCBS,calls 338s + cat segmentByPairedPSCBS,calls.Rout 338s 338s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 338s Copyright (C) 2024 The R Foundation for Statistical Computing 338s Platform: arm-unknown-linux-gnueabihf (32-bit) 338s 338s R is free software and comes with ABSOLUTELY NO WARRANTY. 338s You are welcome to redistribute it under certain conditions. 338s Type 'license()' or 'licence()' for distribution details. 338s 338s R is a collaborative project with many contributors. 338s Type 'contributors()' for more information and 338s 'citation()' on how to cite R or R packages in publications. 338s 338s Type 'demo()' for some demos, 'help()' for on-line help, or 338s 'help.start()' for an HTML browser interface to help. 338s Type 'q()' to quit R. 338s 338s [Previously saved workspace restored] 338s 338s > library("PSCBS") 338s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 338s 338s Attaching package: 'PSCBS' 338s 338s The following objects are masked from 'package:base': 338s 338s append, load 338s 338s > 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Load SNP microarray data 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > data <- PSCBS::exampleData("paired.chr01") 338s > str(data) 338s 'data.frame': 73346 obs. of 6 variables: 338s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 338s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 338s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 338s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 338s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 338s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 338s > 338s > 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Paired PSCBS segmentation 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Drop single-locus outliers 338s > dataS <- dropSegmentationOutliers(data) 338s > 338s > # Find centromere 338s > gaps <- findLargeGaps(dataS, minLength=2e6) 338s > knownSegments <- gapsToSegments(gaps) 338s > 338s > 338s > # Run light-weight tests by default 338s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 338s + # Use only every 5th data point 338s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 338s + # Number of segments (for assertion) 338s + nSegs <- 4L 338s + # Number of bootstrap samples (see below) 338s + B <- 100L 338s + } else { 338s + # Full tests 338s + nSegs <- 11L 338s + B <- 1000L 338s + } 338s > 338s > str(dataS) 338s 'data.frame': 14670 obs. of 6 variables: 338s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 338s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 338s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 338s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 338s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 338s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 338s > 338s > # Paired PSCBS segmentation 338s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 338s + seed=0xBEEF, verbose=-10) 338s Segmenting paired tumor-normal signals using Paired PSCBS... 338s Calling genotypes from normal allele B fractions... 338s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 338s Called genotypes: 338s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 338s - attr(*, "modelFit")=List of 1 338s ..$ :List of 7 338s .. ..$ flavor : chr "density" 338s .. ..$ cn : int 2 338s .. ..$ nbrOfGenotypeGroups: int 3 338s .. ..$ tau : num [1:2] 0.315 0.677 338s .. ..$ n : int 14640 338s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 338s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 338s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 338s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 338s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 338s .. .. ..$ type : chr [1:2] "valley" "valley" 338s .. .. ..$ x : num [1:2] 0.315 0.677 338s .. .. ..$ density: num [1:2] 0.522 0.552 338s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 338s muN 338s 0 0.5 1 338s 5221 4198 5251 338s Calling genotypes from normal allele B fractions...done 338s Normalizing betaT using betaN (TumorBoost)... 338s Normalized BAFs: 338s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 338s - attr(*, "modelFit")=List of 5 338s ..$ method : chr "normalizeTumorBoost" 338s ..$ flavor : chr "v4" 338s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 338s .. ..- attr(*, "modelFit")=List of 1 338s .. .. ..$ :List of 7 338s .. .. .. ..$ flavor : chr "density" 338s .. .. .. ..$ cn : int 2 338s .. .. .. ..$ nbrOfGenotypeGroups: int 3 338s .. .. .. ..$ tau : num [1:2] 0.315 0.677 338s .. .. .. ..$ n : int 14640 338s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 338s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 338s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 338s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 338s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 338s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 338s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 338s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 338s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 338s ..$ preserveScale: logi FALSE 338s ..$ scaleFactor : num NA 338s Normalizing betaT using betaN (TumorBoost)...done 338s Setup up data... 338s 'data.frame': 14670 obs. of 7 variables: 338s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 338s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 338s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 338s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 338s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 338s ..- attr(*, "modelFit")=List of 5 338s .. ..$ method : chr "normalizeTumorBoost" 338s .. ..$ flavor : chr "v4" 338s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 338s .. .. ..- attr(*, "modelFit")=List of 1 338s .. .. .. ..$ :List of 7 338s .. .. .. .. ..$ flavor : chr "density" 338s .. .. .. .. ..$ cn : int 2 338s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 338s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 338s .. .. .. .. ..$ n : int 14640 338s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 338s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 338s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 338s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 338s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 338s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 338s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 338s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 338s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 338s .. ..$ preserveScale: logi FALSE 338s .. ..$ scaleFactor : num NA 338s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 338s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 338s ..- attr(*, "modelFit")=List of 1 338s .. ..$ :List of 7 338s .. .. ..$ flavor : chr "density" 338s .. .. ..$ cn : int 2 338s .. .. ..$ nbrOfGenotypeGroups: int 3 338s .. .. ..$ tau : num [1:2] 0.315 0.677 338s .. .. ..$ n : int 14640 338s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 338s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 338s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 338s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 338s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 338s .. .. .. ..$ type : chr [1:2] "valley" "valley" 338s .. .. .. ..$ x : num [1:2] 0.315 0.677 338s .. .. .. ..$ density: num [1:2] 0.522 0.552 338s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 338s Setup up data...done 338s Dropping loci for which TCNs are missing... 338s Number of loci dropped: 12 338s Dropping loci for which TCNs are missing...done 338s Ordering data along genome... 338s 'data.frame': 14658 obs. of 7 variables: 338s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 338s $ x : num 554484 730720 782343 878522 916294 ... 338s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 338s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 338s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 338s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 338s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 338s Ordering data along genome...done 338s Keeping only current chromosome for 'knownSegments'... 338s Chromosome: 1 338s Known segments for this chromosome: 338s chromosome start end length 338s 1 1 -Inf 120992603 Inf 338s 2 1 120992604 141510002 20517398 338s 3 1 141510003 Inf Inf 338s Keeping only current chromosome for 'knownSegments'...done 338s alphaTCN: 0.009 338s alphaDH: 0.001 338s Number of loci: 14658 338s Calculating DHs... 338s Number of SNPs: 14658 338s Number of heterozygous SNPs: 4196 (28.63%) 338s Normalized DHs: 338s num [1:14658] NA NA NA NA NA ... 338s Calculating DHs...done 338s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 338s Produced 2 seeds from this stream for future usage 338s Identification of change points by total copy numbers... 338s Segmenting by CBS... 338s Chromosome: 1 338s Segmenting multiple segments on current chromosome... 338s Number of segments: 3 338s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 338s Produced 3 seeds from this stream for future usage 338s Segmenting by CBS... 338s Chromosome: 1 338s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 338s Segmenting by CBS...done 338s Segmenting by CBS... 338s Chromosome: 1 338s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 338s Segmenting by CBS...done 338s Segmenting multiple segments on current chromosome...done 338s Segmenting by CBS...done 338s List of 4 338s $ data :'data.frame': 14658 obs. of 4 variables: 338s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 338s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 338s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 338s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 338s $ output :'data.frame': 4 obs. of 6 variables: 338s ..$ sampleName: chr [1:4] NA NA NA NA 338s ..$ chromosome: int [1:4] 1 1 1 1 338s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.42e+08 1.85e+08 338s ..$ end : num [1:4] 1.21e+08 1.42e+08 1.85e+08 2.47e+08 338s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 338s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 338s $ segRows:'data.frame': 4 obs. of 2 variables: 338s ..$ startRow: int [1:4] 1 NA 7587 10268 338s ..$ endRow : int [1:4] 7586 NA 10267 14658 338s $ params :List of 5 338s ..$ alpha : num 0.009 338s ..$ undo : num 0 338s ..$ joinSegments : logi TRUE 338s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 338s .. ..$ chromosome: int [1:4] 1 1 2 1 338s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.42e+08 338s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 338s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 338s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 338s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.484 0 0.484 0 0 338s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 338s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 338s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 338s Identification of change points by total copy numbers...done 338s Restructure TCN segmentation results... 338s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 338s 1 1 554484 120992603 7586 1.3853 338s 2 1 120992604 141510002 0 NA 338s 3 1 141510003 185449813 2681 2.0689 338s 4 1 185449813 24713+ [ 0 != 0 ] 338s + echo Test segmentByPairedPSCBS,calls passed 338s + echo 0 338s + echo Begin test segmentByPairedPSCBS,noNormalBAFs 338s + exitcode=0 338s + R CMD BATCH segmentByPairedPSCBS,noNormalBAFs.R 338s 7334 4391 2.6341 338s Number of TCN segments: 4 338s Restructure TCN segmentation results...done 338s Total CN segment #1 ([ 554484,1.20993e+08]) of 4... 338s Number of TCN loci in segment: 7586 338s Locus data for TCN segment: 338s 'data.frame': 7586 obs. of 9 variables: 338s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 338s $ x : num 554484 730720 782343 878522 916294 ... 338s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 338s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 338s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 338s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 338s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 338s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 338s $ rho : num NA NA NA NA NA ... 338s Number of loci: 7586 338s Number of SNPs: 2108 (27.79%) 338s Number of heterozygous SNPs: 2108 (100.00%) 338s Chromosome: 1 338s Segmenting DH signals... 338s Segmenting by CBS... 338s Chromosome: 1 338s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 338s Segmenting by CBS...done 338s List of 4 338s $ data :'data.frame': 7586 obs. of 4 variables: 338s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 338s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 338s ..$ y : num [1:7586] NA NA NA NA NA ... 338s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 338s $ output :'data.frame': 1 obs. of 6 variables: 338s ..$ sampleName: chr NA 338s ..$ chromosome: int 1 338s ..$ start : num 554484 338s ..$ end : num 1.21e+08 338s ..$ nbrOfLoci : int 2108 338s ..$ mean : num 0.512 338s $ segRows:'data.frame': 1 obs. of 2 variables: 338s ..$ startRow: int 10 338s ..$ endRow : int 7574 338s $ params :List of 5 338s ..$ alpha : num 0.001 338s ..$ undo : num 0 338s ..$ joinSegments : logi TRUE 338s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 338s .. ..$ chromosome: int 1 338s .. ..$ start : num 554484 338s .. ..$ end : num 1.21e+08 338s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 338s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 338s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.045 0 0.045 0 0 338s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 338s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 338s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 338s DH segmentation (locally-indexed) rows: 338s startRow endRow 338s 1 10 7574 338s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 338s DH segmentation rows: 338s startRow endRow 338s 1 10 7574 338s Segmenting DH signals...done 338s DH segmentation table: 338s dhStart dhEnd dhNbrOfLoci dhMean 338s 1 554484 120992603 2108 0.5116 338s startRow endRow 338s 1 10 7574 338s Rows: 338s [1] 1 338s TCN segmentation rows: 338s startRow endRow 338s 1 1 7586 338s TCN and DH segmentation rows: 338s startRow endRow 338s 1 1 7586 338s startRow endRow 338s 1 10 7574 338s NULL 338s TCN segmentation (expanded) rows: 338s startRow endRow 338s 1 1 7586 338s TCN and DH segmentation rows: 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s 3 7587 10267 338s 4 10268 14658 338s startRow endRow 338s 1 10 7574 338s startRow endRow 338s 1 1 7586 338s Total CN segmentation table (expanded): 338s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 338s 1 1 554484 120992603 7586 1.3853 2108 2108 338s (TCN,DH) segmentation for one total CN segment: 338s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 338s 1 2108 554484 120992603 2108 0.5116 338s Total CN segment #1 ([ 554484,1.20993e+08]) of 4...done 338s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4... 338s Number of TCN loci in segment: 0 338s Locus data for TCN segment: 338s 'data.frame': 0 obs. of 9 variables: 338s $ chromosome: int 338s $ x : num 338s $ CT : num 338s $ betaT : num 338s $ betaTN : num 338s $ betaN : num 338s $ muN : num 338s $ index : int 338s $ rho : num 338s Number of loci: 0 338s Number of SNPs: 0 (NaN%) 338s Number of heterozygous SNPs: 0 (NaN%) 338s Chromosome: 1 338s Segmenting DH signals... 338s Segmenting by CBS... 338s Chromosome: NA 338s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 338s Segmenting by CBS...done 338s List of 4 338s $ data :'data.frame': 0 obs. of 4 variables: 338s ..$ chromosome: int(0) 338s ..$ x : num(0) 338s ..$ y : num(0) 338s ..$ index : int(0) 338s $ output :'data.frame': 0 obs. of 6 variables: 338s ..$ sampleName: chr(0) 338s ..$ chromosome: num(0) 338s ..$ start : num(0) 338s ..$ end : num(0) 338s ..$ nbrOfLoci : int(0) 338s ..$ mean : num(0) 338s $ segRows:'data.frame': 0 obs. of 2 variables: 338s ..$ startRow: int(0) 338s ..$ endRow : int(0) 338s $ params :List of 5 338s ..$ alpha : num 0.001 338s ..$ undo : num 0 338s ..$ joinSegments : logi TRUE 338s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 338s .. ..$ chromosome: int(0) 338s .. ..$ start : num(0) 338s .. ..$ end : num(0) 338s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 338s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 338s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.002 0 0.002 0 0 338s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 338s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 338s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 338s DH segmentation (locally-indexed) rows: 338s [1] startRow endRow 338s <0 rows> (or 0-length row.names) 338s int(0) 338s DH segmentation rows: 338s [1] startRow endRow 338s <0 rows> (or 0-length row.names) 338s Segmenting DH signals...done 338s DH segmentation table: 338s dhStart dhEnd dhNbrOfLoci dhMean 338s NA NA NA NA NA 338s startRow endRow 338s NA NA NA 338s Rows: 338s [1] 2 338s TCN segmentation rows: 338s startRow endRow 338s 2 NA NA 338s TCN and DH segmentation rows: 338s startRow endRow 338s 2 NA NA 338s startRow endRow 338s NA NA NA 338s startRow endRow 338s 1 1 7586 338s TCN segmentation (expanded) rows: 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s TCN and DH segmentation rows: 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s 3 7587 10267 338s 4 10268 14658 338s startRow endRow 338s 1 10 7574 338s 2 NA NA 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s Total CN segmentation table (expanded): 338s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 338s 2 1 120992604 141510002 0 NA 0 0 338s (TCN,DH) segmentation for one total CN segment: 338s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 2 2 1 1 120992604 141510002 0 NA 0 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 338s 2 0 NA NA NA NA 338s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4...done 338s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4... 338s Number of TCN loci in segment: 2681 338s Locus data for TCN segment: 338s 'data.frame': 2681 obs. of 9 variables: 338s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 338s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 338s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 338s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 338s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 338s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 338s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 338s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 338s $ rho : num 0.117 0.258 NA NA NA ... 338s Number of loci: 2681 338s Number of SNPs: 777 (28.98%) 338s Number of heterozygous SNPs: 777 (100.00%) 338s Chromosome: 1 338s Segmenting DH signals... 338s Segmenting by CBS... 338s Chromosome: 1 338s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 338s Segmenting by CBS...done 338s List of 4 338s $ data :'data.frame': 2681 obs. of 4 variables: 338s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 338s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 338s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 338s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 338s $ output :'data.frame': 1 obs. of 6 variables: 338s ..$ sampleName: chr NA 338s ..$ chromosome: int 1 338s ..$ start : num 1.42e+08 338s ..$ end : num 1.85e+08 338s ..$ nbrOfLoci : int 777 338s ..$ mean : num 0.0973 338s $ segRows:'data.frame': 1 obs. of 2 variables: 338s ..$ startRow: int 1 338s ..$ endRow : int 2677 338s $ params :List of 5 338s ..$ alpha : num 0.001 338s ..$ undo : num 0 338s ..$ joinSegments : logi TRUE 338s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 338s .. ..$ chromosome: int 1 338s .. ..$ start : num 1.42e+08 338s .. ..$ end : num 1.85e+08 338s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 338s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 338s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.012 0 0.012 0 0 338s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 338s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 338s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 338s DH segmentation (locally-indexed) rows: 338s startRow endRow 338s 1 1 2677 338s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 338s DH segmentation rows: 338s startRow endRow 338s 1 7587 10263 338s Segmenting DH signals...done 338s DH segmentation table: 338s dhStart dhEnd dhNbrOfLoci dhMean 338s 1 141510003 185449813 777 0.0973 338s startRow endRow 338s 1 7587 10263 338s Rows: 338s [1] 3 338s TCN segmentation rows: 338s startRow endRow 338s 3 7587 10267 338s TCN and DH segmentation rows: 338s startRow endRow 338s 3 7587 10267 338s startRow endRow 338s 1 7587 10263 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s TCN segmentation (expanded) rows: 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s 3 7587 10267 338s TCN and DH segmentation rows: 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s 3 7587 10267 338s 4 10268 14658 338s startRow endRow 338s 1 10 7574 338s 2 NA NA 338s 3 7587 10263 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s 3 7587 10267 338s Total CN segmentation table (expanded): 338s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 338s 3 1 141510003 185449813 2681 2.0689 777 777 338s (TCN,DH) segmentation for one total CN segment: 338s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 3 3 1 1 141510003 185449813 2681 2.0689 777 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 338s 3 777 141510003 185449813 777 0.0973 338s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4...done 338s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 338s Number of TCN loci in segment: 4391 338s Locus data for TCN segment: 338s 'data.frame': 4391 obs. of 9 variables: 338s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 338s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 338s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 338s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 338s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 338s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 338s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 338s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 338s $ rho : num NA 0.2186 NA 0.0503 NA ... 338s Number of loci: 4391 338s Number of SNPs: 1311 (29.86%) 338s Number of heterozygous SNPs: 1311 (100.00%) 338s Chromosome: 1 338s Segmenting DH signals... 338s Segmenting by CBS... 338s Chromosome: 1 338s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 338s Segmenting by CBS...done 338s List of 4 338s $ data :'data.frame': 4391 obs. of 4 variables: 338s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 338s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 338s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 338s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 338s $ output :'data.frame': 1 obs. of 6 variables: 338s ..$ sampleName: chr NA 338s ..$ chromosome: int 1 338s ..$ start : num 1.85e+08 338s ..$ end : num 2.47e+08 338s ..$ nbrOfLoci : int 1311 338s ..$ mean : num 0.23 338s $ segRows:'data.frame': 1 obs. of 2 variables: 338s ..$ startRow: int 2 338s ..$ endRow : int 4388 338s $ params :List of 5 338s ..$ alpha : num 0.001 338s ..$ undo : num 0 338s ..$ joinSegments : logi TRUE 338s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 338s .. ..$ chromosome: int 1 338s .. ..$ start : num 1.85e+08 338s .. ..$ end : num 2.47e+08 338s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 338s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 338s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.024 0 0.024 0 0 338s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 338s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 338s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 338s DH segmentation (locally-indexed) rows: 338s startRow endRow 338s 1 2 4388 338s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 338s DH segmentation rows: 338s startRow endRow 338s 1 10269 14655 338s Segmenting DH signals...done 338s DH segmentation table: 338s dhStart dhEnd dhNbrOfLoci dhMean 338s 1 185449813 247137334 1311 0.2295 338s startRow endRow 338s 1 10269 14655 338s Rows: 338s [1] 4 338s TCN segmentation rows: 338s startRow endRow 338s 4 10268 14658 338s TCN and DH segmentation rows: 338s startRow endRow 338s 4 10268 14658 338s startRow endRow 338s 1 10269 14655 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s 3 7587 10267 338s TCN segmentation (expanded) rows: 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s 3 7587 10267 338s 4 10268 14658 338s TCN and DH segmentation rows: 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s 3 7587 10267 338s 4 10268 14658 338s startRow endRow 338s 1 10 7574 338s 2 NA NA 338s 3 7587 10263 338s 4 10269 14655 338s startRow endRow 338s 1 1 7586 338s 2 NA NA 338s 3 7587 10267 338s 4 10268 14658 338s Total CN segmentation table (expanded): 338s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 338s 4 1 185449813 247137334 4391 2.6341 1311 1311 338s (TCN,DH) segmentation for one total CN segment: 338s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 4 4 1 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 338s 4 1311 185449813 247137334 1311 0.2295 338s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 338s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s 2 1 2 1 120992604 141510002 0 NA 0 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 338s 1 2108 554484 120992603 2108 0.5116 338s 2 0 NA NA NA NA 338s 3 777 141510003 185449813 777 0.0973 338s 4 1311 185449813 247137334 1311 0.2295 338s Calculating (C1,C2) per segment... 338s Calculating (C1,C2) per segment...done 338s Number of segments: 4 338s Segmenting paired tumor-normal signals using Paired PSCBS...done 338s Post-segmenting TCNs... 338s Number of segments: 4 338s Number of chromosomes: 1 338s [1] 1 338s Chromosome 1 ('chr01') of 1... 338s Rows: 338s [1] 1 2 3 4 338s Number of segments: 4 338s TCN segment #1 ('1') of 4... 338s Nothing todo. Only one DH segmentation. Skipping. 338s TCN segment #1 ('1') of 4...done 338s TCN segment #2 ('2') of 4... 338s Nothing todo. Only one DH segmentation. Skipping. 338s TCN segment #2 ('2') of 4...done 338s TCN segment #3 ('3') of 4... 338s Nothing todo. Only one DH segmentation. Skipping. 338s TCN segment #3 ('3') of 4...done 338s TCN segment #4 ('4') of 4... 338s Nothing todo. Only one DH segmentation. Skipping. 338s TCN segment #4 ('4') of 4...done 338s Chromosome 1 ('chr01') of 1...done 338s Update (C1,C2) per segment... 338s Update (C1,C2) per segment...done 338s Post-segmenting TCNs...done 338s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s 2 1 2 1 120992604 141510002 0 NA 0 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 338s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 338s 2 0 NA NA NA NA NA NA 338s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 338s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 338s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s 2 1 2 1 120992604 141510002 0 NA 0 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 338s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 338s 2 0 NA NA NA NA NA NA 338s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 338s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 338s > print(fit) 338s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s 2 1 2 1 120992604 141510002 0 NA 0 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 338s 1 2108 2108 0.5116 0.3382903 1.047010 338s 2 0 NA NA NA NA 338s 3 777 777 0.0973 0.9337980 1.135102 338s 4 1311 1311 0.2295 1.0147870 1.619313 338s > 338s > # Plot results 338s > plotTracks(fit) 338s > 338s > # Sanity check 338s > stopifnot(nbrOfSegments(fit) == nSegs) 338s > 338s > 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Bootstrap segment level estimates 338s > # (used by the AB caller, which, if skipped here, 338s > # will do it automatically) 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > fit <- bootstrapTCNandDHByRegion(fit, B=B, verbose=-10) 338s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 338s Already done? 338s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 338s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 338s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 338s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 338s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 338s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 338s Number of loci: 14658 338s Number of SNPs: 4196 338s Number of non-SNPs: 10462 338s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 338s num [1:4, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : NULL 338s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 338s Segment #1 (chr 1, tcnId=1, dhId=1) of 4... 338s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 338s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.04701 338s Number of TCNs: 7586 338s Number of DHs: 2108 338s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 338s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 338s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 338s Identify loci used to bootstrap DH means... 338s Heterozygous SNPs to resample for DH: 338s int [1:2108] 10 12 24 28 31 33 34 39 46 48 ... 338s Identify loci used to bootstrap DH means...done 338s Identify loci used to bootstrap TCN means... 338s SNPs: 338s int [1:2108] 10 12 24 28 31 33 34 39 46 48 ... 338s Non-polymorphic loci: 338s int [1:5478] 1 2 3 4 5 6 7 8 9 11 ... 338s Heterozygous SNPs to resample for TCN: 338s int [1:2108] 10 12 24 28 31 33 34 39 46 48 ... 338s Homozygous SNPs to resample for TCN: 338s int(0) 338s Non-polymorphic loci to resample for TCN: 338s int [1:5478] 1 2 3 4 5 6 7 8 9 11 ... 338s Heterozygous SNPs with non-DH to resample for TCN: 338s int(0) 338s Loci to resample for TCN: 338s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 338s Identify loci used to bootstrap TCN means...done 338s Number of (#hets, #homs, #nonSNPs): (2108,0,5478) 338s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 338s Number of bootstrap samples: 100 338s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 338s Segment #1 (chr 1, tcnId=1, dhId=1) of 4...done 338s Segment #2 (chr 1, tcnId=2, dhId=1) of 4... 338s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 2 1 2 1 120992604 141510002 0 NA 0 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 338s 2 0 NA NA 0 NA NA NA 338s Number of TCNs: 0 338s Number of DHs: 0 338s int 0 338s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 338s int(0) 338s Identify loci used to bootstrap DH means... 338s Heterozygous SNPs to resample for DH: 338s int 0 338s Identify loci used to bootstrap DH means...done 338s Identify loci used to bootstrap TCN means... 338s SNPs: 338s int(0) 338s Non-polymorphic loci: 338s int(0) 338s Heterozygous SNPs to resample for TCN: 338s int(0) 338s Homozygous SNPs to resample for TCN: 338s int(0) 338s Non-polymorphic loci to resample for TCN: 338s int(0) 338s Heterozygous SNPs with non-DH to resample for TCN: 338s int(0) 338s Loci to resample for TCN: 338s int(0) 338s Identify loci used to bootstrap TCN means...done 338s Number of (#hets, #homs, #nonSNPs): (0,0,0) 338s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 338s Number of bootstrap samples: 100 338s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 338s Segment #2 (chr 1, tcnId=2, dhId=1) of 4...done 338s Segment #3 (chr 1, tcnId=3, dhId=1) of 4... 338s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 338s 3 777 141510003 185449813 777 0.0973 0.933798 1.135102 338s Number of TCNs: 2681 338s Number of DHs: 777 338s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 338s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 338s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 338s Identify loci used to bootstrap DH means... 338s Heterozygous SNPs to resample for DH: 338s int [1:777] 7587 7588 7594 7614 7616 7626 7627 7628 7635 7638 ... 338s Identify loci used to bootstrap DH means...done 338s Identify loci used to bootstrap TCN means... 338s SNPs: 338s int [1:777] 7587 7588 7594 7614 7616 7626 7627 7628 7635 7638 ... 338s Non-polymorphic loci: 338s int [1:1904] 7589 7590 7591 7592 7593 7595 7596 7597 7598 7599 ... 338s Heterozygous SNPs to resample for TCN: 338s int [1:777] 7587 7588 7594 7614 7616 7626 7627 7628 7635 7638 ... 338s Homozygous SNPs to resample for TCN: 338s int(0) 338s Non-polymorphic loci to resample for TCN: 338s int [1:1904] 7589 7590 7591 7592 7593 7595 7596 7597 7598 7599 ... 338s Heterozygous SNPs with non-DH to resample for TCN: 338s int(0) 338s Loci to resample for TCN: 338s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 338s Identify loci used to bootstrap TCN means...done 338s Number of (#hets, #homs, #nonSNPs): (777,0,1904) 338s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 338s Number of bootstrap samples: 100 338s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 338s Segment #3 (chr 1, tcnId=3, dhId=1) of 4...done 338s Segment #4 (chr 1, tcnId=4, dhId=1) of 4... 338s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 338s 4 1311 185449813 247137334 1311 0.2295 1.014787 1.619313 338s Number of TCNs: 4391 338s Number of DHs: 1311 338s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 338s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 338s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 338s Identify loci used to bootstrap DH means... 338s Heterozygous SNPs to resample for DH: 338s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 338s Identify loci used to bootstrap DH means...done 338s Identify loci used to bootstrap TCN means... 338s SNPs: 338s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 338s Non-polymorphic loci: 338s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 338s Heterozygous SNPs to resample for TCN: 338s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 338s Homozygous SNPs to resample for TCN: 338s int(0) 338s Non-polymorphic loci to resample for TCN: 338s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 338s Heterozygous SNPs with non-DH to resample for TCN: 338s int(0) 338s Loci to resample for TCN: 338s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 338s Identify loci used to bootstrap TCN means...done 338s Number of (#hets, #homs, #nonSNPs): (1311,0,3080) 338s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 338s Number of bootstrap samples: 100 338s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 338s Segment #4 (chr 1, tcnId=4, dhId=1) of 4...done 338s Bootstrapped segment mean levels 338s num [1:4, 1:100, 1:4] 1.39 NA 2.08 2.63 1.38 ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : NULL 338s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 338s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 338s num [1:4, 1:100, 1:4] 1.39 NA 2.08 2.63 1.38 ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : NULL 338s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 338s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 338s Calculating polar (alpha,radius,manhattan) for change points... 338s num [1:3, 1:100, 1:2] NA NA -0.0752 NA NA ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : NULL 338s ..$ : chr [1:2] "c1" "c2" 338s Bootstrapped change points 338s num [1:3, 1:100, 1:5] NA NA -1.73 NA NA ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : NULL 338s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 338s Calculating polar (alpha,radius,manhattan) for change points...done 338s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 338s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 338s num [1:4, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 338s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 338s Field #1 ('tcn') of 4... 338s Segment #1 of 4... 338s Segment #1 of 4...done 338s Segment #2 of 4... 338s Segment #2 of 4...done 338s Segment #3 of 4... 338s Segment #3 of 4...done 338s Segment #4 of 4... 338s Segment #4 of 4...done 338s Field #1 ('tcn') of 4...done 338s Field #2 ('dh') of 4... 338s Segment #1 of 4... 338s Segment #1 of 4...done 338s Segment #2 of 4... 338s Segment #2 of 4...done 338s Segment #3 of 4... 338s Segment #3 of 4...done 338s Segment #4 of 4... 338s Segment #4 of 4...done 338s Field #2 ('dh') of 4...done 338s Field #3 ('c1') of 4... 338s Segment #1 of 4... 338s Segment #1 of 4...done 338s Segment #2 of 4... 338s Segment #2 of 4...done 338s Segment #3 of 4... 338s Segment #3 of 4...done 338s Segment #4 of 4... 338s Segment #4 of 4...done 338s Field #3 ('c1') of 4...done 338s Field #4 ('c2') of 4... 338s Segment #1 of 4... 338s Segment #1 of 4...done 338s Segment #2 of 4... 338s Segment #2 of 4...done 338s Segment #3 of 4... 338s Segment #3 of 4...done 338s Segment #4 of 4... 338s Segment #4 of 4...done 338s Field #4 ('c2') of 4...done 338s Bootstrap statistics 338s num [1:4, 1:4, 1:4] 1.38 NA 2.06 2.63 1.38 ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 338s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 338s Statistical sanity checks (iff B >= 100)... 338s Available summaries: 2.5%, 5%, 95%, 97.5% 338s Available quantiles: 0.025, 0.05, 0.95, 0.975 338s num [1:4, 1:4, 1:4] 1.38 NA 2.06 2.63 1.38 ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 338s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 338s Field #1 ('tcn') of 4... 338s Seg 1. mean=1.3853, range=[1.37909,1.39287], n=7586 338s Seg 2. mean=NA, range=[NA,NA], n=0 338s Seg 3. mean=2.0689, range=[2.05903,2.079], n=2681 338s Seg 4. mean=2.6341, range=[2.62504,2.64649], n=4391 338s Field #1 ('tcn') of 4...done 338s Field #2 ('dh') of 4... 338s Seg 1. mean=0.5116, range=[0.502148,0.519941], n=2108 338s Seg 2. mean=NA, range=[NA,NA], n=NA 338s Seg 3. mean=0.0973, range=[0.0906366,0.105818], n=777 338s Seg 4. mean=0.2295, range=[0.222919,0.237005], n=1311 338s Field #2 ('dh') of 4...done 338s Field #3 ('c1') of 4... 338s Seg 1. mean=0.33829, range=[0.332209,0.345936], n=2108 338s Seg 2. mean=NA, range=[NA,NA], n=NA 338s Seg 3. mean=0.933798, range=[0.924112,0.941776], n=777 338s Seg 4. mean=1.01479, range=[1.00381,1.02461], n=1311 338s Field #3 ('c1') of 4...done 338s Field #4 ('c2') of 4... 338s Seg 1. mean=1.04701, range=[1.03882,1.05318], n=2108 338s Seg 2. mean=NA, range=[NA,NA], n=NA 338s Seg 3. mean=1.1351, range=[1.12454,1.1465], n=777 338s Seg 4. mean=1.61931, range=[1.60862,1.63328], n=1311 338s Field #4 ('c2') of 4...done 338s Statistical sanity checks (iff B >= 100)...done 338s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 338s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 338s num [1:3, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 338s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 338s Field #1 ('alpha') of 5... 338s Changepoint #1 of 3... 338s Changepoint #1 of 3...done 338s Changepoint #2 of 3... 338s Changepoint #2 of 3...done 338s Changepoint #3 of 3... 338s Changepoint #3 of 3...done 338s Field #1 ('alpha') of 5...done 338s Field #2 ('radius') of 5... 338s Changepoint #1 of 3... 338s Changepoint #1 of 3...done 338s Changepoint #2 of 3... 338s Changepoint #2 of 3...done 338s Changepoint #3 of 3... 338s Changepoint #3 of 3...done 338s Field #2 ('radius') of 5...done 338s Field #3 ('manhattan') of 5... 338s Changepoint #1 of 3... 338s Changepoint #1 of 3...done 338s Changepoint #2 of 3... 338s Changepoint #2 of 3...done 338s Changepoint #3 of 3... 338s Changepoint #3 of 3...done 338s Field #3 ('manhattan') of 5...done 338s Field #4 ('d1') of 5... 338s Changepoint #1 of 3... 338s Changepoint #1 of 3...done 338s Changepoint #2 of 3... 338s Changepoint #2 of 3...done 338s Changepoint #3 of 3... 338s Changepoint #3 of 3...done 338s Field #4 ('d1') of 5...done 338s Field #5 ('d2') of 5... 338s Changepoint #1 of 3... 338s Changepoint #1 of 3...done 338s Changepoint #2 of 3... 338s Changepoint #2 of 3...done 338s Changepoint #3 of 3... 338s Changepoint #3 of 3...done 338s Field #5 ('d2') of 5...done 338s Bootstrap statistics 338s num [1:3, 1:4, 1:5] NA NA -1.77 NA NA ... 338s - attr(*, "dimnames")=List of 3 338s ..$ : NULL 338s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 338s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 338s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 338s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 338s > print(fit) 338s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s 2 1 2 1 120992604 141510002 0 NA 0 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 338s 1 2108 2108 0.5116 0.3382903 1.047010 338s 2 0 NA NA NA NA 338s 3 777 777 0.0973 0.9337980 1.135102 338s 4 1311 1311 0.2295 1.0147870 1.619313 338s > plotTracks(fit) 338s > 338s > 338s > 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Calling segments with run of homozygosity (ROH) 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > fit <- callROH(fit, verbose=-10) 338s Calling ROH... 338s Segment #1 of 4... 338s Calling ROH for a single segment... 338s Number of SNPs: 7586 338s Calling ROH for a single segment...done 338s Segment #1 of 4...done 338s Segment #2 of 4... 338s Calling ROH for a single segment... 338s Number of SNPs: 0 338s Calling ROH for a single segment...done 338s Segment #2 of 4...done 338s Segment #3 of 4... 338s Calling ROH for a single segment... 338s Number of SNPs: 2681 338s Calling ROH for a single segment...done 338s Segment #3 of 4...done 338s Segment #4 of 4... 338s Calling ROH for a single segment... 338s Number of SNPs: 4391 338s Calling ROH for a single segment...done 338s Segment #4 of 4...done 338s ROH calls: 338s logi [1:4] FALSE NA FALSE FALSE 338s Mode FALSE NA's 338s logical 3 1 338s Calling ROH...done 338s > print(fit) 338s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s 2 1 2 1 120992604 141510002 0 NA 0 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall 338s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE 338s 2 0 NA NA NA NA NA 338s 3 777 777 0.0973 0.9337980 1.135102 FALSE 338s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE 338s > plotTracks(fit) 338s > 338s > 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Estimate background 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > kappa <- estimateKappa(fit, verbose=-10) 338s Estimate global background (including normal contamination and more)... 338s Number of segments: 3 338s Estimating threshold Delta0.5 from the empirical density of C1:s... 338s adjust: 1 338s minDensity: 0.2 338s ploidy: 2 338s All peaks: 338s type x density 338s 1 peak 0.3362194 1.101272 338s 3 peak 0.9811492 1.065711 338s C1=0 and C1=1 peaks: 338s type x density 338s 1 peak 0.3362194 1.101272 338s 3 peak 0.9811492 1.065711 338s Estimate of Delta0.5: 0.65868427808456 338s Estimating threshold Delta0.5 from the empirical density of C1:s...done 338s Number of segments with C1 < Delta0.5: 1 338s Estimate of kappa: 0.33829026 338s Estimate global background (including normal contamination and more)...done 338s Warning message: 338s In density.default(c1, weights = weights, adjust = adjust, from = from, : 338s Selecting bandwidth *not* using 'weights' 338s > print(kappa) 338s [1] 0.3382903 338s > ## [1] 0.226011 338s > 338s > 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Calling segments in allelic balance (AB) 338s > # NOTE: Ideally, this should be done on whole-genome data 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Explicitly estimate the threshold in DH for calling AB 338s > # (which be done by default by the caller, if skipped here) 338s > deltaAB <- estimateDeltaAB(fit, flavor="qq(DH)", verbose=-10) 338s Estimating DH threshold for calling allelic imbalances... 338s flavor: qq(DH) 338s scale: 1 338s Estimating DH threshold for AB caller... 338s quantile #1: 0.05 338s Symmetric quantile #2: 0.9 338s Number of segments: 3 338s Weighted 5% quantile of DH: 0.257710 338s Number of segments with small DH: 2 338s Number of data points: 7072 338s Number of finite data points: 2088 338s Estimate of (1-0.9):th and 50% quantiles: (0.0310411,0.163658) 338s Estimate of 0.9:th "symmetric" quantile: 0.296275 338s Estimating DH threshold for AB caller...done 338s Estimated delta: 0.296 338s Estimating DH threshold for calling allelic imbalances...done 338s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 338s + # Ad hoc workaround for not utilizing all of the data 338s + # in the test, which results in a poor estimate 338s + deltaAB <- 0.165 338s + } 338s > print(deltaAB) 338s [1] 0.165 338s > ## [1] 0.1657131 338s > 338s > fit <- callAB(fit, delta=deltaAB, verbose=-10) 338s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 338s delta (offset adjusting for bias in DH): 0.165 338s alpha (CI quantile; significance level): 0.05 338s Calling segments... 338s Number of segments called allelic balance (AB): 1 (25.00%) of 4 338s Calling segments...done 338s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 338s > print(fit) 338s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s 2 1 2 1 120992604 141510002 0 NA 0 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall 338s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE FALSE 338s 2 0 NA NA NA NA NA NA 338s 3 777 777 0.0973 0.9337980 1.135102 FALSE TRUE 338s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE FALSE 338s > plotTracks(fit) 338s > 338s > # Even if not explicitly specified, the estimated 338s > # threshold parameter is returned by the caller 338s > stopifnot(fit$params$deltaAB == deltaAB) 338s > 338s > 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Calling segments in loss-of-heterozygosity (LOH) 338s > # NOTE: Ideally, this should be done on whole-genome data 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Explicitly estimate the threshold in C1 for calling LOH 338s > # (which be done by default by the caller, if skipped here) 338s > deltaLOH <- estimateDeltaLOH(fit, flavor="minC1|nonAB", verbose=-10) 338s Estimating DH threshold for calling LOH... 338s flavor: minC1|nonAB 338s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1... 338s Argument 'midpoint': 0.5 338s Number of segments: 4 338s Number of segments in allelic balance: 1 (25.0%) of 4 338s Number of segments not in allelic balance: 2 (50.0%) of 4 338s Number of segments in allelic balance and TCN <= 3.00: 1 (25.0%) of 4 338s C: 2.07 338s Corrected C1 (=C/2): 1.03 338s Number of DHs: 777 338s Weights: 1 338s Weighted median of (corrected) C1 in allelic balance: 1.034 338s Smallest C1 among segments not in allelic balance: 0.338 338s There are 1 segments with in total 2108 heterozygous SNPs with this level. 338s Midpoint between the two: 0.686 338s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1...done 338s delta: 0.686 338s Estimating DH threshold for calling LOH...done 338s > print(deltaLOH) 338s [1] 0.6863701 338s > ## [1] 0.625175 338s > 338s > fit <- callLOH(fit, delta=deltaLOH, verbose=-10) 338s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 338s delta (offset adjusting for bias in C1): 0.68637013 338s alpha (CI quantile; significance level): 0.05 338s Calling segments... 338s Number of segments called low C1 (LowC1, "LOH_C1"): 1 (25.00%) of 4 338s Calling segments...done 338s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 338s > print(fit) 338s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s 2 1 2 1 120992604 141510002 0 NA 0 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall lohCall 338s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE FALSE TRUE 338s 2 0 NA NA NA NA NA NA NA 338s 3 777 777 0.0973 0.9337980 1.135102 FALSE TRUE FALSE 338s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE FALSE FALSE 338s > plotTracks(fit) 338s > 338s > # Even if not explicitly specified, the estimated 338s > # threshold parameter is returned by the caller 338s > stopifnot(fit$params$deltaLOH == deltaLOH) 338s > 338s > 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > # Calling segments that are gained, copy neutral, and lost 338s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 338s > fit <- callGNL(fit, verbose=-10) 338s Calling gain, neutral, and loss based TCNs of AB segments... 338s Calling neutral TCNs... 338s callCopyNeutralByTCNofAB... 338s Alpha: 0.05 338s Delta CN: 0.33085487 338s Calling copy-neutral segments... 338s Retrieve TCN confidence intervals for all segments... 338s Interval: [0.025,0.975] 338s Retrieve TCN confidence intervals for all segments...done 338s Estimating TCN confidence interval of copy-neutral AB segments... 338s calcStatsForCopyNeutralABs... 338s Identifying copy neutral AB segments... 338s Number of AB segments: 1 338s Identifying segments that are copy neutral states... 338s Number of segments in allelic balance: 1 338s Identifying segments that are copy neutral states...done 338s Number of copy-neutral AB segments: 1 338s Extracting all copy neutral AB segments across all chromosomes into one big segment... 338s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall lohCall 338s 3 777 777 0.0973 0.933798 1.135102 FALSE TRUE FALSE 338s Extracting all copy neutral AB segments across all chromosomes into one big segment...done 338s Identifying copy neutral AB segments...done 338s Bootstrap the identified copy-neutral states... 338s Bootstrap the identified copy-neutral states...done 338s tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets dhNbrOfLoci dhMean c1Mean 338s 3 2681 2.0689 777 777 777 0.0973 0.933798 338s c2Mean tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% 338s 3 1.135102 2.055164 2.057694 2.078831 2.081454 0.08974138 0.09080508 0.1035891 338s dh_97.5% c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% 338s 3 0.1050478 0.923788 0.925412 0.9417056 0.9433752 1.124908 1.126631 1.143571 338s c2_97.5% 338s 3 1.145214 338s calcStatsForCopyNeutralABs...done 338s Bootstrap statistics for copy-neutral AB segments: 338s tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets dhNbrOfLoci dhMean c1Mean 338s 3 2681 2.0689 777 777 777 0.0973 0.933798 338s c2Mean tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% 338s 3 1.135102 2.055164 2.057694 2.078831 2.081454 0.08974138 0.09080508 0.1035891 338s dh_97.5% c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% 338s 3 0.1050478 0.923788 0.925412 0.9417056 0.9433752 1.124908 1.126631 1.143571 338s c2_97.5% 338s 3 1.145214 338s [1] "TCN statistics:" 338s tcnMean tcn_2.5% tcn_5% tcn_95% tcn_97.5% 338s 2.068900 2.055164 2.057694 2.078831 2.081454 338s 95%-confidence interval of TCN mean for the copy-neutral state: [2.05516,2.08145] (mean=2.0689) 338s Estimating TCN confidence interval of copy-neutral AB segments...done 338s Identify all copy-neutral segments... 338s DeltaCN: +/-0.330855 338s Call ("acceptance") region: [1.72431,2.41231] 338s Total number of segments: 4 338s Number of segments called allelic balance: 1 338s Number of segments called copy neutral: 1 338s Number of AB segments called copy neutral: 1 338s Number of non-AB segments called copy neutral: 0 338s Identify all copy-neutral segments...done 338s Calling copy-neutral segments...done 338s callCopyNeutralByTCNofAB...done 338s Calling neutral TCNs...done 338s Number of NTCN calls: 1 (25.00%) of 4 338s Mean TCN of AB segments: 2.06831 338s Calling loss... 338s Number of loss calls: 1 (25.00%) of 4 338s Calling loss...done 338s Calling gain... 338s Number of loss calls: 1 (25.00%) of 4 338s Calling gain...done 338s Calling gain, neutral, and loss based TCNs of AB segments...done 338s Warning message: 338s In density.default(c1, weights = weights, adjust = adjust, from = from, : 338s Selecting bandwidth *not* using 'weights' 338s > print(fit) 338s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 338s 1 1 1 1 554484 120992603 7586 1.3853 2108 338s 2 1 2 1 120992604 141510002 0 NA 0 338s 3 1 3 1 141510003 185449813 2681 2.0689 777 338s 4 1 4 1 185449813 247137334 4391 2.6341 1311 338s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall lohCall 338s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE FALSE TRUE 338s 2 0 NA NA NA NA NA NA NA 338s 3 777 777 0.0973 0.9337980 1.135102 FALSE TRUE FALSE 338s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE FALSE FALSE 338s ntcnCall lossCall gainCall 338s 1 FALSE TRUE FALSE 338s 2 NA NA NA 338s 3 TRUE FALSE FALSE 338s 4 FALSE FALSE TRUE 338s > plotTracks(fit) 338s > 338s > proc.time() 338s user system elapsed 338s 7.218 0.130 7.349 338s Test segmentByPairedPSCBS,calls passed 338s 0 338s Begin test segmentByPairedPSCBS,noNormalBAFs 343s + cat segmentByPairedPSCBS,noNormalBAFs.Rout 343s + [ 0 != 0 ] 343s + echo Test segmentByPairedPSCBS,noNormalBAFs passed 343s + echo 0 343s + echo Begin test segmentByPairedPSCBS,report 343s + exitcode=0 343s + R CMD BATCH segmentByPairedPSCBS,report.R 343s 343s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 343s Copyright (C) 2024 The R Foundation for Statistical Computing 343s Platform: arm-unknown-linux-gnueabihf (32-bit) 343s 343s R is free software and comes with ABSOLUTELY NO WARRANTY. 343s You are welcome to redistribute it under certain conditions. 343s Type 'license()' or 'licence()' for distribution details. 343s 343s R is a collaborative project with many contributors. 343s Type 'contributors()' for more information and 343s 'citation()' on how to cite R or R packages in publications. 343s 343s Type 'demo()' for some demos, 'help()' for on-line help, or 343s 'help.start()' for an HTML browser interface to help. 343s Type 'q()' to quit R. 343s 343s [Previously saved workspace restored] 343s 343s > library("PSCBS") 343s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 343s 343s Attaching package: 'PSCBS' 343s 343s The following objects are masked from 'package:base': 343s 343s append, load 343s 343s > 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > # Load SNP microarray data 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > data <- PSCBS::exampleData("paired.chr01") 343s > str(data) 343s 'data.frame': 73346 obs. of 6 variables: 343s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 343s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 343s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 343s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 343s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 343s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 343s > 343s > # Drop single-locus outliers 343s > dataS <- dropSegmentationOutliers(data) 343s > 343s > # Run light-weight tests by default 343s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 343s + # Use only every 5th data point 343s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 343s + # Number of segments (for assertion) 343s + nSegs <- 3L 343s + # Number of bootstrap samples (see below) 343s + B <- 100L 343s + } else { 343s + # Full tests 343s + nSegs <- 8L 343s + B <- 1000L 343s + } 343s > 343s > str(dataS) 343s 'data.frame': 14670 obs. of 6 variables: 343s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 343s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 343s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 343s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 343s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 343s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 343s > 343s > R.oo::attachLocally(dataS) 343s > 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > # Simulate that genotypes are known by other means 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > library("aroma.light") 343s aroma.light v3.32.0 (2023-10-24) successfully loaded. See ?aroma.light for help. 343s > muN <- aroma.light::callNaiveGenotypes(betaN, censorAt=c(0,1)) 343s > 343s > 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > # Paired PSCBS segmentation 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > fit <- segmentByPairedPSCBS(CT, betaT=betaT, muN=muN, tbn=FALSE, 343s + chromosome=chromosome, x=x, 343s + seed=0xBEEF, verbose=-10) 343s Segmenting paired tumor-normal signals using Paired PSCBS... 343s Setup up data... 343s 'data.frame': 14670 obs. of 6 variables: 343s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 343s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 343s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 343s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 343s $ betaTN : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 343s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 343s ..- attr(*, "modelFit")=List of 1 343s .. ..$ :List of 7 343s .. .. ..$ flavor : chr "density" 343s .. .. ..$ cn : int 2 343s .. .. ..$ nbrOfGenotypeGroups: int 3 343s .. .. ..$ tau : num [1:2] 0.315 0.677 343s .. .. ..$ n : int 14640 343s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 343s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 343s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 343s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 343s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 343s .. .. .. ..$ type : chr [1:2] "valley" "valley" 343s .. .. .. ..$ x : num [1:2] 0.315 0.677 343s .. .. .. ..$ density: num [1:2] 0.522 0.552 343s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 343s Setup up data...done 343s Dropping loci for which TCNs are missing... 343s Number of loci dropped: 12 343s Dropping loci for which TCNs are missing...done 343s Ordering data along genome... 343s 'data.frame': 14658 obs. of 6 variables: 343s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 343s $ x : num 554484 730720 782343 878522 916294 ... 343s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 343s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 343s $ betaTN : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 343s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 343s Ordering data along genome...done 343s Keeping only current chromosome for 'knownSegments'... 343s Chromosome: 1 343s Known segments for this chromosome: 343s [1] chromosome start end 343s <0 rows> (or 0-length row.names) 343s Keeping only current chromosome for 'knownSegments'...done 343s alphaTCN: 0.009 343s alphaDH: 0.001 343s Number of loci: 14658 343s Calculating DHs... 343s Number of SNPs: 14658 343s Number of heterozygous SNPs: 4196 (28.63%) 343s Normalized DHs: 343s num [1:14658] NA NA NA NA NA ... 343s Calculating DHs...done 343s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 343s Produced 2 seeds from this stream for future usage 343s Identification of change points by total copy numbers... 343s Segmenting by CBS... 343s Chromosome: 1 343s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 343s Segmenting by CBS...done 343s List of 4 343s $ data :'data.frame': 14658 obs. of 4 variables: 343s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 343s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 343s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 343s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 343s $ output :'data.frame': 3 obs. of 6 variables: 343s ..$ sampleName: chr [1:3] NA NA NA 343s ..$ chromosome: int [1:3] 1 1 1 343s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 343s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 343s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 343s ..$ mean : num [1:3] 1.39 2.07 2.63 343s $ segRows:'data.frame': 3 obs. of 2 variables: 343s ..$ startRow: int [1:3] 1 7600 10268 343s ..$ endRow : int [1:3] 7599 10267 14658 343s $ params :List of 5 343s ..$ alpha : num 0.009 343s ..$ undo : num 0 343s ..$ joinSegments : logi TRUE 343s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 343s .. ..$ chromosome: int 1 343s .. ..$ start : num -Inf 343s .. ..$ end : num Inf 343s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 343s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 343s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 1.936 0.016 1.962 0 0 343s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 343s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 343s - attr(*, "randomSeed")= int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 343s Identification of change points by total copy numbers...done 343s Restructure TCN segmentation results... 343s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 343s 1 1 554484 143926517 7599 1.3859 343s 2 1 143926517 185449813 2668 2.0704 343s 3 1 185449813 247137334 4391 2.6341 343s Number of TCN segments: 3 343s Restructure TCN segmentation results...done 343s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 343s Number of TCN loci in segment: 7599 343s Locus data for TCN segment: 343s 'data.frame': 7599 obs. of 8 variables: 343s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 343s $ x : num 554484 730720 782343 878522 916294 ... 343s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 343s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 343s $ betaTN : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 343s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 343s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 343s $ rho : num NA NA NA NA NA ... 343s Number of loci: 7599 343s Number of SNPs: 2111 (27.78%) 343s Number of heterozygous SNPs: 2111 (100.00%) 343s Chromosome: 1 343s Segmenting DH signals... 343s Segmenting by CBS... 343s Chromosome: 1 343s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 343s Segmenting by CBS...done 343s List of 4 343s $ data :'data.frame': 7599 obs. of 4 variables: 343s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 343s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 343s ..$ y : num [1:7599] NA NA NA NA NA ... 343s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 343s $ output :'data.frame': 1 obs. of 6 variables: 343s ..$ sampleName: chr NA 343s ..$ chromosome: int 1 343s ..$ start : num 554484 343s ..$ end : num 1.44e+08 343s ..$ nbrOfLoci : int 2111 343s ..$ mean : num 0.524 343s $ segRows:'data.frame': 1 obs. of 2 variables: 343s ..$ startRow: int 10 343s ..$ endRow : int 7594 343s $ params :List of 5 343s ..$ alpha : num 0.001 343s ..$ undo : num 0 343s ..$ joinSegments : logi TRUE 343s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 343s .. ..$ chromosome: int 1 343s .. ..$ start : num 554484 343s .. ..$ end : num 1.44e+08 343s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 343s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 343s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.031 0 0.031 0 0 343s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 343s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 343s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 343s DH segmentation (locally-indexed) rows: 343s startRow endRow 343s 1 10 7594 343s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 343s DH segmentation rows: 343s startRow endRow 343s 1 10 7594 343s Segmenting DH signals...done 343s DH segmentation table: 343s dhStart dhEnd dhNbrOfLoci dhMean 343s 1 554484 143926517 2111 0.5237 343s startRow endRow 343s 1 10 7594 343s Rows: 343s [1] 1 343s TCN segmentation rows: 343s startRow endRow 343s 1 1 7599 343s TCN and DH segmentation rows: 343s startRow endRow 343s 1 1 7599 343s startRow endRow 343s 1 10 7594 343s NULL 343s TCN segmentation (expanded) rows: 343s startRow endRow 343s 1 1 7599 343s TCN and DH segmentation rows: 343s startRow endRow 343s 1 1 7599 343s 2 7600 10267 343s 3 10268 14658 343s startRow endRow 343s 1 10 7594 343s startRow endRow 343s 1 1 7599 343s Total CN segmentation table (expanded): 343s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 343s 1 1 554484 143926517 7599 1.3859 2111 2111 343s (TCN,DH) segmentation for one total CN segment: 343s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 1 1 1 1 554484 143926517 7599 1.3859 2111 343s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 343s 1 2111 554484 143926517 2111 0.5237 343s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 343s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 343s Number of TCN loci in segment: 2668 343s Locus data for TCN segment: 343s 'data.frame': 2668 obs. of 8 variables: 343s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 343s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 343s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 343s $ betaT : num 0.1899 0.909 0.9166 0.1668 0.0308 ... 343s $ betaTN : num 0.1899 0.909 0.9166 0.1668 0.0308 ... 343s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 343s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 343s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 343s Number of loci: 2668 343s Number of SNPs: 774 (29.01%) 343s Number of heterozygous SNPs: 774 (100.00%) 343s Chromosome: 1 343s Segmenting DH signals... 343s Segmenting by CBS... 343s Chromosome: 1 343s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 343s Segmenting by CBS...done 343s List of 4 343s $ data :'data.frame': 2668 obs. of 4 variables: 343s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 343s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 343s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 343s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 343s $ output :'data.frame': 1 obs. of 6 variables: 343s ..$ sampleName: chr NA 343s ..$ chromosome: int 1 343s ..$ start : num 1.44e+08 343s ..$ end : num 1.85e+08 343s ..$ nbrOfLoci : int 774 343s ..$ mean : num 0.154 343s $ segRows:'data.frame': 1 obs. of 2 variables: 343s ..$ startRow: int 15 343s ..$ endRow : int 2664 343s $ params :List of 5 343s ..$ alpha : num 0.001 343s ..$ undo : num 0 343s ..$ joinSegments : logi TRUE 343s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 343s .. ..$ chromosome: int 1 343s .. ..$ start : num 1.44e+08 343s .. ..$ end : num 1.85e+08 343s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 343s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 343s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.015 0 0.016 0 0 343s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 343s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 343s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 343s DH segmentation (locally-indexed) rows: 343s startRow endRow 343s 1 15 2664 343s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 343s DH segmentation rows: 343s startRow endRow 343s 1 7614 10263 343s Segmenting DH signals...done 343s DH segmentation table: 343s dhStart dhEnd dhNbrOfLoci dhMean 343s 1 143926517 185449813 774 0.1542 343s startRow endRow 343s 1 7614 10263 343s Rows: 343s [1] 2 343s TCN segmentation rows: 343s startRow endRow 343s 2 7600 10267 343s TCN and DH segmentation rows: 343s startRow endRow 343s 2 7600 10267 343s startRow endRow 343s 1 7614 10263 343s startRow endRow 343s 1 1 7599 343s TCN segmentation (expanded) rows: 343s startRow endRow 343s 1 1 7599 343s 2 7600 10267 343s TCN and DH segmentation rows: 343s startRow endRow 343s 1 1 7599 343s 2 7600 10267 343s 3 10268 14658 343s startRow endRow 343s 1 10 7594 343s 2 7614 10263 343s startRow endRow 343s 1 1 7599 343s 2 7600 10267 343s Total CN segmentation table (expanded): 343s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 343s 2 1 143926517 185449813 2668 2.0704 774 774 343s (TCN,DH) segmentation for one total CN segment: 343s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 2 2 1 1 143926517 185449813 2668 2.0704 774 343s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 343s 2 774 143926517 185449813 774 0.1542 343s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 343s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 343s Number of TCN loci in segment: 4391 343s Locus data for TCN segment: 343s 'data.frame': 4391 obs. of 8 variables: 343s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 343s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 343s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 343s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 343s $ betaTN : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 343s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 343s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 343s $ rho : num NA 0.0308 NA 0.2533 NA ... 343s Number of loci: 4391 343s Number of SNPs: 1311 (29.86%) 343s Number of heterozygous SNPs: 1311 (100.00%) 343s Chromosome: 1 343s Segmenting DH signals... 343s Segmenting by CBS... 343s Chromosome: 1 343s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 343s Segmenting by CBS...done 343s List of 4 343s $ data :'data.frame': 4391 obs. of 4 variables: 343s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 343s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 343s ..$ y : num [1:4391] NA 0.0308 NA 0.2533 NA ... 343s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 343s $ output :'data.frame': 1 obs. of 6 variables: 343s ..$ sampleName: chr NA 343s ..$ chromosome: int 1 343s ..$ start : num 1.85e+08 343s ..$ end : num 2.47e+08 343s ..$ nbrOfLoci : int 1311 343s ..$ mean : num 0.251 343s $ segRows:'data.frame': 1 obs. of 2 variables: 343s ..$ startRow: int 2 343s ..$ endRow : int 4388 343s $ params :List of 5 343s ..$ alpha : num 0.001 343s ..$ undo : num 0 343s ..$ joinSegments : logi TRUE 343s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 343s .. ..$ chromosome: int 1 343s .. ..$ start : num 1.85e+08 343s .. ..$ end : num 2.47e+08 343s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 343s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 343s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.021 0.004 0.025 0 0 343s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 343s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 343s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 343s DH segmentation (locally-indexed) rows: 343s startRow endRow 343s 1 2 4388 343s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 343s DH segmentation rows: 343s startRow endRow 343s 1 10269 14655 343s Segmenting DH signals...done 343s DH segmentation table: 343s dhStart dhEnd dhNbrOfLoci dhMean 343s 1 185449813 247137334 1311 0.2512 343s startRow endRow 343s 1 10269 14655 343s Rows: 343s [1] 3 343s TCN segmentation rows: 343s startRow endRow 343s 3 10268 14658 343s TCN and DH segmentation rows: 343s startRow endRow 343s 3 10268 14658 343s startRow endRow 343s 1 10269 14655 343s startRow endRow 343s 1 1 7599 343s 2 7600 10267 343s TCN segmentation (expanded) rows: 343s startRow endRow 343s 1 1 7599 343s 2 7600 10267 343s 3 10268 14658 343s TCN and DH segmentation rows: 343s startRow endRow 343s 1 1 7599 343s 2 7600 10267 343s 3 10268 14658 343s startRow endRow 343s 1 10 7594 343s 2 7614 10263 343s 3 10269 14655 343s startRow endRow 343s 1 1 7599 343s 2 7600 10267 343s 3 10268 14658 343s Total CN segmentation table (expanded): 343s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 343s 3 1 185449813 247137334 4391 2.6341 1311 1311 343s (TCN,DH) segmentation for one total CN segment: 343s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 3 3 1 1 185449813 247137334 4391 2.6341 1311 343s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 343s 3 1311 185449813 247137334 1311 0.2512 343s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 343s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 1 1 1 1 554484 143926517 7599 1.3859 2111 343s 2 1 2 1 143926517 185449813 2668 2.0704 774 343s 3 1 3 1 185449813 247137334 4391 2.6341 1311 343s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 343s 1 2111 554484 143926517 2111 0.5237 343s 2 774 143926517 185449813 774 0.1542 343s 3 1311 185449813 247137334 1311 0.2512 343s Calculating (C1,C2) per segment... 343s Calculating (C1,C2) per segment...done 343s Number of segments: 3 343s Segmenting paired tumor-normal signals using Paired PSCBS...done 343s Post-segmenting TCNs... 343s Number of segments: 3 343s Number of chromosomes: 1 343s [1] 1 343s Chromosome 1 ('chr01') of 1... 343s Rows: 343s [1] 1 2 3 343s Number of segments: 3 343s TCN segment #1 ('1') of 3... 343s Nothing todo. Only one DH segmentation. Skipping. 343s TCN segment #1 ('1') of 3...done 343s TCN segment #2 ('2') of 3... 343s Nothing todo. Only one DH segmentation. Skipping. 343s TCN segment #2 ('2') of 3...done 343s TCN segment #3 ('3') of 3... 343s Nothing todo. Only one DH segmentation. Skipping. 343s TCN segment #3 ('3') of 3...done 343s Chromosome 1 ('chr01') of 1...done 343s Update (C1,C2) per segment... 343s Update (C1,C2) per segment...done 343s Post-segmenting TCNs...done 343s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 1 1 1 1 554484 143926517 7599 1.3859 2111 343s 2 1 2 1 143926517 185449813 2668 2.0704 774 343s 3 1 3 1 185449813 247137334 4391 2.6341 1311 343s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 343s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 343s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 343s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 343s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 1 1 1 1 554484 143926517 7599 1.3859 2111 343s 2 1 2 1 143926517 185449813 2668 2.0704 774 343s 3 1 3 1 185449813 247137334 4391 2.6341 1311 343s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 343s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 343s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 343s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 343s > print(fit) 343s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 1 1 1 1 554484 143926517 7599 1.3859 2111 343s 2 1 2 1 143926517 185449813 2668 2.0704 774 343s 3 1 3 1 185449813 247137334 4391 2.6341 1311 343s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 343s 1 2111 2111 0.5237 0.3300521 1.055848 343s 2 774 774 0.1542 0.8755722 1.194828 343s 3 1311 1311 0.2512 0.9862070 1.647893 343s > 343s > # Plot results 343s > plotTracks(fit) 343s > 343s > # Sanity check 343s > stopifnot(nbrOfSegments(fit) == nSegs) 343s > 343s > 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > # Bootstrap segment level estimates 343s > # (used by the AB caller, which, if skipped here, 343s > # will do it automatically) 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > fit <- bootstrapTCNandDHByRegion(fit, B=B, verbose=-10) 343s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 343s Already done? 343s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 343s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 343s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 343s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 343s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 343s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 343s Number of loci: 14658 343s Number of SNPs: 4196 343s Number of non-SNPs: 10462 343s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 343s num [1:3, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : NULL 343s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 343s Segment #1 (chr 1, tcnId=1, dhId=1) of 3... 343s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 1 1 1 1 554484 143926517 7599 1.3859 2111 343s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 343s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 343s Number of TCNs: 7599 343s Number of DHs: 2111 343s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 343s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 343s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 343s Identify loci used to bootstrap DH means... 343s Heterozygous SNPs to resample for DH: 343s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 343s Identify loci used to bootstrap DH means...done 343s Identify loci used to bootstrap TCN means... 343s SNPs: 343s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 343s Non-polymorphic loci: 343s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 343s Heterozygous SNPs to resample for TCN: 343s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 343s Homozygous SNPs to resample for TCN: 343s int(0) 343s Non-polymorphic loci to resample for TCN: 343s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 343s Heterozygous SNPs with non-DH to resample for TCN: 343s int(0) 343s Loci to resample for TCN: 343s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 343s Identify loci used to bootstrap TCN means...done 343s Number of (#hets, #homs, #nonSNPs): (2111,0,5488) 343s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 343s Number of bootstrap samples: 100 343s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 343s Segment #1 (chr 1, tcnId=1, dhId=1) of 3...done 343s Segment #2 (chr 1, tcnId=2, dhId=1) of 3... 343s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 2 1 2 1 143926517 185449813 2668 2.0704 774 343s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 343s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 343s Number of TCNs: 2668 343s Number of DHs: 774 343s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 343s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 343s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 343s Identify loci used to bootstrap DH means... 343s Heterozygous SNPs to resample for DH: 343s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 343s Identify loci used to bootstrap DH means...done 343s Identify loci used to bootstrap TCN means... 343s SNPs: 343s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 343s Non-polymorphic loci: 343s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 343s Heterozygous SNPs to resample for TCN: 343s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 343s Homozygous SNPs to resample for TCN: 343s int(0) 343s Non-polymorphic loci to resample for TCN: 343s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 343s Heterozygous SNPs with non-DH to resample for TCN: 343s int(0) 343s Loci to resample for TCN: 343s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 343s Identify loci used to bootstrap TCN means...done 343s Number of (#hets, #homs, #nonSNPs): (774,0,1894) 343s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 343s Number of bootstrap samples: 100 343s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 343s Segment #2 (chr 1, tcnId=2, dhId=1) of 3...done 343s Segment #3 (chr 1, tcnId=3, dhId=1) of 3... 343s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 3 1 3 1 185449813 247137334 4391 2.6341 1311 343s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 343s 3 1311 185449813 247137334 1311 0.2512 0.986207 1.647893 343s Number of TCNs: 4391 343s Number of DHs: 1311 343s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 343s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 343s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 343s Identify loci used to bootstrap DH means... 343s Heterozygous SNPs to resample for DH: 343s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 343s Identify loci used to bootstrap DH means...done 343s Identify loci used to bootstrap TCN means... 343s SNPs: 343s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 343s Non-polymorphic loci: 343s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 343s Heterozygous SNPs to resample for TCN: 343s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 343s Homozygous SNPs to resample for TCN: 343s int(0) 343s Non-polymorphic loci to resample for TCN: 343s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 343s Heterozygous SNPs with non-DH to resample for TCN: 343s int(0) 343s Loci to resample for TCN: 343s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 343s Identify loci used to bootstrap TCN means...done 343s Number of (#hets, #homs, #nonSNPs): (1311,0,3080) 343s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 343s Number of bootstrap samples: 100 343s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 343s Segment #3 (chr 1, tcnId=3, dhId=1) of 3...done 343s Bootstrapped segment mean levels 343s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : NULL 343s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 343s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 343s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : NULL 343s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 343s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 343s Calculating polar (alpha,radius,manhattan) for change points... 343s num [1:2, 1:100, 1:2] -0.5588 -0.0962 -0.5365 -0.1285 -0.5378 ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : NULL 343s ..$ : chr [1:2] "c1" "c2" 343s Bootstrapped change points 343s num [1:2, 1:100, 1:5] -2.89 -1.78 -2.87 -1.86 -2.88 ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : NULL 343s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 343s Calculating polar (alpha,radius,manhattan) for change points...done 343s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 343s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 343s num [1:3, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 343s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 343s Field #1 ('tcn') of 4... 343s Segment #1 of 3... 343s Segment #1 of 3...done 343s Segment #2 of 3... 343s Segment #2 of 3...done 343s Segment #3 of 3... 343s Segment #3 of 3...done 343s Field #1 ('tcn') of 4...done 343s Field #2 ('dh') of 4... 343s Segment #1 of 3... 343s Segment #1 of 3...done 343s Segment #2 of 3... 343s Segment #2 of 3...done 343s Segment #3 of 3... 343s Segment #3 of 3...done 343s Field #2 ('dh') of 4...done 343s Field #3 ('c1') of 4... 343s Segment #1 of 3... 343s Segment #1 of 3...done 343s Segment #2 of 3... 343s Segment #2 of 3...done 343s Segment #3 of 3... 343s Segment #3 of 3...done 343s Field #3 ('c1') of 4...done 343s Field #4 ('c2') of 4... 343s Segment #1 of 3... 343s Segment #1 of 3...done 343s Segment #2 of 3... 343s Segment #2 of 3...done 343s Segment #3 of 3... 343s Segment #3 of 3...done 343s Field #4 ('c2') of 4...done 343s Bootstrap statistics 343s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 343s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 343s Statistical sanity checks (iff B >= 100)... 343s Available summaries: 2.5%, 5%, 95%, 97.5% 343s Available quantiles: 0.025, 0.05, 0.95, 0.975 343s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 343s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 343s Field #1 ('tcn') of 4... 343s Seg 1. mean=1.3859, range=[1.38092,1.3949], n=7599 343s Seg 2. mean=2.0704, range=[2.05747,2.08326], n=2668 343s Seg 3. mean=2.6341, range=[2.62068,2.64694], n=4391 343s Field #1 ('tcn') of 4...done 343s Field #2 ('dh') of 4... 343s Seg 1. mean=0.5237, range=[0.51753,0.532002], n=2111 343s Seg 2. mean=0.1542, range=[0.144468,0.16453], n=774 343s Seg 3. mean=0.2512, range=[0.242575,0.258832], n=1311 343s Field #2 ('dh') of 4...done 343s Field #3 ('c1') of 4... 343s Seg 1. mean=0.330052, range=[0.323996,0.336038], n=2111 343s Seg 2. mean=0.875572, range=[0.86318,0.887699], n=774 343s Seg 3. mean=0.986207, range=[0.975123,0.998982], n=1311 343s Field #3 ('c1') of 4...done 343s Field #4 ('c2') of 4... 343s Seg 1. mean=1.05585, range=[1.05006,1.06231], n=2111 343s Seg 2. mean=1.19483, range=[1.18417,1.2081], n=774 343s Seg 3. mean=1.64789, range=[1.63403,1.66098], n=1311 343s Field #4 ('c2') of 4...done 343s Statistical sanity checks (iff B >= 100)...done 343s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 343s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 343s num [1:2, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 343s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 343s Field #1 ('alpha') of 5... 343s Changepoint #1 of 2... 343s Changepoint #1 of 2...done 343s Changepoint #2 of 2... 343s Changepoint #2 of 2...done 343s Field #1 ('alpha') of 5...done 343s Field #2 ('radius') of 5... 343s Changepoint #1 of 2... 343s Changepoint #1 of 2...done 343s Changepoint #2 of 2... 343s Changepoint #2 of 2...done 343s Field #2 ('radius') of 5...done 343s Field #3 ('manhattan') of 5... 343s Changepoint #1 of 2... 343s Changepoint #1 of 2...done 343s Changepoint #2 of 2... 343s Changepoint #2 of 2...done 343s Field #3 ('manhattan') of 5...done 343s Field #4 ('d1') of 5... 343s Changepoint #1 of 2... 343s Changepoint #1 of 2...done 343s Changepoint #2 of 2... 343s Changepoint #2 of 2...done 343s Field #4 ('d1') of 5...done 343s Field #5 ('d2') of 5... 343s Changepoint #1 of 2... 343s Changepoint #1 of 2...done 343s Changepoint #2 of 2... 343s Changepoint #2 of 2...done 343s Field #5 ('d2') of 5...done 343s Bootstrap statistics 343s num [1:2, 1:4, 1:5] -2.92 -1.86 -2.91 -1.85 -2.87 ... 343s - attr(*, "dimnames")=List of 3 343s ..$ : NULL 343s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 343s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 343s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 343s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 343s > print(fit) 343s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 1 1 1 1 554484 143926517 7599 1.3859 2111 343s 2 1 2 1 143926517 185449813 2668 2.0704 774 343s 3 1 3 1 185449813 247137334 4391 2.6341 1311 343s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 343s 1 2111 2111 0.5237 0.3300521 1.055848 343s 2 774 774 0.1542 0.8755722 1.194828 343s 3 1311 1311 0.2512 0.9862070 1.647893 343s > plotTracks(fit) 343s > 343s > 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > # Calling segments in allelic balance (AB) and 343s > # in loss-of-heterozygosity (LOH) 343s > # NOTE: Ideally, this should be done on whole-genome data 343s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 343s > fit <- callAB(fit, verbose=-10) 343s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 343s delta (offset adjusting for bias in DH): 0.3466649145302 343s alpha (CI quantile; significance level): 0.05 343s Calling segments... 343s Number of segments called allelic balance (AB): 2 (66.67%) of 3 343s Calling segments...done 343s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 343s > fit <- callLOH(fit, verbose=-10) 343s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 343s delta (offset adjusting for bias in C1): 0.771236438183453 343s alpha (CI quantile; significance level): 0.05 343s Calling segments... 343s Number of segments called low C1 (LowC1, "LOH_C1"): 1 (33.33%) of 3 343s Calling segments...done 343s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 343s > print(fit) 343s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 343s 1 1 1 1 554484 143926517 7599 1.3859 2111 343s 2 1 2 1 143926517 185449813 2668 2.0704 774 343s 3 1 3 1 185449813 247137334 4391 2.6341 1311 343s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall lohCall 343s 1 2111 2111 0.5237 0.3300521 1.055848 FALSE TRUE 343s 2 774 774 0.1542 0.8755722 1.194828 TRUE FALSE 343s 3 1311 1311 0.2512 0.9862070 1.647893 TRUE FALSE 343s > plotTracks(fit) 343s > 343s > proc.time() 343s user system elapsed 343s 4.784 0.150 4.946 343s Test segmentByPairedPSCBS,noNormalBAFs passed 343s 0 343s Begin test segmentByPairedPSCBS,report 344s + cat segmentByPairedPSCBS,report.Rout 344s 344s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 344s Copyright (C) 2024 The R Foundation for Statistical Computing 344s Platform: arm-unknown-linux-gnueabihf (32-bit) 344s 344s R is free software and comes with ABSOLUTELY NO WARRANTY. 344s You are welcome to redistribute it under certain conditions. 344s Type 'license()' or 'licence()' for distribution details. 344s 344s R is a collaborative project with many contributors. 344s Type 'contributors()' for more information and 344s 'citation()' on how to cite R or R packages in publications. 344s 344s Type 'demo()' for some demos, 'help()' for on-line help, or 344s 'help.start()' for an HTML browser interface to help. 344s Type 'q()' to quit R. 344s 344s [Previously saved workspace restored] 344s 344s > # This test script calls a report generator which requires 344s > # the 'ggplot2' package, which in turn will require packages 344s > # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'. 344s > 344s > # Only run this test in full testing mode 344s > if (Sys.getenv("_R_CHECK_FULL_") != "") { 344s + library("PSCBS") 344s + 344s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 344s + # Load SNP microarray data 344s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 344s + data <- PSCBS::exampleData("paired.chr01") 344s + str(data) 344s + 344s + 344s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 344s + # Paired PSCBS segmentation 344s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 344s + # Drop single-locus outliers 344s + dataS <- dropSegmentationOutliers(data) 344s + 344s + # Speed up example by segmenting fewer loci 344s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 344s + 344s + str(dataS) 344s + 344s + gaps <- findLargeGaps(dataS, minLength=2e6) 344s + knownSegments <- gapsToSegments(gaps) 344s + 344s + # Paired PSCBS segmentation 344s + fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 344s + seed=0xBEEF, verbose=-10) 344s + 344s + # Fake a multi-chromosome segmentation 344s + fit1 <- fit 344s + fit2 <- renameChromosomes(fit, from=1, to=2) 344s + fit <- c(fit1, fit2) 344s + 344s + report(fit, sampleName="PairedPSCBS", studyName="PSCBS-Ex", verbose=-10) 344s + 344s + } # if (Sys.getenv("_R_CHECK_FULL_")) 344s > 344s > proc.time() 344s user system elapsed 344s 0.302 0.033 0.325 344s Test segmentByPairedPSCBS,report passed 344s 0 344s Begin test segmentByPairedPSCBS,seqOfSegmentsByDP 344s + [ 0 != 0 ] 344s + echo Test segmentByPairedPSCBS,report passed 344s + echo 0 344s + echo Begin test segmentByPairedPSCBS,seqOfSegmentsByDP 344s + exitcode=0 344s + R CMD BATCH segmentByPairedPSCBS,seqOfSegmentsByDP.R 352s + cat segmentByPairedPSCBS,seqOfSegmentsByDP.Rout 352s 352s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 352s Copyright (C) 2024 The R Foundation for Statistical Computing 352s Platform: arm-unknown-linux-gnueabihf (32-bit) 352s 352s R is free software and comes with ABSOLUTELY NO WARRANTY. 352s You are welcome to redistribute it under certain conditions. 352s Type 'license()' or 'licence()' for distribution details. 352s 352s R is a collaborative project with many contributors. 352s Type 'contributors()' for more information and 352s 'citation()' on how to cite R or R packages in publications. 352s 352s Type 'demo()' for some demos, 'help()' for on-line help, or 352s 'help.start()' for an HTML browser interface to help. 352s Type 'q()' to quit R. 352s 352s [Previously saved workspace restored] 352s 352s > library("PSCBS") 352s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 352s 352s Attaching package: 'PSCBS' 352s 352s The following objects are masked from 'package:base': 352s 352s append, load 352s 352s > subplots <- R.utils::subplots 352s > stext <- R.utils::stext 352s > 352s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 352s > # Load SNP microarray data 352s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 352s > data <- PSCBS::exampleData("paired.chr01") 352s > str(data) 352s 'data.frame': 73346 obs. of 6 variables: 352s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 352s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 352s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 352s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 352s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 352s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 352s > 352s > 352s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 352s > # Paired PSCBS segmentation 352s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 352s > # Drop single-locus outliers 352s > dataS <- dropSegmentationOutliers(data) 352s > 352s > # Run light-weight tests by default 352s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 352s + # Use only every 5th data point 352s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 352s + # Number of segments (for assertion) 352s + nSegs <- 3L 352s + # Number of bootstrap samples (see below) 352s + B <- 100L 352s + } else { 352s + # Full tests 352s + nSegs <- 12L 352s + B <- 1000L 352s + } 352s > 352s > str(dataS) 352s 'data.frame': 14670 obs. of 6 variables: 352s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 352s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 352s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 352s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 352s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 352s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 352s > 352s > R.oo::attachLocally(dataS) 352s > 352s > 352s > gaps <- findLargeGaps(dataS, minLength=2e6) 352s > knownSegments <- gapsToSegments(gaps, dropGaps=TRUE) 352s > 352s > # Paired PSCBS segmentation 352s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 352s + seed=0xBEEF, verbose=-10) 352s Segmenting paired tumor-normal signals using Paired PSCBS... 352s Calling genotypes from normal allele B fractions... 352s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 352s Called genotypes: 352s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 352s - attr(*, "modelFit")=List of 1 352s ..$ :List of 7 352s .. ..$ flavor : chr "density" 352s .. ..$ cn : int 2 352s .. ..$ nbrOfGenotypeGroups: int 3 352s .. ..$ tau : num [1:2] 0.315 0.677 352s .. ..$ n : int 14640 352s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 352s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 352s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 352s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 352s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 352s .. .. ..$ type : chr [1:2] "valley" "valley" 352s .. .. ..$ x : num [1:2] 0.315 0.677 352s .. .. ..$ density: num [1:2] 0.522 0.552 352s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 352s muN 352s 0 0.5 1 352s 5221 4198 5251 352s Calling genotypes from normal allele B fractions...done 352s Normalizing b+ [ 0 != 0 ] 352s + echo Test segmentByPairedPSCBS,seqOfSegmentsByDP passed 352s + echo 0 352s + echo Begin test segmentByPairedPSCBS 352s + exitcode=0 352s + R CMD BATCH segmentByPairedPSCBS.R 352s etaT using betaN (TumorBoost)... 352s Normalized BAFs: 352s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 352s - attr(*, "modelFit")=List of 5 352s ..$ method : chr "normalizeTumorBoost" 352s ..$ flavor : chr "v4" 352s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 352s .. ..- attr(*, "modelFit")=List of 1 352s .. .. ..$ :List of 7 352s .. .. .. ..$ flavor : chr "density" 352s .. .. .. ..$ cn : int 2 352s .. .. .. ..$ nbrOfGenotypeGroups: int 3 352s .. .. .. ..$ tau : num [1:2] 0.315 0.677 352s .. .. .. ..$ n : int 14640 352s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 352s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 352s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 352s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 352s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 352s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 352s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 352s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 352s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 352s ..$ preserveScale: logi FALSE 352s ..$ scaleFactor : num NA 352s Normalizing betaT using betaN (TumorBoost)...done 352s Setup up data... 352s 'data.frame': 14670 obs. of 7 variables: 352s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 352s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 352s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 352s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 352s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 352s ..- attr(*, "modelFit")=List of 5 352s .. ..$ method : chr "normalizeTumorBoost" 352s .. ..$ flavor : chr "v4" 352s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 352s .. .. ..- attr(*, "modelFit")=List of 1 352s .. .. .. ..$ :List of 7 352s .. .. .. .. ..$ flavor : chr "density" 352s .. .. .. .. ..$ cn : int 2 352s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 352s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 352s .. .. .. .. ..$ n : int 14640 352s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 352s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 352s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 352s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 352s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 352s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 352s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 352s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 352s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 352s .. ..$ preserveScale: logi FALSE 352s .. ..$ scaleFactor : num NA 352s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 352s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 352s ..- attr(*, "modelFit")=List of 1 352s .. ..$ :List of 7 352s .. .. ..$ flavor : chr "density" 352s .. .. ..$ cn : int 2 352s .. .. ..$ nbrOfGenotypeGroups: int 3 352s .. .. ..$ tau : num [1:2] 0.315 0.677 352s .. .. ..$ n : int 14640 352s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 352s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 352s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 352s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 352s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 352s .. .. .. ..$ type : chr [1:2] "valley" "valley" 352s .. .. .. ..$ x : num [1:2] 0.315 0.677 352s .. .. .. ..$ density: num [1:2] 0.522 0.552 352s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 352s Setup up data...done 352s Dropping loci for which TCNs are missing... 352s Number of loci dropped: 12 352s Dropping loci for which TCNs are missing...done 352s Ordering data along genome... 352s 'data.frame': 14658 obs. of 7 variables: 352s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 352s $ x : num 554484 730720 782343 878522 916294 ... 352s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 352s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 352s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 352s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 352s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 352s Ordering data along genome...done 352s Keeping only current chromosome for 'knownSegments'... 352s Chromosome: 1 352s Known segments for this chromosome: 352s chromosome start end length 352s 1 1 -Inf 120908858 Inf 352s 2 1 142693888 Inf Inf 352s Keeping only current chromosome for 'knownSegments'...done 352s alphaTCN: 0.009 352s alphaDH: 0.001 352s Number of loci: 14658 352s Calculating DHs... 352s Number of SNPs: 14658 352s Number of heterozygous SNPs: 4196 (28.63%) 352s Normalized DHs: 352s num [1:14658] NA NA NA NA NA ... 352s Calculating DHs...done 352s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 352s Produced 2 seeds from this stream for future usage 352s Identification of change points by total copy numbers... 352s Segmenting by CBS... 352s Chromosome: 1 352s Segmenting multiple segments on current chromosome... 352s Number of segments: 2 352s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 352s Produced 2 seeds from this stream for future usage 352s Segmenting by CBS... 352s Chromosome: 1 352s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 352s Segmenting by CBS...done 352s Segmenting by CBS... 352s Chromosome: 1 352s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 352s Segmenting by CBS...done 352s Segmenting multiple segments on current chromosome...done 352s Segmenting by CBS...done 352s List of 4 352s $ data :'data.frame': 14658 obs. of 4 variables: 352s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 352s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 352s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 352s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 352s $ output :'data.frame': 3 obs. of 6 variables: 352s ..$ sampleName: chr [1:3] NA NA NA 352s ..$ chromosome: int [1:3] 1 1 1 352s ..$ start : num [1:3] 5.54e+05 1.43e+08 1.85e+08 352s ..$ end : num [1:3] 1.21e+08 1.85e+08 2.47e+08 352s ..$ nbrOfLoci : int [1:3] 7586 2681 4391 352s ..$ mean : num [1:3] 1.39 2.07 2.63 352s $ segRows:'data.frame': 3 obs. of 2 variables: 352s ..$ startRow: int [1:3] 1 7587 10268 352s ..$ endRow : int [1:3] 7586 10267 14658 352s $ params :List of 5 352s ..$ alpha : num 0.009 352s ..$ undo : num 0 352s ..$ joinSegments : logi TRUE 352s ..$ knownSegments:'data.frame': 2 obs. of 3 variables: 352s .. ..$ chromosome: int [1:2] 1 1 352s .. ..$ start : num [1:2] -Inf 1.43e+08 352s .. ..$ end : num [1:2] 1.21e+08 Inf 352s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 352s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 352s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.475 0.012 0.489 0 0 352s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 352s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 352s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 352s Identification of change points by total copy numbers...done 352s Restructure TCN segmentation results... 352s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 352s 1 1 554484 120908858 7586 1.3853 352s 2 1 142693888 185449813 2681 2.0689 352s 3 1 185449813 247137334 4391 2.6341 352s Number of TCN segments: 3 352s Restructure TCN segmentation results...done 352s Total CN segment #1 ([ 554484,1.20909e+08]) of 3... 352s Number of TCN loci in segment: 7586 352s Locus data for TCN segment: 352s 'data.frame': 7586 obs. of 9 variables: 352s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 352s $ x : num 554484 730720 782343 878522 916294 ... 352s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 352s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 352s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 352s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 352s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 352s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 352s $ rho : num NA NA NA NA NA ... 352s Number of loci: 7586 352s Number of SNPs: 2108 (27.79%) 352s Number of heterozygous SNPs: 2108 (100.00%) 352s Chromosome: 1 352s Segmenting DH signals... 352s Segmenting by CBS... 352s Chromosome: 1 352s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 352s Segmenting by CBS...done 352s List of 4 352s $ data :'data.frame': 7586 obs. of 4 variables: 352s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 352s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 352s ..$ y : num [1:7586] NA NA NA NA NA ... 352s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 352s $ output :'data.frame': 1 obs. of 6 variables: 352s ..$ sampleName: chr NA 352s ..$ chromosome: int 1 352s ..$ start : num 554484 352s ..$ end : num 1.21e+08 352s ..$ nbrOfLoci : int 2108 352s ..$ mean : num 0.512 352s $ segRows:'data.frame': 1 obs. of 2 variables: 352s ..$ startRow: int 10 352s ..$ endRow : int 7574 352s $ params :List of 5 352s ..$ alpha : num 0.001 352s ..$ undo : num 0 352s ..$ joinSegments : logi TRUE 352s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 352s .. ..$ chromosome: int 1 352s .. ..$ start : num 554484 352s .. ..$ end : num 1.21e+08 352s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 352s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 352s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.045 0 0.045 0 0 352s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 352s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 352s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 352s DH segmentation (locally-indexed) rows: 352s startRow endRow 352s 1 10 7574 352s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 352s DH segmentation rows: 352s startRow endRow 352s 1 10 7574 352s Segmenting DH signals...done 352s DH segmentation table: 352s dhStart dhEnd dhNbrOfLoci dhMean 352s 1 554484 120908858 2108 0.5116 352s startRow endRow 352s 1 10 7574 352s Rows: 352s [1] 1 352s TCN segmentation rows: 352s startRow endRow 352s 1 1 7586 352s TCN and DH segmentation rows: 352s startRow endRow 352s 1 1 7586 352s startRow endRow 352s 1 10 7574 352s NULL 352s TCN segmentation (expanded) rows: 352s startRow endRow 352s 1 1 7586 352s TCN and DH segmentation rows: 352s startRow endRow 352s 1 1 7586 352s 2 7587 10267 352s 3 10268 14658 352s startRow endRow 352s 1 10 7574 352s startRow endRow 352s 1 1 7586 352s Total CN segmentation table (expanded): 352s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 352s 1 1 554484 120908858 7586 1.3853 2108 2108 352s (TCN,DH) segmentation for one total CN segment: 352s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 352s 1 1 1 1 554484 120908858 7586 1.3853 2108 352s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 352s 1 2108 554484 120908858 2108 0.5116 352s Total CN segment #1 ([ 554484,1.20909e+08]) of 3...done 352s Total CN segment #2 ([1.42694e+08,1.8545e+08]) of 3... 352s Number of TCN loci in segment: 2681 352s Locus data for TCN segment: 352s 'data.frame': 2681 obs. of 9 variables: 352s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 352s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 352s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 352s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 352s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 352s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 352s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 352s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 352s $ rho : num 0.117 0.258 NA NA NA ... 352s Number of loci: 2681 352s Number of SNPs: 777 (28.98%) 352s Number of heterozygous SNPs: 777 (100.00%) 352s Chromosome: 1 352s Segmenting DH signals... 352s Segmenting by CBS... 352s Chromosome: 1 352s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 352s Segmenting by CBS...done 352s List of 4 352s $ data :'data.frame': 2681 obs. of 4 variables: 352s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 352s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 352s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 352s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 352s $ output :'data.frame': 1 obs. of 6 variables: 352s ..$ sampleName: chr NA 352s ..$ chromosome: int 1 352s ..$ start : num 1.43e+08 352s ..$ end : num 1.85e+08 352s ..$ nbrOfLoci : int 777 352s ..$ mean : num 0.0973 352s $ segRows:'data.frame': 1 obs. of 2 variables: 352s ..$ startRow: int 1 352s ..$ endRow : int 2677 352s $ params :List of 5 352s ..$ alpha : num 0.001 352s ..$ undo : num 0 352s ..$ joinSegments : logi TRUE 352s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 352s .. ..$ chromosome: int 1 352s .. ..$ start : num 1.43e+08 352s .. ..$ end : num 1.85e+08 352s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 352s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 352s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.012 0 0.012 0 0 352s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 352s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 352s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 352s DH segmentation (locally-indexed) rows: 352s startRow endRow 352s 1 1 2677 352s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 352s DH segmentation rows: 352s startRow endRow 352s 1 7587 10263 352s Segmenting DH signals...done 352s DH segmentation table: 352s dhStart dhEnd dhNbrOfLoci dhMean 352s 1 142693888 185449813 777 0.0973 352s startRow endRow 352s 1 7587 10263 352s Rows: 352s [1] 2 352s TCN segmentation rows: 352s startRow endRow 352s 2 7587 10267 352s TCN and DH segmentation rows: 352s startRow endRow 352s 2 7587 10267 352s startRow endRow 352s 1 7587 10263 352s startRow endRow 352s 1 1 7586 352s TCN segmentation (expanded) rows: 352s startRow endRow 352s 1 1 7586 352s 2 7587 10267 352s TCN and DH segmentation rows: 352s startRow endRow 352s 1 1 7586 352s 2 7587 10267 352s 3 10268 14658 352s startRow endRow 352s 1 10 7574 352s 2 7587 10263 352s startRow endRow 352s 1 1 7586 352s 2 7587 10267 352s Total CN segmentation table (expanded): 352s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 352s 2 1 142693888 185449813 2681 2.0689 777 777 352s (TCN,DH) segmentation for one total CN segment: 352s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 352s 2 2 1 1 142693888 185449813 2681 2.0689 777 352s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 352s 2 777 142693888 185449813 777 0.0973 352s Total CN segment #2 ([1.42694e+08,1.8545e+08]) of 3...done 352s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 352s Number of TCN loci in segment: 4391 352s Locus data for TCN segment: 352s 'data.frame': 4391 obs. of 9 variables: 352s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 352s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 352s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 352s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 352s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 352s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 352s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 352s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 352s $ rho : num NA 0.2186 NA 0.0503 NA ... 352s Number of loci: 4391 352s Number of SNPs: 1311 (29.86%) 352s Number of heterozygous SNPs: 1311 (100.00%) 352s Chromosome: 1 352s Segmenting DH signals... 352s Segmenting by CBS... 352s Chromosome: 1 352s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 352s Segmenting by CBS...done 352s List of 4 352s $ data :'data.frame': 4391 obs. of 4 variables: 352s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 352s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 352s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 352s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 352s $ output :'data.frame': 1 obs. of 6 variables: 352s ..$ sampleName: chr NA 352s ..$ chromosome: int 1 352s ..$ start : num 1.85e+08 352s ..$ end : num 2.47e+08 352s ..$ nbrOfLoci : int 1311 352s ..$ mean : num 0.23 352s $ segRows:'data.frame': 1 obs. of 2 variables: 352s ..$ startRow: int 2 352s ..$ endRow : int 4388 352s $ params :List of 5 352s ..$ alpha : num 0.001 352s ..$ undo : num 0 352s ..$ joinSegments : logi TRUE 352s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 352s .. ..$ chromosome: int 1 352s .. ..$ start : num 1.85e+08 352s .. ..$ end : num 2.47e+08 352s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 352s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 352s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.025 0 0.024 0 0 352s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 352s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 352s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 352s DH segmentation (locally-indexed) rows: 352s startRow endRow 352s 1 2 4388 352s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 352s DH segmentation rows: 352s startRow endRow 352s 1 10269 14655 352s Segmenting DH signals...done 352s DH segmentation table: 352s dhStart dhEnd dhNbrOfLoci dhMean 352s 1 185449813 247137334 1311 0.2295 352s startRow endRow 352s 1 10269 14655 352s Rows: 352s [1] 3 352s TCN segmentation rows: 352s startRow endRow 352s 3 10268 14658 352s TCN and DH segmentation rows: 352s startRow endRow 352s 3 10268 14658 352s startRow endRow 352s 1 10269 14655 352s startRow endRow 352s 1 1 7586 352s 2 7587 10267 352s TCN segmentation (expanded) rows: 352s startRow endRow 352s 1 1 7586 352s 2 7587 10267 352s 3 10268 14658 352s TCN and DH segmentation rows: 352s startRow endRow 352s 1 1 7586 352s 2 7587 10267 352s 3 10268 14658 352s startRow endRow 352s 1 10 7574 352s 2 7587 10263 352s 3 10269 14655 352s startRow endRow 352s 1 1 7586 352s 2 7587 10267 352s 3 10268 14658 352s Total CN segmentation table (expanded): 352s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 352s 3 1 185449813 247137334 4391 2.6341 1311 1311 352s (TCN,DH) segmentation for one total CN segment: 352s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 352s 3 3 1 1 185449813 247137334 4391 2.6341 1311 352s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 352s 3 1311 185449813 247137334 1311 0.2295 352s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 352s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 352s 1 1 1 1 554484 120908858 7586 1.3853 2108 352s 2 1 2 1 142693888 185449813 2681 2.0689 777 352s 3 1 3 1 185449813 247137334 4391 2.6341 1311 352s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 352s 1 2108 554484 120908858 2108 0.5116 352s 2 777 142693888 185449813 777 0.0973 352s 3 1311 185449813 247137334 1311 0.2295 352s Calculating (C1,C2) per segment... 352s Calculating (C1,C2) per segment...done 352s Number of segments: 3 352s Segmenting paired tumor-normal signals using Paired PSCBS...done 352s Post-segmenting TCNs... 352s Number of segments: 3 352s Number of chromosomes: 1 352s [1] 1 352s Chromosome 1 ('chr01') of 1... 352s Rows: 352s [1] 1 2 3 352s Number of segments: 3 352s TCN segment #1 ('1') of 3... 352s Nothing todo. Only one DH segmentation. Skipping. 352s TCN segment #1 ('1') of 3...done 352s TCN segment #2 ('2') of 3... 352s Nothing todo. Only one DH segmentation. Skipping. 352s TCN segment #2 ('2') of 3...done 352s TCN segment #3 ('3') of 3... 352s Nothing todo. Only one DH segmentation. Skipping. 352s TCN segment #3 ('3') of 3...done 352s Chromosome 1 ('chr01') of 1...done 352s Update (C1,C2) per segment... 352s Update (C1,C2) per segment...done 352s Post-segmenting TCNs...done 352s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 352s 1 1 1 1 554484 120908858 7586 1.3853 2108 352s 2 1 2 1 142693888 185449813 2681 2.0689 777 352s 3 1 3 1 185449813 247137334 4391 2.6341 1311 352s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 352s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 352s 2 777 142693888 185449813 777 0.0973 0.9337980 1.135102 352s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 352s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 352s 1 1 1 1 554484 120908858 7586 1.3853 2108 352s 2 1 2 1 142693888 185449813 2681 2.0689 777 352s 3 1 3 1 185449813 247137334 4391 2.6341 1311 352s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 352s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 352s 2 777 142693888 185449813 777 0.0973 0.9337980 1.135102 352s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 352s > print(fit) 352s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 352s 1 1 1 1 554484 120908858 7586 1.3853 2108 352s 2 1 2 1 142693888 185449813 2681 2.0689 777 352s 3 1 3 1 185449813 247137334 4391 2.6341 1311 352s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 352s 1 2108 2108 0.5116 0.3382903 1.047010 352s 2 777 777 0.0973 0.9337980 1.135102 352s 3 1311 1311 0.2295 1.0147870 1.619313 352s > 352s > fit1 <- fit 352s > fit2 <- renameChromosomes(fit1, from=1, to=2) 352s > fit <- c(fit1, fit2) 352s > knownSegments <- tileChromosomes(fit)$params$knownSegments 352s > 352s > segList <- seqOfSegmentsByDP(fit, verbose=-10) 352s Identifying optimal sets of segments via dynamic programming... 352s Shifting TCN levels for every second segment... 352s Split up into non-empty independent regions... 352s Chromosome #1 ('1') of 2... 352s Number of loci on chromosome: 14658 352s Known segments on chromosome: 352s chromosome start end 352s 1 1 -Inf 120908858 352s 2 1 142693888 Inf 352s Known segment #1 of 2... 352s chromosome start end 352s 1 1 -Inf 120908858 352s Known segment #1 of 2...done 352s Known segment #2 of 2... 352s chromosome start end 352s 2 1 142693888 Inf 352s Known segment #2 of 2...done 352s Chromosome #1 ('1') of 2...done 352s Chromosome #2 ('2') of 2... 352s Number of loci on chromosome: 14658 352s Known segments on chromosome: 352s chromosome start end 352s 3 2 -Inf 120908858 352s 4 2 142693888 Inf 352s Known segment #1 of 2... 352s chromosome start end 352s 3 2 -Inf 120908858 352s Known segment #1 of 2...done 352s Known segment #2 of 2... 352s chromosome start end 352s 4 2 142693888 Inf 352s Known segment #2 of 2...done 352s Chromosome #2 ('2') of 2...done 352s Number of independent non-empty regions: 4 352s Split up into non-empty independent regions...done 352s Shift every other region... 352s Shift every other region...done 352s Merge... 352s Merge...done 352s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 352s 1 1 1 1 554484 120908858 7586 101.3853 2108 352s 2 1 2 1 142693888 185449813 2681 2.0689 777 352s 3 1 3 1 185449813 247137334 4391 2.6341 1311 352s 4 2 1 1 554484 120908858 7586 101.3853 2108 352s 5 2 2 1 142693888 185449813 2681 2.0689 777 352s 6 2 3 1 185449813 247137334 4391 2.6341 1311 352s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 352s 1 2108 554484 120908858 2108 0.511612 24.757671 76.627587 352s 2 777 142693888 185449813 777 0.097300 0.933798 1.135102 352s 3 1311 185449813 247137334 1311 0.229500 1.014787 1.619313 352s 4 2108 554484 120908858 2108 0.511612 24.757671 76.627587 352s 5 777 142693888 185449813 777 0.097300 0.933798 1.135102 352s 6 1311 185449813 247137334 1311 0.229500 1.014787 1.619313 352s Shifting TCN levels for every second segment...done 352s Extracting signals for dynamic programming... 352s CT rho 352s Min. : 0.805 Min. :0.000 352s 1st Qu.: 2.407 1st Qu.:0.139 352s Median :100.927 Median :0.293 352s Mean : 53.638 Mean :0.347 352s 3rd Qu.:101.370 3rd Qu.:0.557 352s Max. :103.080 Max. :1.022 352s NA's :20924 352s Extracting signals for dynamic programming...done 352s Dynamic programming... 352s Number of "DP" change points: 5 352s int [1:5] 7586 10267 14658 22244 24925 352s List of 4 352s $ jump :List of 5 352s ..$ : num 22244 352s ..$ : num [1:2] 7586 14658 352s ..$ : num [1:3] 7586 14658 22244 352s ..$ : num [1:4] 7586 10267 14658 22244 352s ..$ : num [1:5] 7586 10267 14658 22244 24925 352s $ rse : num [1:6] 71699116 47249179 35852530 5945 5410 ... 352s $ kbest: num 4 352s $ V : num [1:6, 1:6] 1114 0 0 0 0 ... 352s Dynamic programming...done 352s Excluding cases where known segments no longer correct... 352s Number of independent non-empty regions: 4 352s List of 3 352s $ : num [1:3] 7586 14658 22244 352s $ : num [1:4] 7586 10267 14658 22244 352s $ : num [1:5] 7586 10267 14658 22244 24925 352s Excluding cases where known segments no longer correct...done 352s List of 3 352s $ :'data.frame': 4 obs. of 3 variables: 352s ..$ chromosome: int [1:4] 1 1 2 2 352s ..$ start : num [1:4] 5.54e+05 1.43e+08 5.54e+05 1.43e+08 352s ..$ end : num [1:4] 1.21e+08 2.47e+08 1.21e+08 2.47e+08 352s $ :'data.frame': 5 obs. of 3 variables: 352s ..$ chromosome: int [1:5] 1 1 1 2 2 352s ..$ start : num [1:5] 5.54e+05 1.43e+08 1.85e+08 5.54e+05 1.43e+08 352s ..$ end : num [1:5] 1.21e+08 1.85e+08 2.47e+08 1.21e+08 2.47e+08 352s $ :'data.frame': 6 obs. of 3 variables: 352s ..$ chromosome: int [1:6] 1 1 1 2 2 2 352s ..$ start : num [1:6] 5.54e+05 1.43e+08 1.85e+08 5.54e+05 1.43e+08 ... 352s ..$ end : num [1:6] 1.21e+08 1.85e+08 2.47e+08 1.21e+08 1.85e+08 ... 352s Sequence of number of "DP" change points: 352s [1] 3 4 5 352s Sequence of number of segments: 352s [1] 4 5 6 352s Sequence of number of "discovered" change points: 352s [1] 0 1 2 352s Identifying optimal sets of segments via dynamic programming...done 352s > K <- length(segList) 352s > ks <- seq(from=1, to=K, length.out=min(5,K)) 352s > subplots(length(ks), ncol=1, byrow=TRUE) 352s > par(mar=c(2,1,1,1)) 352s > for (kk in ks) { 352s + knownSegmentsKK <- segList[[kk]] 352s + fitKK <- resegment(fit, knownSegments=knownSegmentsKK, undoTCN=+Inf, undoDH=+Inf) 352s + plotTracks(fitKK, tracks="tcn,c1,c2", Clim=c(0,5), add=TRUE) 352s + abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 352s + stext(side=3, pos=0, sprintf("Number of segments: %d", nrow(knownSegmentsKK))) 352s + } # for (kk ...) 352s > 352s > proc.time() 352s user system elapsed 352s 6.887 0.115 7.008 352s Test segmentByPairedPSCBS,seqOfSegmentsByDP passed 352s 0 352s Begin test segmentByPairedPSCBS 365s + cat segmentByPairedPSCBS.Rout 365s 365s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 365s Copyright (C) 2024 The R Foundation for Statistical Computing 365s Platform: arm-unknown-linux-gnueabihf (32-bit) 365s 365s R is free software and comes with ABSOLUTELY NO WARRANTY. 365s You are welcome to redistribute it under certain conditions. 365s Type 'license()' or 'licence()' for distribution details. 365s 365s R is a collaborative project with many contributors. 365s Type 'contributors()' for more information and 365s 'citation()' on how to cite R or R packages in publications. 365s 365s Type 'demo()' for some demos, 'help()' for on-line help, or 365s 'help.start()' for an HTML browser interface to help. 365s Type 'q()' to quit R. 365s 365s [Previously saved workspace restored] 365s 365s > ########################################################### 365s > # This tests: 365s > # - segmentByPairedPSCBS(...) 365s > # - segmentByPairedPSCBS(..., knownSegments) 365s > # - tileChromosomes() 365s > # - plotTracks() 365s > ########################################################### 365s > library("PSCBS") 365s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 365s 365s Attaching package: 'PSCBS' 365s 365s The following objects are masked from 'package:base': 365s 365s append, load 365s 365s > 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > # Load SNP microarray data 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > data <- PSCBS::exampleData("paired.chr01") 365s > 365s > 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > # Paired PSCBS segmentation 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > # Drop single-locus outliers 365s > dataS <- dropSegmentationOutliers(data) 365s > 365s > # Run light-weight tests by default 365s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 365s + # Use only every 5th data point 365s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 365s + # Number of segments (for assertion) 365s + nSegs <- 4L 365s + } else { 365s + # Full tests 365s + nSegs <- 11L 365s + } 365s > 365s > str(dataS) 365s 'data.frame': 14670 obs. of 6 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 365s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 365s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 365s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 365s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 365s > 365s > fig <- 1 365s > 365s > 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > # (a) Don't segment the centromere (and force a separator) 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > knownSegments <- data.frame( 365s + chromosome = c( 1, 1, 1), 365s + start = c( -Inf, NA, 141510003), 365s + end = c(120992603, NA, +Inf) 365s + ) 365s > 365s > 365s > # Paired PSCBS segmentation 365s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 365s + seed=0xBEEF, verbose=-10) 365s Segmenting paired tumor-normal signals using Paired PSCBS... 365s Calling genotypes from normal allele B fractions... 365s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 365s Called genotypes: 365s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 365s - attr(*, "modelFit")=List of 1 365s ..$ :List of 7 365s .. ..$ flavor : chr "density" 365s .. ..$ cn : int 2 365s .. ..$ nbrOfGenotypeGroups: int 3 365s .. ..$ tau : num [1:2] 0.315 0.677 365s .. ..$ n : int 14640 365s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. ..$ density: num [1:2] 0.522 0.552 365s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s muN 365s 0 0.5 1 365s 5221 4198 5251 365s Calling genotypes from normal allele B fractions...done 365s Normalizing betaT using betaN (TumorBoost)... 365s Nor+ [ 0 != 0 ] 365s + echo Test segmentByPairedPSCBS passed 365s + echo 0 365s + echo Begin test weightedQuantile 365s + exitcode=0 365s + R CMD BATCHmalized BAFs: 365s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 365s - attr(*, "modelFit")=List of 5 365s ..$ method : chr "normalizeTumorBoost" 365s ..$ flavor : chr "v4" 365s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 365s .. ..- attr(*, "modelFit")=List of 1 365s .. .. ..$ :List of 7 365s .. .. .. ..$ flavor : chr "density" 365s .. .. .. ..$ cn : int 2 365s .. .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. .. ..$ n : int 14640 365s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s ..$ preserveScale: logi FALSE 365s ..$ scaleFactor : num NA 365s Normalizing betaT using betaN (TumorBoost)...done 365s Setup up data... 365s 'data.frame': 14670 obs. of 7 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 365s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 365s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 365s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 365s ..- attr(*, "modelFit")=List of 5 365s .. ..$ method : chr "normalizeTumorBoost" 365s .. ..$ flavor : chr "v4" 365s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 365s .. .. ..- attr(*, "modelFit")=List of 1 365s .. .. .. ..$ :List of 7 365s .. .. .. .. ..$ flavor : chr "density" 365s .. .. .. .. ..$ cn : int 2 365s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. .. .. ..$ n : int 14640 365s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s .. ..$ preserveScale: logi FALSE 365s .. ..$ scaleFactor : num NA 365s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 365s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 365s ..- attr(*, "modelFit")=List of 1 365s .. ..$ :List of 7 365s .. .. ..$ flavor : chr "density" 365s .. .. ..$ cn : int 2 365s .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. ..$ n : int 14640 365s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s Setup up data...done 365s Dropping loci for which TCNs are missing... 365s Number of loci dropped: 12 365s Dropping loci for which TCNs are missing...done 365s Ordering data along genome... 365s 'data.frame': 14658 obs. of 7 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 554484 730720 782343 878522 916294 ... 365s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 365s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 365s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 365s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 365s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 365s Ordering data along genome...done 365s Keeping only current chromosome for 'knownSegments'... 365s Chromosome: 1 365s Known segments for this chromosome: 365s chromosome start end 365s 1 1 -Inf 120992603 365s 2 1 NA NA 365s 3 1 141510003 Inf 365s Keeping only current chromosome for 'knownSegments'...done 365s alphaTCN: 0.009 365s alphaDH: 0.001 365s Number of loci: 14658 365s Calculating DHs... 365s Number of SNPs: 14658 365s Number of heterozygous SNPs: 4196 (28.63%) 365s Normalized DHs: 365s num [1:14658] NA NA NA NA NA ... 365s Calculating DHs...done 365s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 365s Produced 2 seeds from this stream for future usage 365s Identification of change points by total copy numbers... 365s Segmenting by CBS... 365s Chromosome: 1 365s Segmenting multiple segments on current chromosome... 365s Number of segments: 3 365s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 365s Produced 3 seeds from this stream for future usage 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s Segmenting multiple segments on current chromosome...done 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 14658 obs. of 4 variables: 365s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 365s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 365s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 4 obs. of 6 variables: 365s ..$ sampleName: chr [1:4] NA NA NA NA 365s ..$ chromosome: int [1:4] 1 NA 1 1 365s ..$ start : num [1:4] 5.54e+05 NA 1.42e+08 1.85e+08 365s ..$ end : num [1:4] 1.21e+08 NA 1.85e+08 2.47e+08 365s ..$ nbrOfLoci : int [1:4] 7586 NA 2681 4391 365s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 365s $ segRows:'data.frame': 4 obs. of 2 variables: 365s ..$ startRow: int [1:4] 1 NA 7587 10268 365s ..$ endRow : int [1:4] 7586 NA 10267 14658 365s $ params :List of 5 365s ..$ alpha : num 0.009 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 365s .. ..$ chromosome: num [1:4] 1 1 2 1 365s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.42e+08 365s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 365s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.487 0 0.488 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s Identification of change points by total copy numbers...done 365s Restructure TCN segmentation results... 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 365s 1 1 554484 120992603 7586 1.3853 365s 2 NA NA NA NA NA 365s 3 1 141510003 185449813 2681 2.0689 365s 4 1 185449813 2471 weightedQuantile.R 365s 37334 4391 2.6341 365s Number of TCN segments: 4 365s Restructure TCN segmentation results...done 365s Total CN segment #1 ([ 554484,1.20993e+08]) of 4... 365s Number of TCN loci in segment: 7586 365s Locus data for TCN segment: 365s 'data.frame': 7586 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 554484 730720 782343 878522 916294 ... 365s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 365s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 365s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 365s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 365s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 365s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 365s $ rho : num NA NA NA NA NA ... 365s Number of loci: 7586 365s Number of SNPs: 2108 (27.79%) 365s Number of heterozygous SNPs: 2108 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 7586 obs. of 4 variables: 365s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 365s ..$ y : num [1:7586] NA NA NA NA NA ... 365s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 554484 365s ..$ end : num 1.21e+08 365s ..$ nbrOfLoci : int 2108 365s ..$ mean : num 0.512 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 10 365s ..$ endRow : int 7574 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 554484 365s .. ..$ end : num 1.21e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.045 0 0.045 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 10 7574 365s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 10 7574 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 554484 120992603 2108 0.5116 365s startRow endRow 365s 1 10 7574 365s Rows: 365s [1] 1 365s TCN segmentation rows: 365s startRow endRow 365s 1 1 7586 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s startRow endRow 365s 1 10 7574 365s NULL 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s startRow endRow 365s 1 10 7574 365s startRow endRow 365s 1 1 7586 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 1 1 554484 120992603 7586 1.3853 2108 2108 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 1 2108 554484 120992603 2108 0.5116 365s Total CN segment #1 ([ 554484,1.20993e+08]) of 4...done 365s Total CN segment #2 ([ NA, NA]) of 4... 365s No signals to segment. Just a "splitter" segment. Skipping. 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s NA 2 1 NA NA NA NA NA 0 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s NA 0 NA NA 0 NA 365s Total CN segment #2 ([ NA, NA]) of 4...done 365s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4... 365s Number of TCN loci in segment: 2681 365s Locus data for TCN segment: 365s 'data.frame': 2681 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 365s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 365s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 365s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 365s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 365s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 365s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 365s $ rho : num 0.117 0.258 NA NA NA ... 365s Number of loci: 2681 365s Number of SNPs: 777 (28.98%) 365s Number of heterozygous SNPs: 777 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 2681 obs. of 4 variables: 365s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 365s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 365s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 1.42e+08 365s ..$ end : num 1.85e+08 365s ..$ nbrOfLoci : int 777 365s ..$ mean : num 0.0973 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 1 365s ..$ endRow : int 2677 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 1.42e+08 365s .. ..$ end : num 1.85e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.012 0 0.013 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 1 2677 365s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 7587 10263 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 141510003 185449813 777 0.0973 365s startRow endRow 365s 1 7587 10263 365s Rows: 365s [1] 3 365s TCN segmentation rows: 365s startRow endRow 365s 3 7587 10267 365s TCN and DH segmentation rows: 365s startRow endRow 365s 3 7587 10267 365s startRow endRow 365s 1 7587 10263 365s startRow endRow 365s 1 1 7586 365s NA NA NA 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s NA NA NA 365s 3 7587 10267 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s startRow endRow 365s 1 10 7574 365s 2 NA NA 365s 3 7587 10263 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 3 1 141510003 185449813 2681 2.0689 777 777 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 3 3 1 1 141510003 185449813 2681 2.0689 777 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 3 777 141510003 185449813 777 0.0973 365s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4...done 365s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 365s Number of TCN loci in segment: 4391 365s Locus data for TCN segment: 365s 'data.frame': 4391 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 365s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 365s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 365s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 365s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 365s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 365s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 365s $ rho : num NA 0.2186 NA 0.0503 NA ... 365s Number of loci: 4391 365s Number of SNPs: 1311 (29.86%) 365s Number of heterozygous SNPs: 1311 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 4391 obs. of 4 variables: 365s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 365s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 365s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 1.85e+08 365s ..$ end : num 2.47e+08 365s ..$ nbrOfLoci : int 1311 365s ..$ mean : num 0.23 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 2 365s ..$ endRow : int 4388 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 1.85e+08 365s .. ..$ end : num 2.47e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.024 0 0.024 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 2 4388 365s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 10269 14655 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 185449813 247137334 1311 0.2295 365s startRow endRow 365s 1 10269 14655 365s Rows: 365s [1] 4 365s TCN segmentation rows: 365s startRow endRow 365s 4 10268 14658 365s TCN and DH segmentation rows: 365s startRow endRow 365s 4 10268 14658 365s startRow endRow 365s 1 10269 14655 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s startRow endRow 365s 1 10 7574 365s 2 NA NA 365s 3 7587 10263 365s 4 10269 14655 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 4 1 185449813 247137334 4391 2.6341 1311 1311 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 4 4 1 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 4 1311 185449813 247137334 1311 0.2295 365s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 NA 2 1 NA NA NA NA 0 365s 3 1 3 1 141510003 185449813 2681 2.0689 777 365s 4 1 4 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 1 2108 554484 120992603 2108 0.5116 365s 2 0 NA NA 0 NA 365s 3 777 141510003 185449813 777 0.0973 365s 4 1311 185449813 247137334 1311 0.2295 365s Calculating (C1,C2) per segment... 365s Calculating (C1,C2) per segment...done 365s Number of segments: 4 365s Segmenting paired tumor-normal signals using Paired PSCBS...done 365s Post-segmenting TCNs... 365s Number of segments: 3 365s Number of chromosomes: 1 365s [1] 1 365s Chromosome 1 ('chr01') of 1... 365s Rows: 365s [1] 1 2 3 365s Number of segments: 3 365s TCN segment #1 ('1') of 3... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #1 ('1') of 3...done 365s TCN segment #2 ('3') of 3... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #2 ('3') of 3...done 365s TCN segment #3 ('4') of 3... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #3 ('4') of 3...done 365s Chromosome 1 ('chr01') of 1...done 365s Update (C1,C2) per segment... 365s Update (C1,C2) per segment...done 365s Post-segmenting TCNs...done 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 NA 2 1 NA NA NA NA 0 365s 3 1 3 1 141510003 185449813 2681 2.0689 777 365s 4 1 4 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 365s 2 0 NA NA 0 NA NA NA 365s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 365s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 NA 2 1 NA NA NA NA 0 365s 3 1 3 1 141510003 185449813 2681 2.0689 777 365s 4 1 4 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 365s 2 0 NA NA 0 NA NA NA 365s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 365s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 365s > print(fit) 365s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 NA 2 1 NA NA NA NA 0 365s 3 1 3 1 141510003 185449813 2681 2.0689 777 365s 4 1 4 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 2108 0.5116 0.3382903 1.047010 365s 2 0 0 NA NA NA 365s 3 777 777 0.0973 0.9337980 1.135102 365s 4 1311 1311 0.2295 1.0147870 1.619313 365s > 365s > # Plot results 365s > dev.set(2L) 365s null device 365s 1 365s > plotTracks(fit) 365s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 365s > 365s > # Sanity check 365s > stopifnot(nbrOfSegments(fit) == nSegs) 365s > 365s > fit1 <- fit 365s > 365s > 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > # (b) Segment also the centromere (which will become NAs) 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > knownSegments <- data.frame( 365s + chromosome = c( 1, 1, 1), 365s + start = c( -Inf, 120992604, 141510003), 365s + end = c(120992603, 141510002, +Inf) 365s + ) 365s > 365s > 365s > # Paired PSCBS segmentation 365s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 365s + seed=0xBEEF, verbose=-10) 365s Segmenting paired tumor-normal signals using Paired PSCBS... 365s Calling genotypes from normal allele B fractions... 365s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 365s Called genotypes: 365s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 365s - attr(*, "modelFit")=List of 1 365s ..$ :List of 7 365s .. ..$ flavor : chr "density" 365s .. ..$ cn : int 2 365s .. ..$ nbrOfGenotypeGroups: int 3 365s .. ..$ tau : num [1:2] 0.315 0.677 365s .. ..$ n : int 14640 365s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. ..$ density: num [1:2] 0.522 0.552 365s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s muN 365s 0 0.5 1 365s 5221 4198 5251 365s Calling genotypes from normal allele B fractions...done 365s Normalizing betaT using betaN (TumorBoost)... 365s Normalized BAFs: 365s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 365s - attr(*, "modelFit")=List of 5 365s ..$ method : chr "normalizeTumorBoost" 365s ..$ flavor : chr "v4" 365s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 365s .. ..- attr(*, "modelFit")=List of 1 365s .. .. ..$ :List of 7 365s .. .. .. ..$ flavor : chr "density" 365s .. .. .. ..$ cn : int 2 365s .. .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. .. ..$ n : int 14640 365s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s ..$ preserveScale: logi FALSE 365s ..$ scaleFactor : num NA 365s Normalizing betaT using betaN (TumorBoost)...done 365s Setup up data... 365s 'data.frame': 14670 obs. of 7 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 365s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 365s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 365s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 365s ..- attr(*, "modelFit")=List of 5 365s .. ..$ method : chr "normalizeTumorBoost" 365s .. ..$ flavor : chr "v4" 365s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 365s .. .. ..- attr(*, "modelFit")=List of 1 365s .. .. .. ..$ :List of 7 365s .. .. .. .. ..$ flavor : chr "density" 365s .. .. .. .. ..$ cn : int 2 365s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. .. .. ..$ n : int 14640 365s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s .. ..$ preserveScale: logi FALSE 365s .. ..$ scaleFactor : num NA 365s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 365s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 365s ..- attr(*, "modelFit")=List of 1 365s .. ..$ :List of 7 365s .. .. ..$ flavor : chr "density" 365s .. .. ..$ cn : int 2 365s .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. ..$ n : int 14640 365s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s Setup up data...done 365s Dropping loci for which TCNs are missing... 365s Number of loci dropped: 12 365s Dropping loci for which TCNs are missing...done 365s Ordering data along genome... 365s 'data.frame': 14658 obs. of 7 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 554484 730720 782343 878522 916294 ... 365s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 365s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 365s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 365s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 365s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 365s Ordering data along genome...done 365s Keeping only current chromosome for 'knownSegments'... 365s Chromosome: 1 365s Known segments for this chromosome: 365s chromosome start end 365s 1 1 -Inf 120992603 365s 2 1 120992604 141510002 365s 3 1 141510003 Inf 365s Keeping only current chromosome for 'knownSegments'...done 365s alphaTCN: 0.009 365s alphaDH: 0.001 365s Number of loci: 14658 365s Calculating DHs... 365s Number of SNPs: 14658 365s Number of heterozygous SNPs: 4196 (28.63%) 365s Normalized DHs: 365s num [1:14658] NA NA NA NA NA ... 365s Calculating DHs...done 365s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 365s Produced 2 seeds from this stream for future usage 365s Identification of change points by total copy numbers... 365s Segmenting by CBS... 365s Chromosome: 1 365s Segmenting multiple segments on current chromosome... 365s Number of segments: 3 365s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 365s Produced 3 seeds from this stream for future usage 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s Segmenting multiple segments on current chromosome...done 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 14658 obs. of 4 variables: 365s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 365s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 365s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 4 obs. of 6 variables: 365s ..$ sampleName: chr [1:4] NA NA NA NA 365s ..$ chromosome: num [1:4] 1 1 1 1 365s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.42e+08 1.85e+08 365s ..$ end : num [1:4] 1.21e+08 1.42e+08 1.85e+08 2.47e+08 365s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 365s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 365s $ segRows:'data.frame': 4 obs. of 2 variables: 365s ..$ startRow: int [1:4] 1 NA 7587 10268 365s ..$ endRow : int [1:4] 7586 NA 10267 14658 365s $ params :List of 5 365s ..$ alpha : num 0.009 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 365s .. ..$ chromosome: num [1:4] 1 1 2 1 365s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.42e+08 365s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 365s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.482 0 0.482 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s Identification of change points by total copy numbers...done 365s Restructure TCN segmentation results... 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 365s 1 1 554484 120992603 7586 1.3853 365s 2 1 120992604 141510002 0 NA 365s 3 1 141510003 185449813 2681 2.0689 365s 4 1 185449813 247137334 4391 2.6341 365s Number of TCN segments: 4 365s Restructure TCN segmentation results...done 365s Total CN segment #1 ([ 554484,1.20993e+08]) of 4... 365s Number of TCN loci in segment: 7586 365s Locus data for TCN segment: 365s 'data.frame': 7586 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 554484 730720 782343 878522 916294 ... 365s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 365s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 365s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 365s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 365s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 365s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 365s $ rho : num NA NA NA NA NA ... 365s Number of loci: 7586 365s Number of SNPs: 2108 (27.79%) 365s Number of heterozygous SNPs: 2108 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 7586 obs. of 4 variables: 365s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 365s ..$ y : num [1:7586] NA NA NA NA NA ... 365s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 554484 365s ..$ end : num 1.21e+08 365s ..$ nbrOfLoci : int 2108 365s ..$ mean : num 0.512 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 10 365s ..$ endRow : int 7574 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 554484 365s .. ..$ end : num 1.21e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.045 0 0.045 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 10 7574 365s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 10 7574 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 554484 120992603 2108 0.5116 365s startRow endRow 365s 1 10 7574 365s Rows: 365s [1] 1 365s TCN segmentation rows: 365s startRow endRow 365s 1 1 7586 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s startRow endRow 365s 1 10 7574 365s NULL 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s startRow endRow 365s 1 10 7574 365s startRow endRow 365s 1 1 7586 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 1 1 554484 120992603 7586 1.3853 2108 2108 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 1 2108 554484 120992603 2108 0.5116 365s Total CN segment #1 ([ 554484,1.20993e+08]) of 4...done 365s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4... 365s Number of TCN loci in segment: 0 365s Locus data for TCN segment: 365s 'data.frame': 0 obs. of 9 variables: 365s $ chromosome: int 365s $ x : num 365s $ CT : num 365s $ betaT : num 365s $ betaTN : num 365s $ betaN : num 365s $ muN : num 365s $ index : int 365s $ rho : num 365s Number of loci: 0 365s Number of SNPs: 0 (NaN%) 365s Number of heterozygous SNPs: 0 (NaN%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: NA 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 0 obs. of 4 variables: 365s ..$ chromosome: int(0) 365s ..$ x : num(0) 365s ..$ y : num(0) 365s ..$ index : int(0) 365s $ output :'data.frame': 0 obs. of 6 variables: 365s ..$ sampleName: chr(0) 365s ..$ chromosome: num(0) 365s ..$ start : num(0) 365s ..$ end : num(0) 365s ..$ nbrOfLoci : int(0) 365s ..$ mean : num(0) 365s $ segRows:'data.frame': 0 obs. of 2 variables: 365s ..$ startRow: int(0) 365s ..$ endRow : int(0) 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 365s .. ..$ chromosome: int(0) 365s .. ..$ start : num(0) 365s .. ..$ end : num(0) 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.002 0 0.002 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s [1] startRow endRow 365s <0 rows> (or 0-length row.names) 365s int(0) 365s DH segmentation rows: 365s [1] startRow endRow 365s <0 rows> (or 0-length row.names) 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s NA NA NA NA NA 365s startRow endRow 365s NA NA NA 365s Rows: 365s [1] 2 365s TCN segmentation rows: 365s startRow endRow 365s 2 NA NA 365s TCN and DH segmentation rows: 365s startRow endRow 365s 2 NA NA 365s startRow endRow 365s NA NA NA 365s startRow endRow 365s 1 1 7586 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s startRow endRow 365s 1 10 7574 365s 2 NA NA 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 2 1 120992604 141510002 0 NA 0 0 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 2 2 1 1 120992604 141510002 0 NA 0 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 2 0 NA NA NA NA 365s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4...done 365s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4... 365s Number of TCN loci in segment: 2681 365s Locus data for TCN segment: 365s 'data.frame': 2681 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 365s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 365s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 365s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 365s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 365s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 365s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 365s $ rho : num 0.117 0.258 NA NA NA ... 365s Number of loci: 2681 365s Number of SNPs: 777 (28.98%) 365s Number of heterozygous SNPs: 777 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 2681 obs. of 4 variables: 365s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 365s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 365s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 1.42e+08 365s ..$ end : num 1.85e+08 365s ..$ nbrOfLoci : int 777 365s ..$ mean : num 0.0973 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 1 365s ..$ endRow : int 2677 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 1.42e+08 365s .. ..$ end : num 1.85e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.012 0 0.013 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 1 2677 365s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 7587 10263 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 141510003 185449813 777 0.0973 365s startRow endRow 365s 1 7587 10263 365s Rows: 365s [1] 3 365s TCN segmentation rows: 365s startRow endRow 365s 3 7587 10267 365s TCN and DH segmentation rows: 365s startRow endRow 365s 3 7587 10267 365s startRow endRow 365s 1 7587 10263 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s startRow endRow 365s 1 10 7574 365s 2 NA NA 365s 3 7587 10263 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 3 1 141510003 185449813 2681 2.0689 777 777 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 3 3 1 1 141510003 185449813 2681 2.0689 777 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 3 777 141510003 185449813 777 0.0973 365s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4...done 365s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 365s Number of TCN loci in segment: 4391 365s Locus data for TCN segment: 365s 'data.frame': 4391 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 365s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 365s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 365s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 365s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 365s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 365s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 365s $ rho : num NA 0.2186 NA 0.0503 NA ... 365s Number of loci: 4391 365s Number of SNPs: 1311 (29.86%) 365s Number of heterozygous SNPs: 1311 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 4391 obs. of 4 variables: 365s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 365s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 365s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 1.85e+08 365s ..$ end : num 2.47e+08 365s ..$ nbrOfLoci : int 1311 365s ..$ mean : num 0.23 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 2 365s ..$ endRow : int 4388 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 1.85e+08 365s .. ..$ end : num 2.47e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.025 0 0.024 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 2 4388 365s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 10269 14655 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 185449813 247137334 1311 0.2295 365s startRow endRow 365s 1 10269 14655 365s Rows: 365s [1] 4 365s TCN segmentation rows: 365s startRow endRow 365s 4 10268 14658 365s TCN and DH segmentation rows: 365s startRow endRow 365s 4 10268 14658 365s startRow endRow 365s 1 10269 14655 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s startRow endRow 365s 1 10 7574 365s 2 NA NA 365s 3 7587 10263 365s 4 10269 14655 365s startRow endRow 365s 1 1 7586 365s 2 NA NA 365s 3 7587 10267 365s 4 10268 14658 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 4 1 185449813 247137334 4391 2.6341 1311 1311 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 4 4 1 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 4 1311 185449813 247137334 1311 0.2295 365s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 1 2 1 120992604 141510002 0 NA 0 365s 3 1 3 1 141510003 185449813 2681 2.0689 777 365s 4 1 4 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 1 2108 554484 120992603 2108 0.5116 365s 2 0 NA NA NA NA 365s 3 777 141510003 185449813 777 0.0973 365s 4 1311 185449813 247137334 1311 0.2295 365s Calculating (C1,C2) per segment... 365s Calculating (C1,C2) per segment...done 365s Number of segments: 4 365s Segmenting paired tumor-normal signals using Paired PSCBS...done 365s Post-segmenting TCNs... 365s Number of segments: 4 365s Number of chromosomes: 1 365s [1] 1 365s Chromosome 1 ('chr01') of 1... 365s Rows: 365s [1] 1 2 3 4 365s Number of segments: 4 365s TCN segment #1 ('1') of 4... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #1 ('1') of 4...done 365s TCN segment #2 ('2') of 4... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #2 ('2') of 4...done 365s TCN segment #3 ('3') of 4... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #3 ('3') of 4...done 365s TCN segment #4 ('4') of 4... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #4 ('4') of 4...done 365s Chromosome 1 ('chr01') of 1...done 365s Update (C1,C2) per segment... 365s Update (C1,C2) per segment...done 365s Post-segmenting TCNs...done 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 1 2 1 120992604 141510002 0 NA 0 365s 3 1 3 1 141510003 185449813 2681 2.0689 777 365s 4 1 4 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 365s 2 0 NA NA NA NA NA NA 365s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 365s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 1 2 1 120992604 141510002 0 NA 0 365s 3 1 3 1 141510003 185449813 2681 2.0689 777 365s 4 1 4 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 365s 2 0 NA NA NA NA NA NA 365s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 365s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 365s > print(fit) 365s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 1 2 1 120992604 141510002 0 NA 0 365s 3 1 3 1 141510003 185449813 2681 2.0689 777 365s 4 1 4 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 2108 0.5116 0.3382903 1.047010 365s 2 0 NA NA NA NA 365s 3 777 777 0.0973 0.9337980 1.135102 365s 4 1311 1311 0.2295 1.0147870 1.619313 365s > 365s > # Plot results 365s > dev.set(3L) 365s pdf 365s 2 365s > plotTracks(fit) 365s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 365s > 365s > # Sanity check [TO FIX: See above] 365s > stopifnot(nbrOfSegments(fit) == nSegs) 365s > 365s > fit2 <- fit 365s > 365s > 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > # (c) Do not segment the centromere (without a separator) 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > knownSegments <- data.frame( 365s + chromosome = c( 1, 1), 365s + start = c( -Inf, 141510003), 365s + end = c(120992603, +Inf) 365s + ) 365s > 365s > # Paired PSCBS segmentation 365s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 365s + seed=0xBEEF, verbose=-10) 365s Segmenting paired tumor-normal signals using Paired PSCBS... 365s Calling genotypes from normal allele B fractions... 365s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 365s Called genotypes: 365s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 365s - attr(*, "modelFit")=List of 1 365s ..$ :List of 7 365s .. ..$ flavor : chr "density" 365s .. ..$ cn : int 2 365s .. ..$ nbrOfGenotypeGroups: int 3 365s .. ..$ tau : num [1:2] 0.315 0.677 365s .. ..$ n : int 14640 365s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. ..$ density: num [1:2] 0.522 0.552 365s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s muN 365s 0 0.5 1 365s 5221 4198 5251 365s Calling genotypes from normal allele B fractions...done 365s Normalizing betaT using betaN (TumorBoost)... 365s Normalized BAFs: 365s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 365s - attr(*, "modelFit")=List of 5 365s ..$ method : chr "normalizeTumorBoost" 365s ..$ flavor : chr "v4" 365s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 365s .. ..- attr(*, "modelFit")=List of 1 365s .. .. ..$ :List of 7 365s .. .. .. ..$ flavor : chr "density" 365s .. .. .. ..$ cn : int 2 365s .. .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. .. ..$ n : int 14640 365s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s ..$ preserveScale: logi FALSE 365s ..$ scaleFactor : num NA 365s Normalizing betaT using betaN (TumorBoost)...done 365s Setup up data... 365s 'data.frame': 14670 obs. of 7 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 365s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 365s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 365s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 365s ..- attr(*, "modelFit")=List of 5 365s .. ..$ method : chr "normalizeTumorBoost" 365s .. ..$ flavor : chr "v4" 365s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 365s .. .. ..- attr(*, "modelFit")=List of 1 365s .. .. .. ..$ :List of 7 365s .. .. .. .. ..$ flavor : chr "density" 365s .. .. .. .. ..$ cn : int 2 365s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. .. .. ..$ n : int 14640 365s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s .. ..$ preserveScale: logi FALSE 365s .. ..$ scaleFactor : num NA 365s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 365s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 365s ..- attr(*, "modelFit")=List of 1 365s .. ..$ :List of 7 365s .. .. ..$ flavor : chr "density" 365s .. .. ..$ cn : int 2 365s .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. ..$ n : int 14640 365s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s Setup up data...done 365s Dropping loci for which TCNs are missing... 365s Number of loci dropped: 12 365s Dropping loci for which TCNs are missing...done 365s Ordering data along genome... 365s 'data.frame': 14658 obs. of 7 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 554484 730720 782343 878522 916294 ... 365s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 365s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 365s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 365s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 365s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 365s Ordering data along genome...done 365s Keeping only current chromosome for 'knownSegments'... 365s Chromosome: 1 365s Known segments for this chromosome: 365s chromosome start end 365s 1 1 -Inf 120992603 365s 2 1 141510003 Inf 365s Keeping only current chromosome for 'knownSegments'...done 365s alphaTCN: 0.009 365s alphaDH: 0.001 365s Number of loci: 14658 365s Calculating DHs... 365s Number of SNPs: 14658 365s Number of heterozygous SNPs: 4196 (28.63%) 365s Normalized DHs: 365s num [1:14658] NA NA NA NA NA ... 365s Calculating DHs...done 365s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 365s Produced 2 seeds from this stream for future usage 365s Identification of change points by total copy numbers... 365s Segmenting by CBS... 365s Chromosome: 1 365s Segmenting multiple segments on current chromosome... 365s Number of segments: 2 365s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 365s Produced 2 seeds from this stream for future usage 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s Segmenting multiple segments on current chromosome...done 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 14658 obs. of 4 variables: 365s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 365s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 365s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 3 obs. of 6 variables: 365s ..$ sampleName: chr [1:3] NA NA NA 365s ..$ chromosome: int [1:3] 1 1 1 365s ..$ start : num [1:3] 5.54e+05 1.42e+08 1.85e+08 365s ..$ end : num [1:3] 1.21e+08 1.85e+08 2.47e+08 365s ..$ nbrOfLoci : int [1:3] 7586 2681 4391 365s ..$ mean : num [1:3] 1.39 2.07 2.63 365s $ segRows:'data.frame': 3 obs. of 2 variables: 365s ..$ startRow: int [1:3] 1 7587 10268 365s ..$ endRow : int [1:3] 7586 10267 14658 365s $ params :List of 5 365s ..$ alpha : num 0.009 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 2 obs. of 3 variables: 365s .. ..$ chromosome: num [1:2] 1 1 365s .. ..$ start : num [1:2] -Inf 1.42e+08 365s .. ..$ end : num [1:2] 1.21e+08 Inf 365s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.48 0 0.48 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s Identification of change points by total copy numbers...done 365s Restructure TCN segmentation results... 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 365s 1 1 554484 120992603 7586 1.3853 365s 2 1 141510003 185449813 2681 2.0689 365s 3 1 185449813 247137334 4391 2.6341 365s Number of TCN segments: 3 365s Restructure TCN segmentation results...done 365s Total CN segment #1 ([ 554484,1.20993e+08]) of 3... 365s Number of TCN loci in segment: 7586 365s Locus data for TCN segment: 365s 'data.frame': 7586 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 554484 730720 782343 878522 916294 ... 365s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 365s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 365s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 365s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 365s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 365s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 365s $ rho : num NA NA NA NA NA ... 365s Number of loci: 7586 365s Number of SNPs: 2108 (27.79%) 365s Number of heterozygous SNPs: 2108 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 7586 obs. of 4 variables: 365s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 365s ..$ y : num [1:7586] NA NA NA NA NA ... 365s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 554484 365s ..$ end : num 1.21e+08 365s ..$ nbrOfLoci : int 2108 365s ..$ mean : num 0.512 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 10 365s ..$ endRow : int 7574 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 554484 365s .. ..$ end : num 1.21e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.045 0 0.045 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 10 7574 365s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 10 7574 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 554484 120992603 2108 0.5116 365s startRow endRow 365s 1 10 7574 365s Rows: 365s [1] 1 365s TCN segmentation rows: 365s startRow endRow 365s 1 1 7586 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s startRow endRow 365s 1 10 7574 365s NULL 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 7587 10267 365s 3 10268 14658 365s startRow endRow 365s 1 10 7574 365s startRow endRow 365s 1 1 7586 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 1 1 554484 120992603 7586 1.3853 2108 2108 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 1 2108 554484 120992603 2108 0.5116 365s Total CN segment #1 ([ 554484,1.20993e+08]) of 3...done 365s Total CN segment #2 ([1.4151e+08,1.8545e+08]) of 3... 365s Number of TCN loci in segment: 2681 365s Locus data for TCN segment: 365s 'data.frame': 2681 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 365s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 365s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 365s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 365s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 365s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 365s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 365s $ rho : num 0.117 0.258 NA NA NA ... 365s Number of loci: 2681 365s Number of SNPs: 777 (28.98%) 365s Number of heterozygous SNPs: 777 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 2681 obs. of 4 variables: 365s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 365s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 365s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 1.42e+08 365s ..$ end : num 1.85e+08 365s ..$ nbrOfLoci : int 777 365s ..$ mean : num 0.0973 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 1 365s ..$ endRow : int 2677 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 1.42e+08 365s .. ..$ end : num 1.85e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.013 0 0.013 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 1 2677 365s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 7587 10263 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 141510003 185449813 777 0.0973 365s startRow endRow 365s 1 7587 10263 365s Rows: 365s [1] 2 365s TCN segmentation rows: 365s startRow endRow 365s 2 7587 10267 365s TCN and DH segmentation rows: 365s startRow endRow 365s 2 7587 10267 365s startRow endRow 365s 1 7587 10263 365s startRow endRow 365s 1 1 7586 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s 2 7587 10267 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 7587 10267 365s 3 10268 14658 365s startRow endRow 365s 1 10 7574 365s 2 7587 10263 365s startRow endRow 365s 1 1 7586 365s 2 7587 10267 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 2 1 141510003 185449813 2681 2.0689 777 777 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 2 2 1 1 141510003 185449813 2681 2.0689 777 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 2 777 141510003 185449813 777 0.0973 365s Total CN segment #2 ([1.4151e+08,1.8545e+08]) of 3...done 365s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 365s Number of TCN loci in segment: 4391 365s Locus data for TCN segment: 365s 'data.frame': 4391 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 365s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 365s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 365s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 365s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 365s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 365s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 365s $ rho : num NA 0.2186 NA 0.0503 NA ... 365s Number of loci: 4391 365s Number of SNPs: 1311 (29.86%) 365s Number of heterozygous SNPs: 1311 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 4391 obs. of 4 variables: 365s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 365s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 365s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 1.85e+08 365s ..$ end : num 2.47e+08 365s ..$ nbrOfLoci : int 1311 365s ..$ mean : num 0.23 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 2 365s ..$ endRow : int 4388 365s $ params :List of 5 365s ..$ alpha : num 0.001 365s ..$ undo : num 0 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 1.85e+08 365s .. ..$ end : num 2.47e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.025 0 0.024 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 2 4388 365s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 10269 14655 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 185449813 247137334 1311 0.2295 365s startRow endRow 365s 1 10269 14655 365s Rows: 365s [1] 3 365s TCN segmentation rows: 365s startRow endRow 365s 3 10268 14658 365s TCN and DH segmentation rows: 365s startRow endRow 365s 3 10268 14658 365s startRow endRow 365s 1 10269 14655 365s startRow endRow 365s 1 1 7586 365s 2 7587 10267 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s 2 7587 10267 365s 3 10268 14658 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 7587 10267 365s 3 10268 14658 365s startRow endRow 365s 1 10 7574 365s 2 7587 10263 365s 3 10269 14655 365s startRow endRow 365s 1 1 7586 365s 2 7587 10267 365s 3 10268 14658 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 3 1 185449813 247137334 4391 2.6341 1311 1311 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 3 3 1 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 3 1311 185449813 247137334 1311 0.2295 365s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 1 2 1 141510003 185449813 2681 2.0689 777 365s 3 1 3 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 1 2108 554484 120992603 2108 0.5116 365s 2 777 141510003 185449813 777 0.0973 365s 3 1311 185449813 247137334 1311 0.2295 365s Calculating (C1,C2) per segment... 365s Calculating (C1,C2) per segment...done 365s Number of segments: 3 365s Segmenting paired tumor-normal signals using Paired PSCBS...done 365s Post-segmenting TCNs... 365s Number of segments: 3 365s Number of chromosomes: 1 365s [1] 1 365s Chromosome 1 ('chr01') of 1... 365s Rows: 365s [1] 1 2 3 365s Number of segments: 3 365s TCN segment #1 ('1') of 3... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #1 ('1') of 3...done 365s TCN segment #2 ('2') of 3... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #2 ('2') of 3...done 365s TCN segment #3 ('3') of 3... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #3 ('3') of 3...done 365s Chromosome 1 ('chr01') of 1...done 365s Update (C1,C2) per segment... 365s Update (C1,C2) per segment...done 365s Post-segmenting TCNs...done 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 1 2 1 141510003 185449813 2681 2.0689 777 365s 3 1 3 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 365s 2 777 141510003 185449813 777 0.0973 0.9337980 1.135102 365s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 1 2 1 141510003 185449813 2681 2.0689 777 365s 3 1 3 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 365s 2 777 141510003 185449813 777 0.0973 0.9337980 1.135102 365s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 365s > print(fit) 365s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.3853 2108 365s 2 1 2 1 141510003 185449813 2681 2.0689 777 365s 3 1 3 1 185449813 247137334 4391 2.6341 1311 365s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 2108 0.5116 0.3382903 1.047010 365s 2 777 777 0.0973 0.9337980 1.135102 365s 3 1311 1311 0.2295 1.0147870 1.619313 365s > 365s > # Plot results 365s > dev.set(4L) 365s pdf 365s 2 365s > plotTracks(fit) 365s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 365s > 365s > # Sanity check 365s > stopifnot(nbrOfSegments(fit) == nSegs-1L) 365s > 365s > fit3 <- fit 365s > 365s > 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > # (d) Skip the identification of new change points 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > knownSegments <- data.frame( 365s + chromosome = c( 1, 1), 365s + start = c( -Inf, 141510003), 365s + end = c(120992603, +Inf) 365s + ) 365s > 365s > # Paired PSCBS segmentation 365s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 365s + undoTCN=Inf, undoDH=Inf, 365s + seed=0xBEEF, verbose=-10) 365s Segmenting paired tumor-normal signals using Paired PSCBS... 365s Calling genotypes from normal allele B fractions... 365s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 365s Called genotypes: 365s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 365s - attr(*, "modelFit")=List of 1 365s ..$ :List of 7 365s .. ..$ flavor : chr "density" 365s .. ..$ cn : int 2 365s .. ..$ nbrOfGenotypeGroups: int 3 365s .. ..$ tau : num [1:2] 0.315 0.677 365s .. ..$ n : int 14640 365s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. ..$ density: num [1:2] 0.522 0.552 365s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s muN 365s 0 0.5 1 365s 5221 4198 5251 365s Calling genotypes from normal allele B fractions...done 365s Normalizing betaT using betaN (TumorBoost)... 365s Normalized BAFs: 365s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 365s - attr(*, "modelFit")=List of 5 365s ..$ method : chr "normalizeTumorBoost" 365s ..$ flavor : chr "v4" 365s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 365s .. ..- attr(*, "modelFit")=List of 1 365s .. .. ..$ :List of 7 365s .. .. .. ..$ flavor : chr "density" 365s .. .. .. ..$ cn : int 2 365s .. .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. .. ..$ n : int 14640 365s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s ..$ preserveScale: logi FALSE 365s ..$ scaleFactor : num NA 365s Normalizing betaT using betaN (TumorBoost)...done 365s Setup up data... 365s 'data.frame': 14670 obs. of 7 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 365s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 365s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 365s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 365s ..- attr(*, "modelFit")=List of 5 365s .. ..$ method : chr "normalizeTumorBoost" 365s .. ..$ flavor : chr "v4" 365s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 365s .. .. ..- attr(*, "modelFit")=List of 1 365s .. .. .. ..$ :List of 7 365s .. .. .. .. ..$ flavor : chr "density" 365s .. .. .. .. ..$ cn : int 2 365s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. .. .. ..$ n : int 14640 365s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s .. ..$ preserveScale: logi FALSE 365s .. ..$ scaleFactor : num NA 365s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 365s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 365s ..- attr(*, "modelFit")=List of 1 365s .. ..$ :List of 7 365s .. .. ..$ flavor : chr "density" 365s .. .. ..$ cn : int 2 365s .. .. ..$ nbrOfGenotypeGroups: int 3 365s .. .. ..$ tau : num [1:2] 0.315 0.677 365s .. .. ..$ n : int 14640 365s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 365s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 365s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 365s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 365s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 365s .. .. .. ..$ type : chr [1:2] "valley" "valley" 365s .. .. .. ..$ x : num [1:2] 0.315 0.677 365s .. .. .. ..$ density: num [1:2] 0.522 0.552 365s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 365s Setup up data...done 365s Dropping loci for which TCNs are missing... 365s Number of loci dropped: 12 365s Dropping loci for which TCNs are missing...done 365s Ordering data along genome... 365s 'data.frame': 14658 obs. of 7 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 554484 730720 782343 878522 916294 ... 365s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 365s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 365s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 365s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 365s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 365s Ordering data along genome...done 365s Keeping only current chromosome for 'knownSegments'... 365s Chromosome: 1 365s Known segments for this chromosome: 365s chromosome start end 365s 1 1 -Inf 120992603 365s 2 1 141510003 Inf 365s Keeping only current chromosome for 'knownSegments'...done 365s alphaTCN: 0.009 365s alphaDH: 0.001 365s Number of loci: 14658 365s Calculating DHs... 365s Number of SNPs: 14658 365s Number of heterozygous SNPs: 4196 (28.63%) 365s Normalized DHs: 365s num [1:14658] NA NA NA NA NA ... 365s Calculating DHs...done 365s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 365s Produced 2 seeds from this stream for future usage 365s Identification of change points by total copy numbers... 365s Segmenting by CBS... 365s Chromosome: 1 365s Segmenting multiple segments on current chromosome... 365s Number of segments: 2 365s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 365s Produced 2 seeds from this stream for future usage 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s Segmenting multiple segments on current chromosome...done 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 14658 obs. of 4 variables: 365s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 365s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 365s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 2 obs. of 6 variables: 365s ..$ sampleName: chr [1:2] NA NA 365s ..$ chromosome: num [1:2] 1 1 365s ..$ start : num [1:2] 5.54e+05 1.42e+08 365s ..$ end : num [1:2] 1.21e+08 2.47e+08 365s ..$ nbrOfLoci : int [1:2] 7586 7072 365s ..$ mean : num [1:2] 1.39 2.42 365s $ segRows:'data.frame': 2 obs. of 2 variables: 365s ..$ startRow: int [1:2] 1 7587 365s ..$ endRow : int [1:2] 7586 14658 365s $ params :List of 7 365s ..$ undo.splits : chr "sdundo" 365s ..$ undo.SD : num Inf 365s ..$ alpha : num 0.009 365s ..$ undo : num Inf 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 2 obs. of 3 variables: 365s .. ..$ chromosome: num [1:2] 1 1 365s .. ..$ start : num [1:2] -Inf 1.42e+08 365s .. ..$ end : num [1:2] 1.21e+08 Inf 365s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.002 0 0.002 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s Identification of change points by total copy numbers...done 365s Restructure TCN segmentation results... 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 365s 1 1 554484 120992603 7586 1.385258 365s 2 1 141510003 247137334 7072 2.419824 365s Number of TCN segments: 2 365s Restructure TCN segmentation results...done 365s Total CN segment #1 ([ 554484,1.20993e+08]) of 2... 365s Number of TCN loci in segment: 7586 365s Locus data for TCN segment: 365s 'data.frame': 7586 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 554484 730720 782343 878522 916294 ... 365s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 365s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 365s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 365s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 365s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 365s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 365s $ rho : num NA NA NA NA NA ... 365s Number of loci: 7586 365s Number of SNPs: 2108 (27.79%) 365s Number of heterozygous SNPs: 2108 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 7586 obs. of 4 variables: 365s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 365s ..$ y : num [1:7586] NA NA NA NA NA ... 365s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 554484 365s ..$ end : num 1.21e+08 365s ..$ nbrOfLoci : int 7586 365s ..$ mean : num 0.512 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 1 365s ..$ endRow : int 7586 365s $ params :List of 7 365s ..$ undo.splits : chr "sdundo" 365s ..$ undo.SD : num Inf 365s ..$ alpha : num 0.001 365s ..$ undo : num Inf 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 554484 365s .. ..$ end : num 1.21e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.002 0 0.003 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 1 7586 365s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 554484 120992603 7586 0.511612 365s startRow endRow 365s 1 1 7586 365s Rows: 365s [1] 1 365s TCN segmentation rows: 365s startRow endRow 365s 1 1 7586 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s startRow endRow 365s 1 1 7586 365s NULL 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 7587 14658 365s startRow endRow 365s 1 1 7586 365s startRow endRow 365s 1 1 7586 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 365s 1 1 554484 120992603 7586 1.385258 2108 2108 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.385258 2108 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 1 2108 554484 120992603 7586 0.511612 365s Total CN segment #1 ([ 554484,1.20993e+08]) of 2...done 365s Total CN segment #2 ([1.4151e+08,2.47137e+08]) of 2... 365s Number of TCN loci in segment: 7072 365s Locus data for TCN segment: 365s 'data.frame': 7072 obs. of 9 variables: 365s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 365s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 365s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 365s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 365s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 365s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 365s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 365s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 365s $ rho : num 0.117 0.258 NA NA NA ... 365s Number of loci: 7072 365s Number of SNPs: 2088 (29.52%) 365s Number of heterozygous SNPs: 2088 (100.00%) 365s Chromosome: 1 365s Segmenting DH signals... 365s Segmenting by CBS... 365s Chromosome: 1 365s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 365s Segmenting by CBS...done 365s List of 4 365s $ data :'data.frame': 7072 obs. of 4 variables: 365s ..$ chromosome: int [1:7072] 1 1 1 1 1 1 1 1 1 1 ... 365s ..$ x : num [1:7072] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 365s ..$ y : num [1:7072] 0.117 0.258 NA NA NA ... 365s ..$ index : int [1:7072] 1 2 3 4 5 6 7 8 9 10 ... 365s $ output :'data.frame': 1 obs. of 6 variables: 365s ..$ sampleName: chr NA 365s ..$ chromosome: int 1 365s ..$ start : num 1.42e+08 365s ..$ end : num 2.47e+08 365s ..$ nbrOfLoci : int 7072 365s ..$ mean : num 0.18 365s $ segRows:'data.frame': 1 obs. of 2 variables: 365s ..$ startRow: int 1 365s ..$ endRow : int 7072 365s $ params :List of 7 365s ..$ undo.splits : chr "sdundo" 365s ..$ undo.SD : num Inf 365s ..$ alpha : num 0.001 365s ..$ undo : num Inf 365s ..$ joinSegments : logi TRUE 365s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 365s .. ..$ chromosome: int 1 365s .. ..$ start : num 1.42e+08 365s .. ..$ end : num 2.47e+08 365s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 365s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.002 0 0.002 0 0 365s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 365s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 365s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 365s DH segmentation (locally-indexed) rows: 365s startRow endRow 365s 1 1 7072 365s int [1:7072] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 365s DH segmentation rows: 365s startRow endRow 365s 1 7587 14658 365s Segmenting DH signals...done 365s DH segmentation table: 365s dhStart dhEnd dhNbrOfLoci dhMean 365s 1 141510003 247137334 7072 0.1803011 365s startRow endRow 365s 1 7587 14658 365s Rows: 365s [1] 2 365s TCN segmentation rows: 365s startRow endRow 365s 2 7587 14658 365s TCN and DH segmentation rows: 365s startRow endRow 365s 2 7587 14658 365s startRow endRow 365s 1 7587 14658 365s startRow endRow 365s 1 1 7586 365s TCN segmentation (expanded) rows: 365s startRow endRow 365s 1 1 7586 365s 2 7587 14658 365s TCN and DH segmentation rows: 365s startRow endRow 365s 1 1 7586 365s 2 7587 14658 365s startRow endRow 365s 1 1 7586 365s 2 7587 14658 365s startRow endRow 365s 1 1 7586 365s 2 7587 14658 365s Total CN segmentation table (expanded): 365s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 2 1 141510003 247137334 7072 2.419824 2088 365s tcnNbrOfHets 365s 2 2088 365s (TCN,DH) segmentation for one total CN segment: 365s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 2 2 1 1 141510003 247137334 7072 2.419824 2088 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 2 2088 141510003 247137334 7072 0.1803011 365s Total CN segment #2 ([1.4151e+08,2.47137e+08]) of 2...done 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.385258 2108 365s 2 1 2 1 141510003 247137334 7072 2.419824 2088 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 365s 1 2108 554484 120992603 7586 0.5116120 365s 2 2088 141510003 247137334 7072 0.1803011 365s Calculating (C1,C2) per segment... 365s Calculating (C1,C2) per segment...done 365s Number of segments: 2 365s Segmenting paired tumor-normal signals using Paired PSCBS...done 365s Post-segmenting TCNs... 365s Number of segments: 2 365s Number of chromosomes: 1 365s [1] 1 365s Chromosome 1 ('chr01') of 1... 365s Rows: 365s [1] 1 2 365s Number of segments: 2 365s TCN segment #1 ('1') of 2... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #1 ('1') of 2...done 365s TCN segment #2 ('2') of 2... 365s Nothing todo. Only one DH segmentation. Skipping. 365s TCN segment #2 ('2') of 2...done 365s Chromosome 1 ('chr01') of 1...done 365s Update (C1,C2) per segment... 365s Update (C1,C2) per segment...done 365s Post-segmenting TCNs...done 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.385258 2108 365s 2 1 2 1 141510003 247137334 7072 2.419824 2088 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 554484 120992603 7586 0.5116120 0.3382717 1.046986 365s 2 2088 141510003 247137334 7072 0.1803011 0.9917635 1.428060 365s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.385258 2108 365s 2 1 2 1 141510003 247137334 7072 2.419824 2088 365s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 554484 120992603 7586 0.5116120 0.3382717 1.046986 365s 2 2088 141510003 247137334 7072 0.1803011 0.9917635 1.428060 365s > print(fit) 365s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 365s 1 1 1 1 554484 120992603 7586 1.385258 2108 365s 2 1 2 1 141510003 247137334 7072 2.419824 2088 365s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 365s 1 2108 7586 0.5116120 0.3382717 1.046986 365s 2 2088 7072 0.1803011 0.9917635 1.428060 365s > 365s > # Plot results 365s > dev.set(5L) 365s pdf 365s 2 365s > plotTracks(fit) 365s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 365s > 365s > # Sanity check 365s > stopifnot(nbrOfSegments(fit) == nrow(knownSegments)) 365s > 365s > fit4 <- fit 365s > 365s > 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > # Tiling multiple chromosomes 365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 365s > # Simulate multiple chromosomes 365s > fit1 <- fit 365s > fit2 <- renameChromosomes(fit, from=1, to=2) 365s > fitM <- c(fit1, fit2) 365s > 365s > # Tile chromosomes 365s > fitT <- tileChromosomes(fitM) 365s > fitTb <- tileChromosomes(fitT) 365s > stopifnot(identical(fitTb, fitT)) 365s > 365s > # Plotting multiple chromosomes 365s > plotTracks(fitT) 365s > 365s > proc.time() 365s user system elapsed 365s 11.587 0.128 11.717 365s Test segmentByPairedPSCBS passed 365s 0 365s Begin test weightedQuantile 368s + cat weightedQuantile.Rout 368s 368s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 368s Copyright (C) 2024 The R Foundation for Statistical Computing 368s Platform: arm-unknown-linux-gnueabihf (32-bit) 368s 368s R is free software and comes with ABSOLUTELY NO WARRANTY. 368s You are welcome to redistribute it under certain conditions. 368s Type 'license()' or 'licence()' for distribution details. 368s 368s R is a collaborative project with many contributors. 368s Type 'contributors()' for more information and 368s 'citation()' on how to cite R or R packages in publications. 368s 368s Type 'demo()' for some demos, 'help()' for on-line help, or 368s 'help.start()' for an HTML browser interface to help. 368s Type 'q()' to quit R. 368s 368s [Previously saved workspace restored] 368s 368s > library("PSCBS") 368s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 368s 368s Attaching package: 'PSCBS' 368s 368s The following objects are masked from 'package:base': 368s 368s append, load 368s 368s > library("stats") 368s > 368s > message("weightedQuantile() ...") 368s weightedQuantile() ... 368s > 368s > if (requireNamespace("Hmisc")) { 368s + message(" - assert identical results to Hmisc::wtd.quantile()") 368s + wtd.quantile <- Hmisc::wtd.quantile 368s + for (kk in 1:100) { 368s + n <- 5L + sample.int(995, size = 1L) 368s + x <- rnorm(n, mean = 0.0, sd = 1.0) 368s + w <- runif(n, min = 0.5, max = 2.0) ## Non-normalized weights 368s + probs <- c(0.0, 0.25, 0.50, 0.75, 1.0) 368s + q0 <- wtd.quantile(x, weights = w, probs = probs, normwt = TRUE) 368s + q <- weightedQuantile(x, w = w, probs = probs) 368s + if (!isTRUE(all.equal(q, q0))) { 368s + print(q0) 368s + print(q) 368s + stopifnot(all.equal(q, q0)) 368s + } 368s + } 368s + } 368s Loading required namespace: Hmisc 368s - assert identical results to Hmisc::wtd.quantile() 368s > 368s > message("weightedQuantile() ... DONE") 368s weightedQuantile() ... DONE 368s > 368s > proc.time() 368s user system elapsed 368s 1.921 0.083 2.006 368s Test weightedQuantile passed 368s 0 368s + [ 0 != 0 ] 368s + echo Test weightedQuantile passed 368s + echo 0 368s + rm -f /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/PairedPSCBS,boot.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/PairedPSCBS,boot.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/Rplots.pdf /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/findLargeGaps.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/findLargeGaps.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/randomSeed.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/randomSeed.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,calls.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,calls.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,median.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,median.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,prune.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,prune.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,report.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,report.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,shiftTCN.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,shiftTCN.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,weights.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS,weights.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByCBS.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByNonPairedPSCBS,medianDH.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByNonPairedPSCBS,medianDH.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,DH.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,DH.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,calls.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,calls.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,noNormalBAFs.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,noNormalBAFs.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,report.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,report.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,seqOfSegmentsByDP.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS,seqOfSegmentsByDP.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/segmentByPairedPSCBS.Rout /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/weightedQuantile.R /tmp/autopkgtest.0xi9ix/autopkgtest_tmp/weightedQuantile.Rout 368s autopkgtest [01:51:24]: test run-unit-test: -----------------------] 372s autopkgtest [01:51:28]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 372s run-unit-test PASS 375s autopkgtest [01:51:31]: @@@@@@@@@@@@@@@@@@@@ summary 375s run-unit-test PASS