0s autopkgtest [01:24:26]: starting date and time: 2024-03-28 01:24:26+0000 0s autopkgtest [01:24:26]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [01:24:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u_7pjsk5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-21.secgroup --name adt-noble-s390x-r-cran-pscbs-20240328-012426-juju-7f2275-prod-proposed-migration-environment-2-9ea40968-96ef-4947-8f9b-7a3063c31717 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 114s autopkgtest [01:26:20]: testbed dpkg architecture: s390x 114s autopkgtest [01:26:20]: testbed apt version: 2.7.12 114s autopkgtest [01:26:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 115s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 116s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 116s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B] 116s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [55.9 kB] 116s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3958 kB] 118s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [651 kB] 118s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 118s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 118s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 118s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4042 kB] 120s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 120s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.2 kB] 120s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 122s Fetched 9364 kB in 6s (1644 kB/s) 122s Reading package lists... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade... 124s The following packages will be upgraded: 124s binutils binutils-common binutils-s390x-linux-gnu dmsetup gcc-13-base 124s gcc-14-base initramfs-tools initramfs-tools-bin initramfs-tools-core jq 124s libbinutils libctf-nobfd0 libctf0 libdevmapper1.02.1 libexpat1 libftdi1-2 124s libgcc-s1 libjq1 libpam-modules libpam-modules-bin libpam-runtime libpam0g 124s libseccomp2 libsframe1 libstdc++6 libusb-1.0-0 124s 26 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Need to get 5444 kB of archives. 124s After this operation, 17.4 kB of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libpam0g s390x 1.5.3-5ubuntu3 [69.8 kB] 125s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules-bin s390x 1.5.3-5ubuntu3 [57.4 kB] 125s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules s390x 1.5.3-5ubuntu3 [289 kB] 125s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x gcc-14-base s390x 14-20240315-1ubuntu1 [47.0 kB] 125s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++6 s390x 14-20240315-1ubuntu1 [908 kB] 126s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-s1 s390x 14-20240315-1ubuntu1 [35.9 kB] 126s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] 126s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libseccomp2 s390x 2.5.5-1ubuntu2 [53.4 kB] 126s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libdevmapper1.02.1 s390x 2:1.02.185-3ubuntu2 [142 kB] 126s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x dmsetup s390x 2:1.02.185-3ubuntu2 [80.4 kB] 126s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libexpat1 s390x 2.6.1-2 [94.8 kB] 126s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libusb-1.0-0 s390x 2:1.0.27-1 [54.8 kB] 126s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libctf0 s390x 2.42-4ubuntu1 [98.4 kB] 126s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libctf-nobfd0 s390x 2.42-4ubuntu1 [100 kB] 126s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x binutils-s390x-linux-gnu s390x 2.42-4ubuntu1 [2270 kB] 127s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libbinutils s390x 2.42-4ubuntu1 [477 kB] 127s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x binutils s390x 2.42-4ubuntu1 [3056 B] 127s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x binutils-common s390x 2.42-4ubuntu1 [217 kB] 127s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libsframe1 s390x 2.42-4ubuntu1 [14.2 kB] 127s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-base s390x 13.2.0-21ubuntu1 [48.3 kB] 127s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x initramfs-tools all 0.142ubuntu23 [9058 B] 127s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x initramfs-tools-core all 0.142ubuntu23 [50.1 kB] 127s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x initramfs-tools-bin s390x 0.142ubuntu23 [20.5 kB] 127s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x jq s390x 1.7.1-3 [66.5 kB] 127s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libjq1 s390x 1.7.1-3 [168 kB] 127s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libftdi1-2 s390x 1.5-6build4 [29.3 kB] 128s Preconfiguring packages ... 128s Fetched 5444 kB in 3s (1611 kB/s) 128s (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 ... 52167 files and directories currently installed.) 128s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_s390x.deb ... 128s Unpacking libpam0g:s390x (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 128s Setting up libpam0g:s390x (1.5.3-5ubuntu3) ... 128s (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 ... 52167 files and directories currently installed.) 128s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_s390x.deb ... 128s Unpacking libpam-modules-bin (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 128s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ... 128s pam_namespace.service is a disabled or a static unit not running, not starting it. 128s (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 ... 52167 files and directories currently installed.) 128s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu3_s390x.deb ... 129s Unpacking libpam-modules:s390x (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 129s Setting up libpam-modules:s390x (1.5.3-5ubuntu3) ... 129s Installing new version of config file /etc/security/namespace.init ... 129s (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 ... 52165 files and directories currently installed.) 129s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_s390x.deb ... 129s Unpacking gcc-14-base:s390x (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 129s Setting up gcc-14-base:s390x (14-20240315-1ubuntu1) ... 129s (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 ... 52165 files and directories currently installed.) 129s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_s390x.deb ... 129s Unpacking libstdc++6:s390x (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 129s Setting up libstdc++6:s390x (14-20240315-1ubuntu1) ... 129s (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 ... 52165 files and directories currently installed.) 129s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_s390x.deb ... 129s Unpacking libgcc-s1:s390x (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 129s Setting up libgcc-s1:s390x (14-20240315-1ubuntu1) ... 129s (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 ... 52165 files and directories currently installed.) 129s Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu3_all.deb ... 129s Unpacking libpam-runtime (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 129s Setting up libpam-runtime (1.5.3-5ubuntu3) ... 129s (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 ... 52165 files and directories currently installed.) 129s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu2_s390x.deb ... 129s Unpacking libseccomp2:s390x (2.5.5-1ubuntu2) over (2.5.5-1ubuntu1) ... 129s Setting up libseccomp2:s390x (2.5.5-1ubuntu2) ... 129s (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 ... 52165 files and directories currently installed.) 129s Preparing to unpack .../00-libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_s390x.deb ... 129s Unpacking libdevmapper1.02.1:s390x (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 129s Preparing to unpack .../01-dmsetup_2%3a1.02.185-3ubuntu2_s390x.deb ... 129s Unpacking dmsetup (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 129s Preparing to unpack .../02-libexpat1_2.6.1-2_s390x.deb ... 129s Unpacking libexpat1:s390x (2.6.1-2) over (2.6.0-1) ... 129s Preparing to unpack .../03-libusb-1.0-0_2%3a1.0.27-1_s390x.deb ... 129s Unpacking libusb-1.0-0:s390x (2:1.0.27-1) over (2:1.0.26-1) ... 129s Preparing to unpack .../04-libctf0_2.42-4ubuntu1_s390x.deb ... 129s Unpacking libctf0:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 129s Preparing to unpack .../05-libctf-nobfd0_2.42-4ubuntu1_s390x.deb ... 129s Unpacking libctf-nobfd0:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 129s Preparing to unpack .../06-binutils-s390x-linux-gnu_2.42-4ubuntu1_s390x.deb ... 129s Unpacking binutils-s390x-linux-gnu (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 129s Preparing to unpack .../07-libbinutils_2.42-4ubuntu1_s390x.deb ... 129s Unpacking libbinutils:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 129s Preparing to unpack .../08-binutils_2.42-4ubuntu1_s390x.deb ... 129s Unpacking binutils (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 129s Preparing to unpack .../09-binutils-common_2.42-4ubuntu1_s390x.deb ... 129s Unpacking binutils-common:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 129s Preparing to unpack .../10-libsframe1_2.42-4ubuntu1_s390x.deb ... 129s Unpacking libsframe1:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 129s Preparing to unpack .../11-gcc-13-base_13.2.0-21ubuntu1_s390x.deb ... 129s Unpacking gcc-13-base:s390x (13.2.0-21ubuntu1) over (13.2.0-17ubuntu2) ... 129s Preparing to unpack .../12-initramfs-tools_0.142ubuntu23_all.deb ... 129s Unpacking initramfs-tools (0.142ubuntu23) over (0.142ubuntu20) ... 129s Preparing to unpack .../13-initramfs-tools-core_0.142ubuntu23_all.deb ... 129s Unpacking initramfs-tools-core (0.142ubuntu23) over (0.142ubuntu20) ... 130s Preparing to unpack .../14-initramfs-tools-bin_0.142ubuntu23_s390x.deb ... 130s Unpacking initramfs-tools-bin (0.142ubuntu23) over (0.142ubuntu20) ... 130s Preparing to unpack .../15-jq_1.7.1-3_s390x.deb ... 130s Unpacking jq (1.7.1-3) over (1.7.1-2) ... 130s Preparing to unpack .../16-libjq1_1.7.1-3_s390x.deb ... 130s Unpacking libjq1:s390x (1.7.1-3) over (1.7.1-2) ... 130s Preparing to unpack .../17-libftdi1-2_1.5-6build4_s390x.deb ... 130s Unpacking libftdi1-2:s390x (1.5-6build4) over (1.5-6build3) ... 130s Setting up libexpat1:s390x (2.6.1-2) ... 130s Setting up libjq1:s390x (1.7.1-3) ... 130s Setting up binutils-common:s390x (2.42-4ubuntu1) ... 130s Setting up libctf-nobfd0:s390x (2.42-4ubuntu1) ... 130s Setting up libsframe1:s390x (2.42-4ubuntu1) ... 130s Setting up gcc-13-base:s390x (13.2.0-21ubuntu1) ... 130s Setting up libdevmapper1.02.1:s390x (2:1.02.185-3ubuntu2) ... 130s Setting up dmsetup (2:1.02.185-3ubuntu2) ... 130s Setting up jq (1.7.1-3) ... 130s Setting up libusb-1.0-0:s390x (2:1.0.27-1) ... 130s Setting up libbinutils:s390x (2.42-4ubuntu1) ... 130s Setting up initramfs-tools-bin (0.142ubuntu23) ... 130s Setting up libctf0:s390x (2.42-4ubuntu1) ... 130s Setting up binutils-s390x-linux-gnu (2.42-4ubuntu1) ... 130s Setting up binutils (2.42-4ubuntu1) ... 130s Setting up libftdi1-2:s390x (1.5-6build4) ... 130s Setting up initramfs-tools-core (0.142ubuntu23) ... 130s Setting up initramfs-tools (0.142ubuntu23) ... 130s update-initramfs: deferring update (trigger activated) 130s Processing triggers for man-db (2.12.0-3) ... 130s Processing triggers for libc-bin (2.39-0ubuntu6) ... 130s Processing triggers for initramfs-tools (0.142ubuntu23) ... 130s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 130s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 134s Using config file '/etc/zipl.conf' 134s Building bootmap in '/boot' 134s Adding IPL section 'ubuntu' (default) 134s Preparing boot device for LD-IPL: vda (0000). 134s Done. 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 218 not upgraded. 135s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 135s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 135s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 135s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 136s Reading package lists... 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Calculating upgrade... 137s The following packages were automatically installed and are no longer required: 137s libaio1 libnetplan0 python3-distutils python3-lib2to3 137s Use 'sudo apt autoremove' to remove them. 137s The following packages will be REMOVED: 137s libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1 137s libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11 137s libhogweed6 libmagic1 libnettle8 libnpth0 libnvme1 libparted2 libperl5.38 137s libpng16-16 libpsl5 libreadline8 libreiserfscore0 libssl3 libtirpc3 liburcu8 137s libuv1 137s The following NEW packages will be installed: 137s bpfcc-tools bpftrace fontconfig-config fonts-dejavu-core fonts-dejavu-mono 137s hwdata ieee-data libaio1t64 libapt-pkg6.0t64 libarchive13t64 libatm1t64 137s libbpfcc libc-dev-bin libc-devtools libc6-dev libclang-cpp18 libclang1-18 137s libcrypt-dev libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libdeflate0 137s libdw1t64 libelf1t64 libext2fs2t64 libfontconfig1 libfreetype6 libgd3 137s libgdbm-compat4t64 libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libgpgme11t64 137s libhogweed6t64 libjbig0 libjpeg-turbo8 libjpeg8 libllvm18 libmagic1t64 137s libnetplan1 libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64 137s libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64 libreiserfscore0t64 137s libsharpyuv0 libssl3t64 libtiff6 libtirpc3t64 liburcu8t64 libuv1t64 libwebp7 137s libxpm4 linux-headers-6.8.0-20 linux-headers-6.8.0-20-generic 137s linux-image-6.8.0-20-generic linux-libc-dev linux-modules-6.8.0-20-generic 137s linux-modules-extra-6.8.0-20-generic linux-tools-6.8.0-20 137s linux-tools-6.8.0-20-generic linux-tools-common manpages manpages-dev 137s python3-bpfcc python3-netaddr rpcsvc-proto ubuntu-kernel-accessories 137s xdg-user-dirs 137s The following packages have been kept back: 137s s390-tools 137s The following packages will be upgraded: 137s apparmor apt apt-utils base-files bash bind9-dnsutils bind9-host bind9-libs 137s bolt bsdextrautils bsdutils btrfs-progs coreutils cryptsetup-bin curl dbus 137s dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common 137s dbus-user-session dhcpcd-base dirmngr dpkg dpkg-dev e2fsprogs e2fsprogs-l10n 137s eject fdisk file ftp fwupd gawk gir1.2-girepository-2.0 gir1.2-glib-2.0 137s gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv 137s groff-base ibverbs-providers inetutils-telnet info install-info iproute2 137s keyboxd kmod kpartx krb5-locales libapparmor1 libaudit-common libaudit1 137s libblkid1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 137s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 137s libblockdev-utils3 libblockdev3 libbpf1 libbrotli1 libcap-ng0 libcom-err2 137s libcryptsetup12 libdbus-1-3 libdebconfclient0 libdpkg-perl 137s libevent-core-2.1-7 libfdisk1 libfido2-1 libfwupd2 libgirepository-1.0-1 137s libglib2.0-data libgssapi-krb5-2 libgudev-1.0-0 libgusb2 libibverbs1 137s libjcat1 libjson-glib-1.0-0 libjson-glib-1.0-common libk5crypto3 libkmod2 137s libkrb5-3 libkrb5support0 libldap-common libldap2 liblocale-gettext-perl 137s liblzma5 libmagic-mgc libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 137s libnghttp2-14 libnsl2 libnss-systemd libpam-systemd libplymouth5 137s libpolkit-agent-1-0 libpolkit-gobject-1-0 libproc2-0 libprotobuf-c1 137s libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib 137s libpython3.12-minimal libpython3.12-stdlib libqmi-glib5 libqmi-proxy 137s libqrtr-glib0 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db 137s libselinux1 libsemanage-common libsemanage2 libslang2 libsmartcols1 137s libsqlite3-0 libss2 libssh-4 libsystemd-shared libsystemd0 137s libtext-charwidth-perl libtext-iconv-perl libtirpc-common libudev1 137s libudisks2-0 libuuid1 libvolume-key1 libxml2 libxmlb2 libxmuu1 linux-generic 137s linux-headers-generic linux-headers-virtual linux-image-generic 137s linux-image-virtual linux-virtual logsave lshw lsof man-db motd-news-config 137s mount mtr-tiny multipath-tools netplan-generator netplan.io openssh-client 137s openssh-server openssh-sftp-server openssl parted perl perl-base 137s perl-modules-5.38 pinentry-curses plymouth plymouth-theme-ubuntu-text procps 137s python-apt-common python3 python3-apt python3-cryptography python3-dbus 137s python3-distutils python3-gdbm python3-gi python3-lib2to3 python3-minimal 137s python3-netplan python3-pkg-resources python3-pyrsistent python3-setuptools 137s python3-typing-extensions python3-yaml python3.11 python3.11-minimal 137s python3.12 python3.12-minimal readline-common rsync rsyslog s390-tools-data 137s shared-mime-info sudo systemd systemd-dev systemd-resolved systemd-sysv 137s systemd-timesyncd tcpdump telnet tnftp ubuntu-pro-client 137s ubuntu-pro-client-l10n udev udisks2 usb.ids util-linux uuid-runtime 137s vim-common vim-tiny wget xxd xz-utils zlib1g 137s 217 upgraded, 73 newly installed, 28 to remove and 1 not upgraded. 137s Need to get 223 MB of archives. 137s After this operation, 524 MB of additional disk space will be used. 137s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x motd-news-config all 13ubuntu8 [5098 B] 137s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x base-files s390x 13ubuntu8 [74.2 kB] 138s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bash s390x 5.2.21-2ubuntu3 [845 kB] 138s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdutils s390x 1:2.39.3-9ubuntu2 [96.1 kB] 139s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbrotli1 s390x 1.1.0-2build1 [375 kB] 139s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgssapi-krb5-2 s390x 1.20.1-6ubuntu1 [149 kB] 139s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5-3 s390x 1.20.1-6ubuntu1 [360 kB] 139s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5support0 s390x 1.20.1-6ubuntu1 [34.6 kB] 139s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libk5crypto3 s390x 1.20.1-6ubuntu1 [90.3 kB] 139s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcom-err2 s390x 1.47.0-2.4~exp1ubuntu2 [22.9 kB] 139s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g s390x 1:1.3.dfsg-3.1ubuntu1 [75.7 kB] 139s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build6 [58.4 kB] 139s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x udisks2 s390x 2.10.1-6 [298 kB] 139s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libudisks2-0 s390x 2.10.1-6 [179 kB] 139s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblkid1 s390x 2.39.3-9ubuntu2 [128 kB] 139s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblzma5 s390x 5.6.0-0.2 [137 kB] 140s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main s390x kmod s390x 31+20240202-2ubuntu4 [107 kB] 140s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkmod2 s390x 31+20240202-2ubuntu4 [56.3 kB] 140s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-dev all 255.4-1ubuntu5 [103 kB] 140s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-timesyncd s390x 255.4-1ubuntu5 [35.3 kB] 140s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB] 140s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-sysv s390x 255.4-1ubuntu5 [11.9 kB] 140s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-systemd s390x 255.4-1ubuntu5 [242 kB] 140s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-user-session s390x 1.14.10-4ubuntu2 [9960 B] 140s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapparmor1 s390x 4.0.0-beta3-0ubuntu2 [50.8 kB] 140s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libaudit-common all 1:3.1.2-2.1 [5674 B] 140s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcap-ng0 s390x 0.8.4-2build1 [15.7 kB] 140s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libaudit1 s390x 1:3.1.2-2.1 [48.9 kB] 140s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libselinux1 s390x 3.5-2ubuntu1 [84.7 kB] 140s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl4t64 s390x 8.5.0-2ubuntu8 [363 kB] 140s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main s390x curl s390x 8.5.0-2ubuntu8 [227 kB] 140s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpsl5t64 s390x 0.21.2-1.1 [57.6 kB] 140s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main s390x wget s390x 1.21.4-1ubuntu2 [351 kB] 140s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main s390x tnftp s390x 20230507-2build1 [107 kB] 140s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main s390x tcpdump s390x 4.99.4-3ubuntu2 [490 kB] 141s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd-shared s390x 255.4-1ubuntu5 [2131 kB] 141s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-resolved s390x 255.4-1ubuntu5 [304 kB] 141s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main s390x sudo s390x 1.9.15p5-3ubuntu3 [968 kB] 141s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main s390x rsync s390x 3.2.7-1build1 [446 kB] 142s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-cryptography s390x 41.0.7-4build2 [918 kB] 142s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 142s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssh-sftp-server s390x 1:9.6p1-3ubuntu11 [39.0 kB] 142s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssh-client s390x 1:9.6p1-3ubuntu11 [935 kB] 142s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssh-server s390x 1:9.6p1-3ubuntu11 [529 kB] 142s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssh-4 s390x 0.10.6-2build1 [189 kB] 142s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsasl2-modules s390x 2.1.28+dfsg1-5ubuntu1 [76.6 kB] 142s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.12 s390x 3.12.2-4build3 [645 kB] 143s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.12-minimal s390x 3.12.2-4build3 [2419 kB] 143s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.12-minimal s390x 3.12.2-4build3 [829 kB] 143s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libparted2t64 s390x 3.6-3.1build2 [172 kB] 143s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main s390x parted s390x 3.6-3.1build2 [44.6 kB] 143s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.11 s390x 3.11.8-1build4 [589 kB] 143s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.11-minimal s390x 3.11.8-1build4 [2280 kB] 144s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.11-minimal s390x 3.11.8-1build4 [838 kB] 144s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.11-stdlib s390x 3.11.8-1build4 [1944 kB] 144s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x shared-mime-info s390x 2.4-1build1 [474 kB] 145s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gir1.2-girepository-2.0 s390x 1.79.1-1ubuntu6 [24.5 kB] 145s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gir1.2-glib-2.0 s390x 2.79.3-3ubuntu5 [180 kB] 145s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgirepository-1.0-1 s390x 1.79.1-1ubuntu6 [84.0 kB] 145s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-gi s390x 3.47.0-3build1 [236 kB] 145s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-dbus s390x 1.3.2-5build2 [100 kB] 145s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnetplan1 s390x 1.0-1 [123 kB] 145s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-netplan s390x 1.0-1 [23.0 kB] 145s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main s390x netplan-generator s390x 1.0-1 [59.1 kB] 145s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main s390x netplan.io s390x 1.0-1 [65.4 kB] 145s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxmlb2 s390x 0.3.15-1build1 [70.6 kB] 145s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgpgme11t64 s390x 1.18.0-4.1ubuntu3 [150 kB] 145s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libvolume-key1 s390x 0.3.12-7build1 [40.8 kB] 145s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libqrtr-glib0 s390x 1.2.2-1ubuntu3 [17.5 kB] 145s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libqmi-glib5 s390x 1.35.2-0ubuntu1 [918 kB] 145s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libqmi-proxy s390x 1.35.2-0ubuntu1 [6122 B] 145s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpolkit-agent-1-0 s390x 124-1ubuntu1 [17.8 kB] 145s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpolkit-gobject-1-0 s390x 124-1ubuntu1 [48.3 kB] 145s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmm-glib0 s390x 1.23.4-0ubuntu1 [251 kB] 145s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmbim-glib4 s390x 1.31.2-0ubuntu2 [238 kB] 145s Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmbim-proxy s390x 1.31.2-0ubuntu2 [6154 B] 145s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjson-glib-1.0-common all 1.8.0-2build1 [4210 B] 145s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjson-glib-1.0-0 s390x 1.8.0-2build1 [68.4 kB] 145s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgusb2 s390x 0.4.8-1build1 [39.0 kB] 145s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgudev-1.0-0 s390x 1:238-3ubuntu2 [15.7 kB] 145s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libarchive13t64 s390x 3.7.2-1.1ubuntu2 [419 kB] 146s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main s390x fwupd s390x 1.9.15-2 [4435 kB] 147s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl3t64-gnutls s390x 8.5.0-2ubuntu8 [356 kB] 147s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfwupd2 s390x 1.9.15-2 [136 kB] 147s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev3 s390x 3.1.0-1build1 [52.3 kB] 147s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-utils3 s390x 3.1.0-1build1 [19.2 kB] 147s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-swap3 s390x 3.1.0-1build1 [7778 B] 147s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-part3 s390x 3.1.0-1build1 [15.4 kB] 147s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnvme1t64 s390x 1.8-3 [78.7 kB] 147s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-nvme3 s390x 3.1.0-1build1 [18.3 kB] 147s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-mdraid3 s390x 3.1.0-1build1 [13.2 kB] 147s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-loop3 s390x 3.1.0-1build1 [7138 B] 147s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main s390x logsave s390x 1.47.0-2.4~exp1ubuntu2 [22.5 kB] 147s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main s390x e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B] 147s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libext2fs2t64 s390x 1.47.0-2.4~exp1ubuntu2 [235 kB] 147s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main s390x e2fsprogs s390x 1.47.0-2.4~exp1ubuntu2 [615 kB] 147s Get:97 http://ftpmaster.internal/ubuntu noble/main s390x libreiserfscore0t64 s390x 1:3.6.27-7.1 [85.5 kB] 147s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main s390x btrfs-progs s390x 6.6.3-1.1build1 [959 kB] 148s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-fs3 s390x 3.1.0-1build1 [36.5 kB] 148s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-crypto3 s390x 3.1.0-1build1 [21.6 kB] 148s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bolt s390x 0.9.6-2build1 [142 kB] 148s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-0t64 s390x 2.79.3-3ubuntu5 [1566 kB] 149s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjcat1 s390x 0.2.0-2build2 [34.4 kB] 149s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libldap2 s390x 2.6.7+dfsg-1~exp1ubuntu6 [202 kB] 149s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ubuntu-pro-client-l10n s390x 31.2.2 [19.4 kB] 149s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ubuntu-pro-client s390x 31.2.2 [214 kB] 149s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gnupg-utils s390x 2.4.4-2ubuntu15 [116 kB] 149s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main s390x keyboxd s390x 2.4.4-2ubuntu15 [83.1 kB] 149s Get:109 http://ftpmaster.internal/ubuntu noble/main s390x libnpth0t64 s390x 1.6-3.1 [8148 B] 149s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgv s390x 2.4.4-2ubuntu15 [165 kB] 149s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg-wks-client s390x 2.4.4-2ubuntu15 [76.8 kB] 149s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg-agent s390x 2.4.4-2ubuntu15 [240 kB] 149s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg s390x 2.4.4-2ubuntu15 [589 kB] 149s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dirmngr s390x 2.4.4-2ubuntu15 [340 kB] 149s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gnupg all 2.4.4-2ubuntu15 [359 kB] 149s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-apt s390x 2.7.7 [171 kB] 149s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt-utils s390x 2.7.14 [214 kB] 149s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapt-pkg6.0t64 s390x 2.7.14 [1014 kB] 149s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnettle8t64 s390x 3.9.1-2.2 [210 kB] 149s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libhogweed6t64 s390x 3.9.1-2.2 [204 kB] 149s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgnutls30t64 s390x 3.8.3-1.1ubuntu2 [1044 kB] 150s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt s390x 2.7.14 [1390 kB] 150s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgconf s390x 2.4.4-2ubuntu15 [111 kB] 150s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgsm s390x 2.4.4-2ubuntu15 [244 kB] 150s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libreadline8t64 s390x 8.2-4 [170 kB] 150s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gawk s390x 1:5.2.1-2build2 [496 kB] 150s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main s390x fdisk s390x 2.39.3-9ubuntu2 [124 kB] 150s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.12-stdlib s390x 3.12.2-4build3 [2046 kB] 150s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-base s390x 5.38.2-3.2 [1961 kB] 150s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 151s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-gdbm s390x 3.12.2-3ubuntu1.1 [19.0 kB] 151s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main s390x man-db s390x 2.12.0-3build4 [1246 kB] 151s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm6t64 s390x 1.23-5.1 [36.4 kB] 151s Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm-compat4t64 s390x 1.23-5.1 [6880 B] 151s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libperl5.38t64 s390x 5.38.2-3.2 [5007 kB] 151s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl s390x 5.38.2-3.2 [231 kB] 151s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-6 [763 kB] 151s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsasl2-modules-db s390x 2.1.28+dfsg1-5ubuntu1 [21.1 kB] 151s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsasl2-2 s390x 2.1.28+dfsg1-5ubuntu1 [57.8 kB] 151s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfido2-1 s390x 1.14.0-1build1 [81.0 kB] 151s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu2 [264 kB] 151s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dhcpcd-base s390x 1:10.0.6-1ubuntu2 [217 kB] 151s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libuv1t64 s390x 1.48.0-1.1 [101 kB] 151s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bind9-host s390x 1:9.18.24-0ubuntu3 [50.5 kB] 151s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bind9-dnsutils s390x 1:9.18.24-0ubuntu3 [162 kB] 151s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bind9-libs s390x 1:9.18.24-0ubuntu3 [1243 kB] 151s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 151s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnss-systemd s390x 255.4-1ubuntu5 [166 kB] 152s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libudev1 s390x 255.4-1ubuntu5 [178 kB] 152s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd s390x 255.4-1ubuntu5 [3533 kB] 152s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main s390x udev s390x 255.4-1ubuntu5 [1887 kB] 152s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd0 s390x 255.4-1ubuntu5 [443 kB] 152s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB] 152s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-bin s390x 1.14.10-4ubuntu2 [41.4 kB] 152s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus s390x 1.14.10-4ubuntu2 [24.3 kB] 152s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-daemon s390x 1.14.10-4ubuntu2 [118 kB] 152s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdbus-1-3 s390x 1.14.10-4ubuntu2 [213 kB] 152s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmount1 s390x 2.39.3-9ubuntu2 [138 kB] 152s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libuuid1 s390x 2.39.3-9ubuntu2 [35.6 kB] 152s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfdisk1 s390x 2.39.3-9ubuntu2 [151 kB] 152s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main s390x mount s390x 2.39.3-9ubuntu2 [119 kB] 152s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu1 [747 kB] 152s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg s390x 1.22.6ubuntu5 [1278 kB] 152s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-minimal s390x 3.12.2-0ubuntu1 [27.1 kB] 152s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3 s390x 3.12.2-0ubuntu1 [24.1 kB] 152s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3-stdlib s390x 3.12.2-0ubuntu1 [9804 B] 152s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsmartcols1 s390x 2.39.3-9ubuntu2 [67.9 kB] 152s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdextrautils s390x 2.39.3-9ubuntu2 [76.3 kB] 152s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main s390x groff-base s390x 1.23.0-3build1 [1049 kB] 152s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main s390x pinentry-curses s390x 1.2.1-3ubuntu4 [37.6 kB] 152s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main s390x readline-common all 8.2-4 [56.4 kB] 152s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxml2 s390x 2.9.14+dfsg-1.3ubuntu2 [818 kB] 152s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbpf1 s390x 1:1.3.0-2build1 [176 kB] 152s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libelf1t64 s390x 0.190-1.1build2 [69.7 kB] 152s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc-common all 1.3.4+ds-1.1 [8018 B] 152s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main s390x lsof s390x 4.95.0-1build2 [248 kB] 152s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnsl2 s390x 1.3.0-3build2 [44.1 kB] 152s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc3t64 s390x 1.3.4+ds-1.1 [85.8 kB] 153s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main s390x iproute2 s390x 6.1.0-1ubuntu5 [1156 kB] 153s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-yaml s390x 6.0.1-2build1 [121 kB] 153s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libprotobuf-c1 s390x 1.4.1-1ubuntu3 [23.4 kB] 153s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnghttp2-14 s390x 1.59.0-1build1 [77.8 kB] 153s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu2 [60.1 kB] 153s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main s390x procps s390x 2:4.0.4-4ubuntu2 [724 kB] 153s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main s390x coreutils s390x 9.4-3ubuntu3 [1482 kB] 153s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main s390x util-linux s390x 2.39.3-9ubuntu2 [1143 kB] 153s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main s390x file s390x 1:5.45-3 [22.2 kB] 153s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmagic-mgc s390x 1:5.45-3 [305 kB] 153s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmagic1t64 s390x 1:5.45-3 [93.1 kB] 153s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libplymouth5 s390x 24.004.60-1ubuntu6 [151 kB] 153s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpng16-16t64 s390x 1.6.43-3 [200 kB] 153s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main s390x multipath-tools s390x 0.9.4-5ubuntu6 [318 kB] 153s Get:193 http://ftpmaster.internal/ubuntu noble/main s390x liburcu8t64 s390x 0.14.0-3.1 [67.3 kB] 153s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblocale-gettext-perl s390x 1.07-6ubuntu4 [15.8 kB] 153s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main s390x uuid-runtime s390x 2.39.3-9ubuntu2 [33.4 kB] 153s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdebconfclient0 s390x 0.271ubuntu2 [11.4 kB] 153s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsemanage-common all 3.5-1build4 [10.1 kB] 153s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsemanage2 s390x 3.5-1build4 [96.7 kB] 153s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main s390x install-info s390x 7.1-3build1 [64.5 kB] 153s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libss2 s390x 1.47.0-2.4~exp1ubuntu2 [17.2 kB] 153s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main s390x eject s390x 2.39.3-9ubuntu2 [26.2 kB] 153s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main s390x krb5-locales all 1.20.1-6ubuntu1 [13.8 kB] 153s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 153s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libslang2 s390x 2.3.3-3build1 [501 kB] 154s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtext-charwidth-perl s390x 0.04-11build2 [9484 B] 154s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtext-iconv-perl s390x 1.7-8build2 [13.8 kB] 154s Get:207 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python-apt-common all 2.7.7 [19.8 kB] 154s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-setuptools all 68.1.2-2ubuntu1 [396 kB] 154s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB] 154s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main s390x rsyslog s390x 8.2312.0-3ubuntu7 [536 kB] 155s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main s390x vim-tiny s390x 2:9.1.0016-1ubuntu6 [879 kB] 155s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main s390x vim-common all 2:9.1.0016-1ubuntu6 [385 kB] 155s Get:213 http://ftpmaster.internal/ubuntu noble/main s390x xdg-user-dirs s390x 0.18-1 [18.5 kB] 155s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main s390x xxd s390x 2:9.1.0016-1ubuntu6 [63.5 kB] 155s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apparmor s390x 4.0.0-beta3-0ubuntu2 [710 kB] 156s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ftp all 20230507-2build1 [4724 B] 156s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main s390x inetutils-telnet s390x 2:2.5-3ubuntu3 [105 kB] 156s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main s390x info s390x 7.1-3build1 [152 kB] 156s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxmuu1 s390x 2:1.1.3-3build1 [8860 B] 156s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main s390x lshw s390x 02.19.git.2021.06.19.996aaad9c7-2build2 [346 kB] 156s Get:221 http://ftpmaster.internal/ubuntu noble/main s390x manpages all 6.05.01-1 [1340 kB] 156s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main s390x mtr-tiny s390x 0.95-1.1build1 [57.0 kB] 156s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main s390x plymouth-theme-ubuntu-text s390x 24.004.60-1ubuntu6 [10.2 kB] 156s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main s390x plymouth s390x 24.004.60-1ubuntu6 [147 kB] 156s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main s390x telnet all 0.17+2.5-3ubuntu3 [3682 B] 156s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main s390x usb.ids all 2024.03.18-1 [223 kB] 156s Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main s390x xz-utils s390x 5.6.0-0.2 [274 kB] 156s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libllvm18 s390x 1:18.1.2-1ubuntu2 [33.4 MB] 160s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libclang-cpp18 s390x 1:18.1.2-1ubuntu2 [16.1 MB] 162s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libbpfcc s390x 0.29.1+ds-1ubuntu4 [697 kB] 162s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x python3-bpfcc all 0.29.1+ds-1ubuntu4 [40.2 kB] 162s Get:232 http://ftpmaster.internal/ubuntu noble/main s390x ieee-data all 20220827.1 [2113 kB] 162s Get:233 http://ftpmaster.internal/ubuntu noble/main s390x python3-netaddr all 0.8.0-2ubuntu1 [319 kB] 162s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x bpfcc-tools all 0.29.1+ds-1ubuntu4 [687 kB] 162s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libclang1-18 s390x 1:18.1.2-1ubuntu2 [9349 kB] 163s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdw1t64 s390x 0.190-1.1build2 [286 kB] 163s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x bpftrace s390x 0.20.2-1ubuntu1 [1139 kB] 163s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main s390x cryptsetup-bin s390x 2:2.7.0-1ubuntu2 [211 kB] 163s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg-dev all 1.22.6ubuntu5 [1074 kB] 163s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdpkg-perl all 1.22.6ubuntu5 [269 kB] 163s Get:241 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 163s Get:242 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 163s Get:243 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu1 [37.4 kB] 163s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB] 163s Get:245 http://ftpmaster.internal/ubuntu noble/main s390x hwdata all 0.379-1 [29.1 kB] 163s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libibverbs1 s390x 50.0-2build1 [70.0 kB] 163s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ibverbs-providers s390x 50.0-2build1 [408 kB] 163s Get:248 http://ftpmaster.internal/ubuntu noble/main s390x libaio1t64 s390x 0.3.113-6 [7290 B] 163s Get:249 http://ftpmaster.internal/ubuntu noble/main s390x libatm1t64 s390x 1:2.5.1-5.1 [24.5 kB] 163s Get:250 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.39-0ubuntu6 [20.2 kB] 163s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfreetype6 s390x 2.13.2+dfsg-1build2 [437 kB] 163s Get:252 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu1 [150 kB] 163s Get:253 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 163s Get:254 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 163s Get:255 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 163s Get:256 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 163s Get:257 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsharpyuv0 s390x 1.3.2-0.4build2 [14.9 kB] 163s Get:258 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libwebp7 s390x 1.3.2-0.4build2 [207 kB] 163s Get:259 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu1 [218 kB] 163s Get:260 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxpm4 s390x 1:3.5.17-1build1 [41.4 kB] 163s Get:261 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgd3 s390x 2.3.3-9ubuntu3 [141 kB] 163s Get:262 http://ftpmaster.internal/ubuntu noble/main s390x libc-devtools s390x 2.39-0ubuntu6 [30.6 kB] 163s Get:263 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-libc-dev s390x 6.8.0-20.20 [1592 kB] 164s Get:264 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4 [135 kB] 164s Get:265 http://ftpmaster.internal/ubuntu noble/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu6 [64.7 kB] 164s Get:266 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.39-0ubuntu6 [1629 kB] 164s Get:267 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libevent-core-2.1-7 s390x 2.1.12-stable-9build1 [94.3 kB] 164s Get:268 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB] 164s Get:269 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-modules-6.8.0-20-generic s390x 6.8.0-20.20 [21.0 MB] 166s Get:270 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-image-6.8.0-20-generic s390x 6.8.0-20.20 [9872 kB] 166s Get:271 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-modules-extra-6.8.0-20-generic s390x 6.8.0-20.20 [11.7 MB] 167s Get:272 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-generic s390x 6.8.0-20.20+1 [1734 B] 167s Get:273 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-image-generic s390x 6.8.0-20.20+1 [9688 B] 167s Get:274 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-virtual s390x 6.8.0-20.20+1 [1682 B] 167s Get:275 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-image-virtual s390x 6.8.0-20.20+1 [9700 B] 167s Get:276 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-headers-virtual s390x 6.8.0-20.20+1 [1642 B] 167s Get:277 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-headers-6.8.0-20 all 6.8.0-20.20 [13.6 MB] 168s Get:278 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-headers-6.8.0-20-generic s390x 6.8.0-20.20 [2579 kB] 169s Get:279 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-headers-generic s390x 6.8.0-20.20+1 [9608 B] 169s Get:280 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-tools-common all 6.8.0-20.20 [437 kB] 169s Get:281 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-tools-6.8.0-20 s390x 6.8.0-20.20 [2674 kB] 169s Get:282 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-tools-6.8.0-20-generic s390x 6.8.0-20.20 [1724 B] 169s Get:283 http://ftpmaster.internal/ubuntu noble/main s390x manpages-dev all 6.05.01-1 [2018 kB] 169s Get:284 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-distutils all 3.12.2-3ubuntu1.1 [133 kB] 169s Get:285 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-lib2to3 all 3.12.2-3ubuntu1.1 [79.1 kB] 169s Get:286 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-pyrsistent s390x 0.20.0-1build1 [55.8 kB] 169s Get:287 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-typing-extensions all 4.10.0-1 [60.7 kB] 169s Get:288 http://ftpmaster.internal/ubuntu noble-proposed/main s390x s390-tools-data all 2.31.0-0ubuntu3 [17.8 kB] 169s Get:289 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-kernel-accessories s390x 1.536build1 [10.5 kB] 169s Get:290 http://ftpmaster.internal/ubuntu noble-proposed/main s390x kpartx s390x 0.9.4-5ubuntu6 [32.8 kB] 170s Preconfiguring packages ... 170s Fetched 223 MB in 32s (6934 kB/s) 170s (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 ... 52166 files and directories currently installed.) 170s Preparing to unpack .../motd-news-config_13ubuntu8_all.deb ... 170s Unpacking motd-news-config (13ubuntu8) over (13ubuntu7) ... 170s Preparing to unpack .../base-files_13ubuntu8_s390x.deb ... 170s Unpacking base-files (13ubuntu8) over (13ubuntu7) ... 170s Setting up base-files (13ubuntu8) ... 171s motd-news.service is a disabled or a static unit not running, not starting it. 171s (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 ... 52166 files and directories currently installed.) 171s Preparing to unpack .../bash_5.2.21-2ubuntu3_s390x.deb ... 171s Unpacking bash (5.2.21-2ubuntu3) over (5.2.21-2ubuntu2) ... 171s Setting up bash (5.2.21-2ubuntu3) ... 171s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 171s (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 ... 52166 files and directories currently installed.) 171s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_s390x.deb ... 171s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ... 171s Setting up bsdutils (1:2.39.3-9ubuntu2) ... 171s (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 ... 52166 files and directories currently installed.) 171s Preparing to unpack .../0-libbrotli1_1.1.0-2build1_s390x.deb ... 171s Unpacking libbrotli1:s390x (1.1.0-2build1) over (1.1.0-2) ... 171s Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-6ubuntu1_s390x.deb ... 171s Unpacking libgssapi-krb5-2:s390x (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 171s Preparing to unpack .../2-libkrb5-3_1.20.1-6ubuntu1_s390x.deb ... 171s Unpacking libkrb5-3:s390x (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 171s Preparing to unpack .../3-libkrb5support0_1.20.1-6ubuntu1_s390x.deb ... 171s Unpacking libkrb5support0:s390x (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 171s Preparing to unpack .../4-libk5crypto3_1.20.1-6ubuntu1_s390x.deb ... 171s Unpacking libk5crypto3:s390x (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 171s Preparing to unpack .../5-libcom-err2_1.47.0-2.4~exp1ubuntu2_s390x.deb ... 171s Unpacking libcom-err2:s390x (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 171s Preparing to unpack .../6-zlib1g_1%3a1.3.dfsg-3.1ubuntu1_s390x.deb ... 171s Unpacking zlib1g:s390x (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ... 171s Setting up zlib1g:s390x (1:1.3.dfsg-3.1ubuntu1) ... 171s (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 ... 52166 files and directories currently installed.) 171s Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-2build6_s390x.deb ... 171s Unpacking librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ... 171s Preparing to unpack .../udisks2_2.10.1-6_s390x.deb ... 171s Unpacking udisks2 (2.10.1-6) over (2.10.1-1ubuntu2) ... 171s Preparing to unpack .../libudisks2-0_2.10.1-6_s390x.deb ... 171s Unpacking libudisks2-0:s390x (2.10.1-6) over (2.10.1-1ubuntu2) ... 171s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_s390x.deb ... 171s Unpacking libblkid1:s390x (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 171s Setting up libblkid1:s390x (2.39.3-9ubuntu2) ... 172s (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 ... 52166 files and directories currently installed.) 172s Preparing to unpack .../liblzma5_5.6.0-0.2_s390x.deb ... 172s Unpacking liblzma5:s390x (5.6.0-0.2) over (5.4.5-0.3) ... 172s Setting up liblzma5:s390x (5.6.0-0.2) ... 172s (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 ... 52166 files and directories currently installed.) 172s Preparing to unpack .../0-kmod_31+20240202-2ubuntu4_s390x.deb ... 172s Unpacking kmod (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 172s Preparing to unpack .../1-libkmod2_31+20240202-2ubuntu4_s390x.deb ... 172s Unpacking libkmod2:s390x (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 172s Preparing to unpack .../2-systemd-dev_255.4-1ubuntu5_all.deb ... 172s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 172s Preparing to unpack .../3-systemd-timesyncd_255.4-1ubuntu5_s390x.deb ... 172s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 172s Preparing to unpack .../4-dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ... 172s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 172s Preparing to unpack .../5-systemd-sysv_255.4-1ubuntu5_s390x.deb ... 172s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 172s Preparing to unpack .../6-libpam-systemd_255.4-1ubuntu5_s390x.deb ... 172s Unpacking libpam-systemd:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 172s Preparing to unpack .../7-dbus-user-session_1.14.10-4ubuntu2_s390x.deb ... 172s Unpacking dbus-user-session (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 172s Preparing to unpack .../8-libapparmor1_4.0.0-beta3-0ubuntu2_s390x.deb ... 172s Unpacking libapparmor1:s390x (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 172s Preparing to unpack .../9-libaudit-common_1%3a3.1.2-2.1_all.deb ... 172s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ... 172s Setting up libaudit-common (1:3.1.2-2.1) ... 172s (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 ... 52166 files and directories currently installed.) 172s Preparing to unpack .../libcap-ng0_0.8.4-2build1_s390x.deb ... 172s Unpacking libcap-ng0:s390x (0.8.4-2build1) over (0.8.4-2) ... 172s Setting up libcap-ng0:s390x (0.8.4-2build1) ... 172s (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 ... 52166 files and directories currently installed.) 172s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_s390x.deb ... 172s Unpacking libaudit1:s390x (1:3.1.2-2.1) over (1:3.1.2-2) ... 172s Setting up libaudit1:s390x (1:3.1.2-2.1) ... 172s (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 ... 52166 files and directories currently installed.) 172s Preparing to unpack .../libselinux1_3.5-2ubuntu1_s390x.deb ... 172s Unpacking libselinux1:s390x (3.5-2ubuntu1) over (3.5-2build1) ... 172s Setting up libselinux1:s390x (3.5-2ubuntu1) ... 172s dpkg: libcurl4:s390x: dependency problems, but removing anyway as you requested: 172s s390-tools depends on libcurl4 (>= 7.16.2). 172s curl depends on libcurl4 (= 8.5.0-2ubuntu2). 172s 172s (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 ... 52166 files and directories currently installed.) 172s Removing libcurl4:s390x (8.5.0-2ubuntu2) ... 172s Selecting previously unselected package libcurl4t64:s390x. 172s (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 ... 52161 files and directories currently installed.) 172s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu8_s390x.deb ... 172s Unpacking libcurl4t64:s390x (8.5.0-2ubuntu8) ... 172s Preparing to unpack .../curl_8.5.0-2ubuntu8_s390x.deb ... 172s Unpacking curl (8.5.0-2ubuntu8) over (8.5.0-2ubuntu2) ... 172s dpkg: libpsl5:s390x: dependency problems, but removing anyway as you requested: 172s wget depends on libpsl5 (>= 0.16.0). 172s libcurl3-gnutls:s390x depends on libpsl5 (>= 0.16.0). 172s 172s (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 ... 52167 files and directories currently installed.) 172s Removing libpsl5:s390x (0.21.2-1build1) ... 172s Selecting previously unselected package libpsl5t64:s390x. 172s (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 ... 52162 files and directories currently installed.) 172s Preparing to unpack .../00-libpsl5t64_0.21.2-1.1_s390x.deb ... 172s Unpacking libpsl5t64:s390x (0.21.2-1.1) ... 172s Preparing to unpack .../01-wget_1.21.4-1ubuntu2_s390x.deb ... 172s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ... 172s Preparing to unpack .../02-tnftp_20230507-2build1_s390x.deb ... 172s Unpacking tnftp (20230507-2build1) over (20230507-2) ... 172s Preparing to unpack .../03-tcpdump_4.99.4-3ubuntu2_s390x.deb ... 172s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ... 172s Preparing to unpack .../04-libsystemd-shared_255.4-1ubuntu5_s390x.deb ... 172s Unpacking libsystemd-shared:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 172s Preparing to unpack .../05-systemd-resolved_255.4-1ubuntu5_s390x.deb ... 172s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 172s Preparing to unpack .../06-sudo_1.9.15p5-3ubuntu3_s390x.deb ... 172s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ... 172s Preparing to unpack .../07-rsync_3.2.7-1build1_s390x.deb ... 172s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ... 172s Preparing to unpack .../08-python3-cryptography_41.0.7-4build2_s390x.deb ... 173s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ... 173s Preparing to unpack .../09-openssl_3.0.13-0ubuntu2_s390x.deb ... 173s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 173s Preparing to unpack .../10-openssh-sftp-server_1%3a9.6p1-3ubuntu11_s390x.deb ... 173s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 173s Preparing to unpack .../11-openssh-client_1%3a9.6p1-3ubuntu11_s390x.deb ... 173s Unpacking openssh-client (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 173s Preparing to unpack .../12-openssh-server_1%3a9.6p1-3ubuntu11_s390x.deb ... 173s Unpacking openssh-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 173s Preparing to unpack .../13-libssh-4_0.10.6-2build1_s390x.deb ... 173s Unpacking libssh-4:s390x (0.10.6-2build1) over (0.10.6-2) ... 173s Preparing to unpack .../14-libsasl2-modules_2.1.28+dfsg1-5ubuntu1_s390x.deb ... 173s Unpacking libsasl2-modules:s390x (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 173s Preparing to unpack .../15-python3.12_3.12.2-4build3_s390x.deb ... 173s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ... 173s Preparing to unpack .../16-python3.12-minimal_3.12.2-4build3_s390x.deb ... 173s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ... 173s Preparing to unpack .../17-libpython3.12-minimal_3.12.2-4build3_s390x.deb ... 173s Unpacking libpython3.12-minimal:s390x (3.12.2-4build3) over (3.12.2-1) ... 173s dpkg: libparted2:s390x: dependency problems, but removing anyway as you requested: 173s parted depends on libparted2 (= 3.6-3). 173s 173s (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 ... 52168 files and directories currently installed.) 173s Removing libparted2:s390x (3.6-3) ... 173s Selecting previously unselected package libparted2t64:s390x. 173s (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 ... 52162 files and directories currently installed.) 173s Preparing to unpack .../00-libparted2t64_3.6-3.1build2_s390x.deb ... 173s Unpacking libparted2t64:s390x (3.6-3.1build2) ... 173s Preparing to unpack .../01-parted_3.6-3.1build2_s390x.deb ... 173s Unpacking parted (3.6-3.1build2) over (3.6-3) ... 173s Preparing to unpack .../02-python3.11_3.11.8-1build4_s390x.deb ... 173s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ... 173s Preparing to unpack .../03-python3.11-minimal_3.11.8-1build4_s390x.deb ... 173s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ... 173s Preparing to unpack .../04-libpython3.11-minimal_3.11.8-1build4_s390x.deb ... 173s Unpacking libpython3.11-minimal:s390x (3.11.8-1build4) over (3.11.8-1) ... 174s Preparing to unpack .../05-libpython3.11-stdlib_3.11.8-1build4_s390x.deb ... 174s Unpacking libpython3.11-stdlib:s390x (3.11.8-1build4) over (3.11.8-1) ... 174s Preparing to unpack .../06-shared-mime-info_2.4-1build1_s390x.deb ... 174s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ... 174s Preparing to unpack .../07-gir1.2-girepository-2.0_1.79.1-1ubuntu6_s390x.deb ... 174s Unpacking gir1.2-girepository-2.0:s390x (1.79.1-1ubuntu6) over (1.79.1-1) ... 174s Preparing to unpack .../08-gir1.2-glib-2.0_2.79.3-3ubuntu5_s390x.deb ... 174s Unpacking gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 174s Preparing to unpack .../09-libgirepository-1.0-1_1.79.1-1ubuntu6_s390x.deb ... 174s Unpacking libgirepository-1.0-1:s390x (1.79.1-1ubuntu6) over (1.79.1-1) ... 174s Preparing to unpack .../10-python3-gi_3.47.0-3build1_s390x.deb ... 174s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ... 174s Preparing to unpack .../11-python3-dbus_1.3.2-5build2_s390x.deb ... 174s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ... 174s Selecting previously unselected package libnetplan1:s390x. 174s Preparing to unpack .../12-libnetplan1_1.0-1_s390x.deb ... 174s Unpacking libnetplan1:s390x (1.0-1) ... 174s Preparing to unpack .../13-python3-netplan_1.0-1_s390x.deb ... 174s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ... 174s Preparing to unpack .../14-netplan-generator_1.0-1_s390x.deb ... 174s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 174s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ... 174s Preparing to unpack .../15-netplan.io_1.0-1_s390x.deb ... 174s Unpacking netplan.io (1.0-1) over (0.107.1-3) ... 174s Preparing to unpack .../16-libxmlb2_0.3.15-1build1_s390x.deb ... 174s Unpacking libxmlb2:s390x (0.3.15-1build1) over (0.3.15-1) ... 174s dpkg: libgpgme11:s390x: dependency problems, but removing anyway as you requested: 174s libvolume-key1:s390x depends on libgpgme11 (>= 1.4.1). 174s libjcat1:s390x depends on libgpgme11 (>= 1.2.0). 174s 174s (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 ... 52170 files and directories currently installed.) 174s Removing libgpgme11:s390x (1.18.0-4ubuntu1) ... 174s Selecting previously unselected package libgpgme11t64:s390x. 174s (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 ... 52164 files and directories currently installed.) 174s Preparing to unpack .../00-libgpgme11t64_1.18.0-4.1ubuntu3_s390x.deb ... 174s Unpacking libgpgme11t64:s390x (1.18.0-4.1ubuntu3) ... 174s Preparing to unpack .../01-libvolume-key1_0.3.12-7build1_s390x.deb ... 174s Unpacking libvolume-key1:s390x (0.3.12-7build1) over (0.3.12-5build2) ... 174s Preparing to unpack .../02-libqrtr-glib0_1.2.2-1ubuntu3_s390x.deb ... 174s Unpacking libqrtr-glib0:s390x (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ... 174s Preparing to unpack .../03-libqmi-glib5_1.35.2-0ubuntu1_s390x.deb ... 174s Unpacking libqmi-glib5:s390x (1.35.2-0ubuntu1) over (1.34.0-2) ... 174s Preparing to unpack .../04-libqmi-proxy_1.35.2-0ubuntu1_s390x.deb ... 174s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ... 175s Preparing to unpack .../05-libpolkit-agent-1-0_124-1ubuntu1_s390x.deb ... 175s Unpacking libpolkit-agent-1-0:s390x (124-1ubuntu1) over (124-1) ... 175s Preparing to unpack .../06-libpolkit-gobject-1-0_124-1ubuntu1_s390x.deb ... 175s Unpacking libpolkit-gobject-1-0:s390x (124-1ubuntu1) over (124-1) ... 175s Preparing to unpack .../07-libmm-glib0_1.23.4-0ubuntu1_s390x.deb ... 175s Unpacking libmm-glib0:s390x (1.23.4-0ubuntu1) over (1.22.0-3) ... 175s Preparing to unpack .../08-libmbim-glib4_1.31.2-0ubuntu2_s390x.deb ... 175s Unpacking libmbim-glib4:s390x (1.31.2-0ubuntu2) over (1.30.0-1) ... 175s Preparing to unpack .../09-libmbim-proxy_1.31.2-0ubuntu2_s390x.deb ... 175s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ... 175s Preparing to unpack .../10-libjson-glib-1.0-common_1.8.0-2build1_all.deb ... 175s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ... 175s Preparing to unpack .../11-libjson-glib-1.0-0_1.8.0-2build1_s390x.deb ... 175s Unpacking libjson-glib-1.0-0:s390x (1.8.0-2build1) over (1.8.0-2) ... 175s Preparing to unpack .../12-libgusb2_0.4.8-1build1_s390x.deb ... 175s Unpacking libgusb2:s390x (0.4.8-1build1) over (0.4.8-1) ... 175s Preparing to unpack .../13-libgudev-1.0-0_1%3a238-3ubuntu2_s390x.deb ... 175s Unpacking libgudev-1.0-0:s390x (1:238-3ubuntu2) over (1:238-3) ... 175s dpkg: libarchive13:s390x: dependency problems, but removing anyway as you requested: 175s fwupd depends on libarchive13 (>= 3.2.1). 175s 175s (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 ... 52171 files and directories currently installed.) 175s Removing libarchive13:s390x (3.7.2-1ubuntu2) ... 175s Selecting previously unselected package libarchive13t64:s390x. 175s (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 ... 52165 files and directories currently installed.) 175s Preparing to unpack .../libarchive13t64_3.7.2-1.1ubuntu2_s390x.deb ... 175s Unpacking libarchive13t64:s390x (3.7.2-1.1ubuntu2) ... 175s Preparing to unpack .../fwupd_1.9.15-2_s390x.deb ... 175s Unpacking fwupd (1.9.15-2) over (1.9.14-1) ... 175s dpkg: libcurl3-gnutls:s390x: dependency problems, but removing anyway as you requested: 175s libfwupd2:s390x depends on libcurl3-gnutls (>= 7.63.0). 175s 175s (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 ... 52172 files and directories currently installed.) 175s Removing libcurl3-gnutls:s390x (8.5.0-2ubuntu2) ... 175s Selecting previously unselected package libcurl3t64-gnutls:s390x. 175s (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 ... 52165 files and directories currently installed.) 175s Preparing to unpack .../0-libcurl3t64-gnutls_8.5.0-2ubuntu8_s390x.deb ... 175s Unpacking libcurl3t64-gnutls:s390x (8.5.0-2ubuntu8) ... 175s Preparing to unpack .../1-libfwupd2_1.9.15-2_s390x.deb ... 175s Unpacking libfwupd2:s390x (1.9.15-2) over (1.9.14-1) ... 175s Preparing to unpack .../2-libblockdev3_3.1.0-1build1_s390x.deb ... 175s Unpacking libblockdev3:s390x (3.1.0-1build1) over (3.1.0-1) ... 175s Preparing to unpack .../3-libblockdev-utils3_3.1.0-1build1_s390x.deb ... 175s Unpacking libblockdev-utils3:s390x (3.1.0-1build1) over (3.1.0-1) ... 175s Preparing to unpack .../4-libblockdev-swap3_3.1.0-1build1_s390x.deb ... 175s Unpacking libblockdev-swap3:s390x (3.1.0-1build1) over (3.1.0-1) ... 175s Preparing to unpack .../5-libblockdev-part3_3.1.0-1build1_s390x.deb ... 175s Unpacking libblockdev-part3:s390x (3.1.0-1build1) over (3.1.0-1) ... 175s dpkg: libnvme1: dependency problems, but removing anyway as you requested: 175s libblockdev-nvme3:s390x depends on libnvme1 (>= 1.7.1). 175s 175s (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 ... 52172 files and directories currently installed.) 175s Removing libnvme1 (1.8-2) ... 175s Selecting previously unselected package libnvme1t64. 175s (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 ... 52165 files and directories currently installed.) 175s Preparing to unpack .../0-libnvme1t64_1.8-3_s390x.deb ... 175s Unpacking libnvme1t64 (1.8-3) ... 175s Preparing to unpack .../1-libblockdev-nvme3_3.1.0-1build1_s390x.deb ... 175s Unpacking libblockdev-nvme3:s390x (3.1.0-1build1) over (3.1.0-1) ... 175s Preparing to unpack .../2-libblockdev-mdraid3_3.1.0-1build1_s390x.deb ... 175s Unpacking libblockdev-mdraid3:s390x (3.1.0-1build1) over (3.1.0-1) ... 175s Preparing to unpack .../3-libblockdev-loop3_3.1.0-1build1_s390x.deb ... 175s Unpacking libblockdev-loop3:s390x (3.1.0-1build1) over (3.1.0-1) ... 175s Preparing to unpack .../4-logsave_1.47.0-2.4~exp1ubuntu2_s390x.deb ... 175s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 175s Preparing to unpack .../5-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ... 175s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 175s dpkg: libext2fs2:s390x: dependency problems, but removing anyway as you requested: 175s libblockdev-fs3:s390x depends on libext2fs2 (>= 1.42.11). 175s e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1). 175s btrfs-progs depends on libext2fs2 (>= 1.42). 175s 175s (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 ... 52173 files and directories currently installed.) 175s Removing libext2fs2:s390x (1.47.0-2ubuntu1) ... 175s Selecting previously unselected package libext2fs2t64:s390x. 175s (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 ... 52166 files and directories currently installed.) 175s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_s390x.deb ... 175s Adding 'diversion of /lib/s390x-linux-gnu/libe2p.so.2 to /lib/s390x-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' 175s Adding 'diversion of /lib/s390x-linux-gnu/libe2p.so.2.3 to /lib/s390x-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' 175s Adding 'diversion of /lib/s390x-linux-gnu/libext2fs.so.2 to /lib/s390x-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' 175s Adding 'diversion of /lib/s390x-linux-gnu/libext2fs.so.2.4 to /lib/s390x-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' 175s Unpacking libext2fs2t64:s390x (1.47.0-2.4~exp1ubuntu2) ... 175s Setting up libcom-err2:s390x (1.47.0-2.4~exp1ubuntu2) ... 175s Setting up libext2fs2t64:s390x (1.47.0-2.4~exp1ubuntu2) ... 175s (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 ... 52182 files and directories currently installed.) 175s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_s390x.deb ... 175s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 175s dpkg: libreiserfscore0: dependency problems, but removing anyway as you requested: 175s btrfs-progs depends on libreiserfscore0 (>= 1:3.6.27). 175s 176s (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 ... 52182 files and directories currently installed.) 176s Removing libreiserfscore0 (1:3.6.27-7) ... 176s Selecting previously unselected package libreiserfscore0t64. 176s (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 ... 52177 files and directories currently installed.) 176s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_s390x.deb ... 176s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ... 176s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_s390x.deb ... 176s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ... 176s Preparing to unpack .../libblockdev-fs3_3.1.0-1build1_s390x.deb ... 176s Unpacking libblockdev-fs3:s390x (3.1.0-1build1) over (3.1.0-1) ... 176s Preparing to unpack .../libblockdev-crypto3_3.1.0-1build1_s390x.deb ... 176s Unpacking libblockdev-crypto3:s390x (3.1.0-1build1) over (3.1.0-1) ... 176s Preparing to unpack .../bolt_0.9.6-2build1_s390x.deb ... 176s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ... 176s dpkg: libglib2.0-0:s390x: dependency problems, but removing anyway as you requested: 176s s390-tools depends on libglib2.0-0 (>= 2.77.0). 176s libnetplan0:s390x depends on libglib2.0-0 (>= 2.75.3). 176s libjcat1:s390x depends on libglib2.0-0 (>= 2.75.3). 176s 176s (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 ... 52183 files and directories currently installed.) 176s Removing libglib2.0-0:s390x (2.79.2-1~ubuntu1) ... 176s Selecting previously unselected package libglib2.0-0t64:s390x. 176s (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 ... 52158 files and directories currently installed.) 176s Preparing to unpack .../0-libglib2.0-0t64_2.79.3-3ubuntu5_s390x.deb ... 176s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:s390x.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 176s removed '/var/lib/dpkg/info/libglib2.0-0:s390x.postrm' 176s Unpacking libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ... 176s Preparing to unpack .../1-libjcat1_0.2.0-2build2_s390x.deb ... 176s Unpacking libjcat1:s390x (0.2.0-2build2) over (0.2.0-2) ... 176s Preparing to unpack .../2-libldap2_2.6.7+dfsg-1~exp1ubuntu6_s390x.deb ... 176s Unpacking libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 176s Preparing to unpack .../3-ubuntu-pro-client-l10n_31.2.2_s390x.deb ... 176s Unpacking ubuntu-pro-client-l10n (31.2.2) over (31.1) ... 176s Preparing to unpack .../4-ubuntu-pro-client_31.2.2_s390x.deb ... 176s Unpacking ubuntu-pro-client (31.2.2) over (31.1) ... 176s Preparing to unpack .../5-gnupg-utils_2.4.4-2ubuntu15_s390x.deb ... 176s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 176s Preparing to unpack .../6-keyboxd_2.4.4-2ubuntu15_s390x.deb ... 176s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 176s dpkg: libnpth0:s390x: dependency problems, but removing anyway as you requested: 176s gpgv depends on libnpth0 (>= 0.90). 176s gpgsm depends on libnpth0 (>= 0.90). 176s gpg-agent depends on libnpth0 (>= 0.90). 176s gpg depends on libnpth0 (>= 0.90). 176s dirmngr depends on libnpth0 (>= 0.90). 176s 176s (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 ... 52183 files and directories currently installed.) 176s Removing libnpth0:s390x (1.6-3build2) ... 176s Selecting previously unselected package libnpth0t64:s390x. 176s (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 ... 52178 files and directories currently installed.) 176s Preparing to unpack .../libnpth0t64_1.6-3.1_s390x.deb ... 176s Unpacking libnpth0t64:s390x (1.6-3.1) ... 176s Setting up libnpth0t64:s390x (1.6-3.1) ... 176s (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 ... 52184 files and directories currently installed.) 176s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_s390x.deb ... 176s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 176s Setting up gpgv (2.4.4-2ubuntu15) ... 176s (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 ... 52184 files and directories currently installed.) 176s Preparing to unpack .../0-gpg-wks-client_2.4.4-2ubuntu15_s390x.deb ... 176s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 176s Preparing to unpack .../1-gpg-agent_2.4.4-2ubuntu15_s390x.deb ... 176s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 176s Preparing to unpack .../2-gpg_2.4.4-2ubuntu15_s390x.deb ... 176s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 176s Preparing to unpack .../3-dirmngr_2.4.4-2ubuntu15_s390x.deb ... 176s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 176s Preparing to unpack .../4-gnupg_2.4.4-2ubuntu15_all.deb ... 176s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 176s Preparing to unpack .../5-python3-apt_2.7.7_s390x.deb ... 176s Unpacking python3-apt (2.7.7) over (2.7.6) ... 176s Preparing to unpack .../6-apt-utils_2.7.14_s390x.deb ... 176s Unpacking apt-utils (2.7.14) over (2.7.12) ... 177s dpkg: libapt-pkg6.0:s390x: dependency problems, but removing anyway as you requested: 177s apt depends on libapt-pkg6.0 (>= 2.7.12). 177s 177s (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 ... 52182 files and directories currently installed.) 177s Removing libapt-pkg6.0:s390x (2.7.12) ... 177s dpkg: libnettle8:s390x: dependency problems, but removing anyway as you requested: 177s libhogweed6:s390x depends on libnettle8. 177s libgnutls30:s390x depends on libnettle8 (>= 3.9~). 177s 177s Removing libnettle8:s390x (3.9.1-2) ... 177s Selecting previously unselected package libapt-pkg6.0t64:s390x. 177s (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 ... 52126 files and directories currently installed.) 177s Preparing to unpack .../libapt-pkg6.0t64_2.7.14_s390x.deb ... 177s Unpacking libapt-pkg6.0t64:s390x (2.7.14) ... 177s Setting up libapt-pkg6.0t64:s390x (2.7.14) ... 177s Selecting previously unselected package libnettle8t64:s390x. 177s (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 ... 52176 files and directories currently installed.) 177s Preparing to unpack .../libnettle8t64_3.9.1-2.2_s390x.deb ... 177s Unpacking libnettle8t64:s390x (3.9.1-2.2) ... 177s Setting up libnettle8t64:s390x (3.9.1-2.2) ... 177s dpkg: libhogweed6:s390x: dependency problems, but removing anyway as you requested: 177s libgnutls30:s390x depends on libhogweed6 (>= 3.6). 177s 177s (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 ... 52184 files and directories currently installed.) 177s Removing libhogweed6:s390x (3.9.1-2) ... 177s Selecting previously unselected package libhogweed6t64:s390x. 177s (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 ... 52179 files and directories currently installed.) 177s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_s390x.deb ... 177s Unpacking libhogweed6t64:s390x (3.9.1-2.2) ... 177s Setting up libhogweed6t64:s390x (3.9.1-2.2) ... 177s dpkg: libgnutls30:s390x: dependency problems, but removing anyway as you requested: 177s apt depends on libgnutls30 (>= 3.8.1). 177s 177s (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 ... 52185 files and directories currently installed.) 177s Removing libgnutls30:s390x (3.8.3-1ubuntu1) ... 177s Selecting previously unselected package libgnutls30t64:s390x. 177s (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 ... 52176 files and directories currently installed.) 177s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_s390x.deb ... 177s Unpacking libgnutls30t64:s390x (3.8.3-1.1ubuntu2) ... 177s Setting up libgnutls30t64:s390x (3.8.3-1.1ubuntu2) ... 177s (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 ... 52204 files and directories currently installed.) 177s Preparing to unpack .../archives/apt_2.7.14_s390x.deb ... 177s Unpacking apt (2.7.14) over (2.7.12) ... 177s Setting up apt (2.7.14) ... 178s (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 ... 52204 files and directories currently installed.) 178s Preparing to unpack .../gpgconf_2.4.4-2ubuntu15_s390x.deb ... 178s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 178s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_s390x.deb ... 178s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 178s dpkg: libreadline8:s390x: dependency problems, but removing anyway as you requested: 178s libpython3.12-stdlib:s390x depends on libreadline8 (>= 7.0~beta). 178s gawk depends on libreadline8 (>= 6.0). 178s fdisk depends on libreadline8 (>= 6.0). 178s 178s (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 ... 52204 files and directories currently installed.) 178s Removing libreadline8:s390x (8.2-3) ... 178s Selecting previously unselected package libreadline8t64:s390x. 178s (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 ... 52192 files and directories currently installed.) 178s Preparing to unpack .../libreadline8t64_8.2-4_s390x.deb ... 178s Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8 to /lib/s390x-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 178s Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8.2 to /lib/s390x-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 178s Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8 to /lib/s390x-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 178s Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8.2 to /lib/s390x-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 178s Unpacking libreadline8t64:s390x (8.2-4) ... 178s Setting up libreadline8t64:s390x (8.2-4) ... 178s (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 ... 52212 files and directories currently installed.) 178s Preparing to unpack .../gawk_1%3a5.2.1-2build2_s390x.deb ... 178s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ... 178s Preparing to unpack .../fdisk_2.39.3-9ubuntu2_s390x.deb ... 178s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 178s Preparing to unpack .../libpython3.12-stdlib_3.12.2-4build3_s390x.deb ... 178s Unpacking libpython3.12-stdlib:s390x (3.12.2-4build3) over (3.12.2-1) ... 178s Preparing to unpack .../perl-base_5.38.2-3.2_s390x.deb ... 178s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 178s Setting up perl-base (5.38.2-3.2) ... 178s (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 ... 52210 files and directories currently installed.) 178s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 178s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 179s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu1.1_s390x.deb ... 179s Unpacking python3-gdbm:s390x (3.12.2-3ubuntu1.1) over (3.11.5-1) ... 179s Preparing to unpack .../man-db_2.12.0-3build4_s390x.deb ... 179s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ... 179s dpkg: libgdbm-compat4:s390x: dependency problems, but removing anyway as you requested: 179s libperl5.38:s390x depends on libgdbm-compat4 (>= 1.18-3). 179s 179s (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 ... 52210 files and directories currently installed.) 179s Removing libgdbm-compat4:s390x (1.23-5) ... 179s dpkg: libgdbm6:s390x: dependency problems, but removing anyway as you requested: 179s libperl5.38:s390x depends on libgdbm6 (>= 1.21). 179s 179s Removing libgdbm6:s390x (1.23-5) ... 179s Selecting previously unselected package libgdbm6t64:s390x. 179s (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 ... 52200 files and directories currently installed.) 179s Preparing to unpack .../libgdbm6t64_1.23-5.1_s390x.deb ... 179s Unpacking libgdbm6t64:s390x (1.23-5.1) ... 179s Selecting previously unselected package libgdbm-compat4t64:s390x. 179s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_s390x.deb ... 179s Unpacking libgdbm-compat4t64:s390x (1.23-5.1) ... 179s dpkg: libperl5.38:s390x: dependency problems, but removing anyway as you requested: 179s perl depends on libperl5.38 (= 5.38.2-3). 179s 179s (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 ... 52212 files and directories currently installed.) 179s Removing libperl5.38:s390x (5.38.2-3) ... 179s Selecting previously unselected package libperl5.38t64:s390x. 179s (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 ... 51690 files and directories currently installed.) 179s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_s390x.deb ... 179s Unpacking libperl5.38t64:s390x (5.38.2-3.2) ... 179s Preparing to unpack .../perl_5.38.2-3.2_s390x.deb ... 179s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ... 179s dpkg: libdb5.3:s390x: dependency problems, but removing anyway as you requested: 179s libsasl2-modules-db:s390x depends on libdb5.3. 179s iproute2 depends on libdb5.3. 179s 179s (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 ... 52212 files and directories currently installed.) 179s Removing libdb5.3:s390x (5.3.28+dfsg2-4) ... 179s Selecting previously unselected package libdb5.3t64:s390x. 179s (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 ... 52206 files and directories currently installed.) 179s Preparing to unpack .../0-libdb5.3t64_5.3.28+dfsg2-6_s390x.deb ... 179s Unpacking libdb5.3t64:s390x (5.3.28+dfsg2-6) ... 179s Preparing to unpack .../1-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu1_s390x.deb ... 179s Unpacking libsasl2-modules-db:s390x (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 179s Preparing to unpack .../2-libsasl2-2_2.1.28+dfsg1-5ubuntu1_s390x.deb ... 179s Unpacking libsasl2-2:s390x (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 179s Preparing to unpack .../3-libfido2-1_1.14.0-1build1_s390x.deb ... 179s Unpacking libfido2-1:s390x (1.14.0-1build1) over (1.14.0-1) ... 179s Preparing to unpack .../4-libcryptsetup12_2%3a2.7.0-1ubuntu2_s390x.deb ... 179s Unpacking libcryptsetup12:s390x (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 179s Preparing to unpack .../5-dhcpcd-base_1%3a10.0.6-1ubuntu2_s390x.deb ... 179s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ... 179s dpkg: libuv1:s390x: dependency problems, but removing anyway as you requested: 179s bind9-libs:s390x depends on libuv1 (>= 1.40.0). 179s 179s (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 ... 52212 files and directories currently installed.) 179s Removing libuv1:s390x (1.48.0-1) ... 179s Selecting previously unselected package libuv1t64:s390x. 179s (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 ... 52207 files and directories currently installed.) 179s Preparing to unpack .../libuv1t64_1.48.0-1.1_s390x.deb ... 179s Unpacking libuv1t64:s390x (1.48.0-1.1) ... 179s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_s390x.deb ... 179s Unpacking bind9-host (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 179s Preparing to unpack .../bind9-dnsutils_1%3a9.18.24-0ubuntu3_s390x.deb ... 179s Unpacking bind9-dnsutils (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 179s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_s390x.deb ... 179s Unpacking bind9-libs:s390x (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 180s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 180s systemd depends on libssl3 (>= 3.0.0). 180s s390-tools depends on libssl3 (>= 3.0.0). 180s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 180s 180s (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 ... 52213 files and directories currently installed.) 180s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 180s Selecting previously unselected package libssl3t64:s390x. 180s (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 ... 52202 files and directories currently installed.) 180s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 180s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 180s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 180s (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 ... 52215 files and directories currently installed.) 180s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_s390x.deb ... 180s Unpacking libnss-systemd:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 180s Preparing to unpack .../libudev1_255.4-1ubuntu5_s390x.deb ... 180s Unpacking libudev1:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 180s Setting up libudev1:s390x (255.4-1ubuntu5) ... 180s (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 ... 52215 files and directories currently installed.) 180s Preparing to unpack .../systemd_255.4-1ubuntu5_s390x.deb ... 180s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 180s Preparing to unpack .../udev_255.4-1ubuntu5_s390x.deb ... 180s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 180s Preparing to unpack .../libsystemd0_255.4-1ubuntu5_s390x.deb ... 180s Unpacking libsystemd0:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 180s Setting up libsystemd0:s390x (255.4-1ubuntu5) ... 180s (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 ... 52215 files and directories currently installed.) 180s Preparing to unpack .../0-dbus-system-bus-common_1.14.10-4ubuntu2_all.deb ... 180s Unpacking dbus-system-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 180s Preparing to unpack .../1-dbus-bin_1.14.10-4ubuntu2_s390x.deb ... 180s Unpacking dbus-bin (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 180s Preparing to unpack .../2-dbus_1.14.10-4ubuntu2_s390x.deb ... 180s Unpacking dbus (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 180s Preparing to unpack .../3-dbus-daemon_1.14.10-4ubuntu2_s390x.deb ... 180s Unpacking dbus-daemon (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 180s Preparing to unpack .../4-libdbus-1-3_1.14.10-4ubuntu2_s390x.deb ... 180s Unpacking libdbus-1-3:s390x (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 180s Preparing to unpack .../5-libmount1_2.39.3-9ubuntu2_s390x.deb ... 180s Unpacking libmount1:s390x (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 180s Setting up libmount1:s390x (2.39.3-9ubuntu2) ... 180s (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 ... 52215 files and directories currently installed.) 180s Preparing to unpack .../libuuid1_2.39.3-9ubuntu2_s390x.deb ... 180s Unpacking libuuid1:s390x (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 180s Setting up libuuid1:s390x (2.39.3-9ubuntu2) ... 180s (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 ... 52215 files and directories currently installed.) 180s Preparing to unpack .../libfdisk1_2.39.3-9ubuntu2_s390x.deb ... 180s Unpacking libfdisk1:s390x (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 180s Preparing to unpack .../mount_2.39.3-9ubuntu2_s390x.deb ... 180s Unpacking mount (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 180s Preparing to unpack .../libsqlite3-0_3.45.1-1ubuntu1_s390x.deb ... 180s Unpacking libsqlite3-0:s390x (3.45.1-1ubuntu1) over (3.45.1-1) ... 180s Preparing to unpack .../dpkg_1.22.6ubuntu5_s390x.deb ... 180s Unpacking dpkg (1.22.6ubuntu5) over (1.22.4ubuntu5) ... 181s Setting up dpkg (1.22.6ubuntu5) ... 181s Setting up libpython3.12-minimal:s390x (3.12.2-4build3) ... 181s Setting up python3.12-minimal (3.12.2-4build3) ... 182s (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 ... 52215 files and directories currently installed.) 182s Preparing to unpack .../python3-minimal_3.12.2-0ubuntu1_s390x.deb ... 182s Unpacking python3-minimal (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 182s Setting up python3-minimal (3.12.2-0ubuntu1) ... 182s (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 ... 52215 files and directories currently installed.) 182s Preparing to unpack .../python3_3.12.2-0ubuntu1_s390x.deb ... 182s Unpacking python3 (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 182s Preparing to unpack .../libpython3-stdlib_3.12.2-0ubuntu1_s390x.deb ... 182s Unpacking libpython3-stdlib:s390x (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 182s Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu2_s390x.deb ... 182s Unpacking libsmartcols1:s390x (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 182s Setting up libsmartcols1:s390x (2.39.3-9ubuntu2) ... 182s (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 ... 52215 files and directories currently installed.) 182s Preparing to unpack .../0-bsdextrautils_2.39.3-9ubuntu2_s390x.deb ... 182s Unpacking bsdextrautils (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 182s Preparing to unpack .../1-groff-base_1.23.0-3build1_s390x.deb ... 182s Unpacking groff-base (1.23.0-3build1) over (1.23.0-3) ... 182s Preparing to unpack .../2-pinentry-curses_1.2.1-3ubuntu4_s390x.deb ... 182s Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-3ubuntu1) ... 183s Preparing to unpack .../3-readline-common_8.2-4_all.deb ... 183s Unpacking readline-common (8.2-4) over (8.2-3) ... 183s Preparing to unpack .../4-libxml2_2.9.14+dfsg-1.3ubuntu2_s390x.deb ... 183s Unpacking libxml2:s390x (2.9.14+dfsg-1.3ubuntu2) over (2.9.14+dfsg-1.3ubuntu1) ... 183s Preparing to unpack .../5-libbpf1_1%3a1.3.0-2build1_s390x.deb ... 183s Unpacking libbpf1:s390x (1:1.3.0-2build1) over (1:1.3.0-2) ... 183s dpkg: libelf1:s390x: dependency problems, but removing anyway as you requested: 183s linux-headers-6.8.0-11-generic depends on libelf1 (>= 0.144). 183s iproute2 depends on libelf1 (>= 0.131). 183s 183s (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 ... 52215 files and directories currently installed.) 183s Removing libelf1:s390x (0.190-1) ... 183s Selecting previously unselected package libelf1t64:s390x. 183s (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 ... 52210 files and directories currently installed.) 183s Preparing to unpack .../libelf1t64_0.190-1.1build2_s390x.deb ... 183s Unpacking libelf1t64:s390x (0.190-1.1build2) ... 183s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 183s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 183s Preparing to unpack .../lsof_4.95.0-1build2_s390x.deb ... 183s Unpacking lsof (4.95.0-1build2) over (4.95.0-1build1) ... 183s Preparing to unpack .../libnsl2_1.3.0-3build2_s390x.deb ... 183s Unpacking libnsl2:s390x (1.3.0-3build2) over (1.3.0-3) ... 183s dpkg: libtirpc3:s390x: dependency problems, but removing anyway as you requested: 183s iproute2 depends on libtirpc3 (>= 1.0.2). 183s 183s (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 ... 52215 files and directories currently installed.) 183s Removing libtirpc3:s390x (1.3.4+ds-1build1) ... 183s Selecting previously unselected package libtirpc3t64:s390x. 183s (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 ... 52209 files and directories currently installed.) 183s Preparing to unpack .../0-libtirpc3t64_1.3.4+ds-1.1_s390x.deb ... 183s Adding 'diversion of /lib/s390x-linux-gnu/libtirpc.so.3 to /lib/s390x-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 183s Adding 'diversion of /lib/s390x-linux-gnu/libtirpc.so.3.0.0 to /lib/s390x-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 183s Unpacking libtirpc3t64:s390x (1.3.4+ds-1.1) ... 183s Preparing to unpack .../1-iproute2_6.1.0-1ubuntu5_s390x.deb ... 183s Unpacking iproute2 (6.1.0-1ubuntu5) over (6.1.0-1ubuntu2) ... 183s Preparing to unpack .../2-python3-yaml_6.0.1-2build1_s390x.deb ... 183s Unpacking python3-yaml (6.0.1-2build1) over (6.0.1-2) ... 183s Preparing to unpack .../3-libprotobuf-c1_1.4.1-1ubuntu3_s390x.deb ... 183s Unpacking libprotobuf-c1:s390x (1.4.1-1ubuntu3) over (1.4.1-1ubuntu2) ... 183s Preparing to unpack .../4-libnghttp2-14_1.59.0-1build1_s390x.deb ... 183s Unpacking libnghttp2-14:s390x (1.59.0-1build1) over (1.59.0-1) ... 183s Preparing to unpack .../5-libproc2-0_2%3a4.0.4-4ubuntu2_s390x.deb ... 183s Unpacking libproc2-0:s390x (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 183s Preparing to unpack .../6-procps_2%3a4.0.4-4ubuntu2_s390x.deb ... 183s Unpacking procps (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ... 183s Preparing to unpack .../7-coreutils_9.4-3ubuntu3_s390x.deb ... 183s Unpacking coreutils (9.4-3ubuntu3) over (9.4-2ubuntu4) ... 183s Setting up coreutils (9.4-3ubuntu3) ... 183s (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 ... 52220 files and directories currently installed.) 183s Preparing to unpack .../util-linux_2.39.3-9ubuntu2_s390x.deb ... 183s Unpacking util-linux (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 183s Setting up util-linux (2.39.3-9ubuntu2) ... 184s fstrim.service is a disabled or a static unit not running, not starting it. 184s (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 ... 52220 files and directories currently installed.) 184s Removing libatm1:s390x (1:2.5.1-5) ... 184s (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 ... 52215 files and directories currently installed.) 184s Preparing to unpack .../file_1%3a5.45-3_s390x.deb ... 184s Unpacking file (1:5.45-3) over (1:5.45-2) ... 184s (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 ... 52215 files and directories currently installed.) 184s Removing libmagic1:s390x (1:5.45-2) ... 184s (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 ... 52205 files and directories currently installed.) 184s Preparing to unpack .../libmagic-mgc_1%3a5.45-3_s390x.deb ... 184s Unpacking libmagic-mgc (1:5.45-3) over (1:5.45-2) ... 184s Selecting previously unselected package libmagic1t64:s390x. 184s Preparing to unpack .../libmagic1t64_1%3a5.45-3_s390x.deb ... 184s Unpacking libmagic1t64:s390x (1:5.45-3) ... 184s Preparing to unpack .../libplymouth5_24.004.60-1ubuntu6_s390x.deb ... 184s Unpacking libplymouth5:s390x (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 184s (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 ... 52216 files and directories currently installed.) 184s Removing libpng16-16:s390x (1.6.43-1) ... 184s Selecting previously unselected package libpng16-16t64:s390x. 184s (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 ... 52206 files and directories currently installed.) 184s Preparing to unpack .../libpng16-16t64_1.6.43-3_s390x.deb ... 184s Unpacking libpng16-16t64:s390x (1.6.43-3) ... 184s Preparing to unpack .../multipath-tools_0.9.4-5ubuntu6_s390x.deb ... 184s Unpacking multipath-tools (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ... 184s dpkg: liburcu8:s390x: dependency problems, but removing anyway as you requested: 184s xfsprogs depends on liburcu8 (>= 0.13.0). 184s 184s (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 ... 52216 files and directories currently installed.) 184s Removing liburcu8:s390x (0.14.0-3) ... 184s Selecting previously unselected package liburcu8t64:s390x. 184s (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 ... 52197 files and directories currently installed.) 184s Preparing to unpack .../liburcu8t64_0.14.0-3.1_s390x.deb ... 184s Unpacking liburcu8t64:s390x (0.14.0-3.1) ... 185s Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu4_s390x.deb ... 185s Unpacking liblocale-gettext-perl (1.07-6ubuntu4) over (1.07-6build1) ... 185s Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu2_s390x.deb ... 185s Unpacking uuid-runtime (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 185s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_s390x.deb ... 185s Unpacking libdebconfclient0:s390x (0.271ubuntu2) over (0.271ubuntu1) ... 185s Setting up libdebconfclient0:s390x (0.271ubuntu2) ... 185s (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 ... 52217 files and directories currently installed.) 185s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ... 185s Unpacking libsemanage-common (3.5-1build4) over (3.5-1build2) ... 185s Setting up libsemanage-common (3.5-1build4) ... 185s (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 ... 52217 files and directories currently installed.) 185s Preparing to unpack .../libsemanage2_3.5-1build4_s390x.deb ... 185s Unpacking libsemanage2:s390x (3.5-1build4) over (3.5-1build2) ... 185s Setting up libsemanage2:s390x (3.5-1build4) ... 185s (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 ... 52217 files and directories currently installed.) 185s Preparing to unpack .../install-info_7.1-3build1_s390x.deb ... 185s Unpacking install-info (7.1-3build1) over (7.1-3) ... 185s Setting up install-info (7.1-3build1) ... 185s (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 ... 52217 files and directories currently installed.) 185s Preparing to unpack .../00-libss2_1.47.0-2.4~exp1ubuntu2_s390x.deb ... 185s Unpacking libss2:s390x (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 185s Preparing to unpack .../01-eject_2.39.3-9ubuntu2_s390x.deb ... 185s Unpacking eject (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 185s Preparing to unpack .../02-krb5-locales_1.20.1-6ubuntu1_all.deb ... 185s Unpacking krb5-locales (1.20.1-6ubuntu1) over (1.20.1-5build1) ... 185s Preparing to unpack .../03-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 185s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 185s Preparing to unpack .../04-libslang2_2.3.3-3build1_s390x.deb ... 185s Unpacking libslang2:s390x (2.3.3-3build1) over (2.3.3-3) ... 185s Preparing to unpack .../05-libtext-charwidth-perl_0.04-11build2_s390x.deb ... 185s Unpacking libtext-charwidth-perl:s390x (0.04-11build2) over (0.04-11build1) ... 185s Preparing to unpack .../06-libtext-iconv-perl_1.7-8build2_s390x.deb ... 185s Unpacking libtext-iconv-perl:s390x (1.7-8build2) over (1.7-8build1) ... 185s Preparing to unpack .../07-python-apt-common_2.7.7_all.deb ... 185s Unpacking python-apt-common (2.7.7) over (2.7.6) ... 185s Preparing to unpack .../08-python3-setuptools_68.1.2-2ubuntu1_all.deb ... 185s Unpacking python3-setuptools (68.1.2-2ubuntu1) over (68.1.2-2) ... 185s Preparing to unpack .../09-python3-pkg-resources_68.1.2-2ubuntu1_all.deb ... 185s Unpacking python3-pkg-resources (68.1.2-2ubuntu1) over (68.1.2-2) ... 185s Preparing to unpack .../10-rsyslog_8.2312.0-3ubuntu7_s390x.deb ... 185s Unpacking rsyslog (8.2312.0-3ubuntu7) over (8.2312.0-3ubuntu3) ... 185s Preparing to unpack .../11-vim-tiny_2%3a9.1.0016-1ubuntu6_s390x.deb ... 185s Unpacking vim-tiny (2:9.1.0016-1ubuntu6) over (2:9.1.0016-1ubuntu2) ... 185s Preparing to unpack .../12-vim-common_2%3a9.1.0016-1ubuntu6_all.deb ... 185s Unpacking vim-common (2:9.1.0016-1ubuntu6) over (2:9.1.0016-1ubuntu2) ... 185s Selecting previously unselected package xdg-user-dirs. 185s Preparing to unpack .../13-xdg-user-dirs_0.18-1_s390x.deb ... 185s Unpacking xdg-user-dirs (0.18-1) ... 185s Preparing to unpack .../14-xxd_2%3a9.1.0016-1ubuntu6_s390x.deb ... 185s Unpacking xxd (2:9.1.0016-1ubuntu6) over (2:9.1.0016-1ubuntu2) ... 185s Preparing to unpack .../15-apparmor_4.0.0-beta3-0ubuntu2_s390x.deb ... 186s Unpacking apparmor (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 186s Preparing to unpack .../16-ftp_20230507-2build1_all.deb ... 186s Unpacking ftp (20230507-2build1) over (20230507-2) ... 186s Preparing to unpack .../17-inetutils-telnet_2%3a2.5-3ubuntu3_s390x.deb ... 186s Unpacking inetutils-telnet (2:2.5-3ubuntu3) over (2:2.5-3ubuntu1) ... 186s Preparing to unpack .../18-info_7.1-3build1_s390x.deb ... 186s Unpacking info (7.1-3build1) over (7.1-3) ... 186s Preparing to unpack .../19-libxmuu1_2%3a1.1.3-3build1_s390x.deb ... 186s Unpacking libxmuu1:s390x (2:1.1.3-3build1) over (2:1.1.3-3) ... 186s Preparing to unpack .../20-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_s390x.deb ... 186s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ... 186s Selecting previously unselected package manpages. 186s Preparing to unpack .../21-manpages_6.05.01-1_all.deb ... 186s Unpacking manpages (6.05.01-1) ... 186s Preparing to unpack .../22-mtr-tiny_0.95-1.1build1_s390x.deb ... 186s Unpacking mtr-tiny (0.95-1.1build1) over (0.95-1.1) ... 186s Preparing to unpack .../23-plymouth-theme-ubuntu-text_24.004.60-1ubuntu6_s390x.deb ... 186s Unpacking plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 186s Preparing to unpack .../24-plymouth_24.004.60-1ubuntu6_s390x.deb ... 186s Unpacking plymouth (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 186s Preparing to unpack .../25-telnet_0.17+2.5-3ubuntu3_all.deb ... 186s Unpacking telnet (0.17+2.5-3ubuntu3) over (0.17+2.5-3ubuntu1) ... 186s Preparing to unpack .../26-usb.ids_2024.03.18-1_all.deb ... 186s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ... 186s Preparing to unpack .../27-xz-utils_5.6.0-0.2_s390x.deb ... 186s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ... 186s Selecting previously unselected package libllvm18:s390x. 186s Preparing to unpack .../28-libllvm18_1%3a18.1.2-1ubuntu2_s390x.deb ... 186s Unpacking libllvm18:s390x (1:18.1.2-1ubuntu2) ... 187s Selecting previously unselected package libclang-cpp18. 187s Preparing to unpack .../29-libclang-cpp18_1%3a18.1.2-1ubuntu2_s390x.deb ... 187s Unpacking libclang-cpp18 (1:18.1.2-1ubuntu2) ... 188s Selecting previously unselected package libbpfcc:s390x. 188s Preparing to unpack .../30-libbpfcc_0.29.1+ds-1ubuntu4_s390x.deb ... 188s Unpacking libbpfcc:s390x (0.29.1+ds-1ubuntu4) ... 188s Selecting previously unselected package python3-bpfcc. 188s Preparing to unpack .../31-python3-bpfcc_0.29.1+ds-1ubuntu4_all.deb ... 188s Unpacking python3-bpfcc (0.29.1+ds-1ubuntu4) ... 188s Selecting previously unselected package ieee-data. 188s Preparing to unpack .../32-ieee-data_20220827.1_all.deb ... 188s Unpacking ieee-data (20220827.1) ... 188s Selecting previously unselected package python3-netaddr. 188s Preparing to unpack .../33-python3-netaddr_0.8.0-2ubuntu1_all.deb ... 188s Unpacking python3-netaddr (0.8.0-2ubuntu1) ... 188s Selecting previously unselected package bpfcc-tools. 188s Preparing to unpack .../34-bpfcc-tools_0.29.1+ds-1ubuntu4_all.deb ... 188s Unpacking bpfcc-tools (0.29.1+ds-1ubuntu4) ... 188s Selecting previously unselected package libclang1-18. 188s Preparing to unpack .../35-libclang1-18_1%3a18.1.2-1ubuntu2_s390x.deb ... 188s Unpacking libclang1-18 (1:18.1.2-1ubuntu2) ... 189s Selecting previously unselected package libdw1t64:s390x. 189s Preparing to unpack .../36-libdw1t64_0.190-1.1build2_s390x.deb ... 189s Unpacking libdw1t64:s390x (0.190-1.1build2) ... 189s Selecting previously unselected package bpftrace. 189s Preparing to unpack .../37-bpftrace_0.20.2-1ubuntu1_s390x.deb ... 189s Unpacking bpftrace (0.20.2-1ubuntu1) ... 189s Preparing to unpack .../38-cryptsetup-bin_2%3a2.7.0-1ubuntu2_s390x.deb ... 189s Unpacking cryptsetup-bin (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 189s Preparing to unpack .../39-dpkg-dev_1.22.6ubuntu5_all.deb ... 189s Unpacking dpkg-dev (1.22.6ubuntu5) over (1.22.4ubuntu5) ... 189s Preparing to unpack .../40-libdpkg-perl_1.22.6ubuntu5_all.deb ... 189s Unpacking libdpkg-perl (1.22.6ubuntu5) over (1.22.4ubuntu5) ... 189s Selecting previously unselected package fonts-dejavu-mono. 189s Preparing to unpack .../41-fonts-dejavu-mono_2.37-8_all.deb ... 189s Unpacking fonts-dejavu-mono (2.37-8) ... 189s Selecting previously unselected package fonts-dejavu-core. 189s Preparing to unpack .../42-fonts-dejavu-core_2.37-8_all.deb ... 189s Unpacking fonts-dejavu-core (2.37-8) ... 189s Selecting previously unselected package fontconfig-config. 189s Preparing to unpack .../43-fontconfig-config_2.15.0-1.1ubuntu1_s390x.deb ... 189s Unpacking fontconfig-config (2.15.0-1.1ubuntu1) ... 189s Preparing to unpack .../44-gnupg-l10n_2.4.4-2ubuntu15_all.deb ... 189s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 189s Selecting previously unselected package hwdata. 189s Preparing to unpack .../45-hwdata_0.379-1_all.deb ... 189s Unpacking hwdata (0.379-1) ... 189s Preparing to unpack .../46-libibverbs1_50.0-2build1_s390x.deb ... 189s Unpacking libibverbs1:s390x (50.0-2build1) over (50.0-2) ... 189s Preparing to unpack .../47-ibverbs-providers_50.0-2build1_s390x.deb ... 189s Unpacking ibverbs-providers:s390x (50.0-2build1) over (50.0-2) ... 189s Selecting previously unselected package libaio1t64:s390x. 189s Preparing to unpack .../48-libaio1t64_0.3.113-6_s390x.deb ... 189s Unpacking libaio1t64:s390x (0.3.113-6) ... 189s Selecting previously unselected package libatm1t64:s390x. 189s Preparing to unpack .../49-libatm1t64_1%3a2.5.1-5.1_s390x.deb ... 189s Unpacking libatm1t64:s390x (1:2.5.1-5.1) ... 189s Selecting previously unselected package libc-dev-bin. 189s Preparing to unpack .../50-libc-dev-bin_2.39-0ubuntu6_s390x.deb ... 189s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 189s Selecting previously unselected package libfreetype6:s390x. 189s Preparing to unpack .../51-libfreetype6_2.13.2+dfsg-1build2_s390x.deb ... 189s Unpacking libfreetype6:s390x (2.13.2+dfsg-1build2) ... 189s Selecting previously unselected package libfontconfig1:s390x. 189s Preparing to unpack .../52-libfontconfig1_2.15.0-1.1ubuntu1_s390x.deb ... 189s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu1) ... 189s Selecting previously unselected package libjpeg-turbo8:s390x. 189s Preparing to unpack .../53-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 189s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 189s Selecting previously unselected package libjpeg8:s390x. 189s Preparing to unpack .../54-libjpeg8_8c-2ubuntu11_s390x.deb ... 189s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 189s Selecting previously unselected package libdeflate0:s390x. 189s Preparing to unpack .../55-libdeflate0_1.19-1_s390x.deb ... 189s Unpacking libdeflate0:s390x (1.19-1) ... 189s Selecting previously unselected package libjbig0:s390x. 189s Preparing to unpack .../56-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 189s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 189s Selecting previously unselected package libsharpyuv0:s390x. 189s Preparing to unpack .../57-libsharpyuv0_1.3.2-0.4build2_s390x.deb ... 189s Unpacking libsharpyuv0:s390x (1.3.2-0.4build2) ... 189s Selecting previously unselected package libwebp7:s390x. 189s Preparing to unpack .../58-libwebp7_1.3.2-0.4build2_s390x.deb ... 189s Unpacking libwebp7:s390x (1.3.2-0.4build2) ... 189s Selecting previously unselected package libtiff6:s390x. 189s Preparing to unpack .../59-libtiff6_4.5.1+git230720-4ubuntu1_s390x.deb ... 189s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu1) ... 189s Selecting previously unselected package libxpm4:s390x. 189s Preparing to unpack .../60-libxpm4_1%3a3.5.17-1build1_s390x.deb ... 189s Unpacking libxpm4:s390x (1:3.5.17-1build1) ... 189s Selecting previously unselected package libgd3:s390x. 189s Preparing to unpack .../61-libgd3_2.3.3-9ubuntu3_s390x.deb ... 189s Unpacking libgd3:s390x (2.3.3-9ubuntu3) ... 189s Selecting previously unselected package libc-devtools. 189s Preparing to unpack .../62-libc-devtools_2.39-0ubuntu6_s390x.deb ... 189s Unpacking libc-devtools (2.39-0ubuntu6) ... 189s Selecting previously unselected package linux-libc-dev:s390x. 189s Preparing to unpack .../63-linux-libc-dev_6.8.0-20.20_s390x.deb ... 189s Unpacking linux-libc-dev:s390x (6.8.0-20.20) ... 189s Selecting previously unselected package libcrypt-dev:s390x. 189s Preparing to unpack .../64-libcrypt-dev_1%3a4.4.36-4_s390x.deb ... 189s Unpacking libcrypt-dev:s390x (1:4.4.36-4) ... 190s Selecting previously unselected package rpcsvc-proto. 190s Preparing to unpack .../65-rpcsvc-proto_1.4.2-0ubuntu6_s390x.deb ... 190s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 190s Selecting previously unselected package libc6-dev:s390x. 190s Preparing to unpack .../66-libc6-dev_2.39-0ubuntu6_s390x.deb ... 190s Unpacking libc6-dev:s390x (2.39-0ubuntu6) ... 190s Preparing to unpack .../67-libevent-core-2.1-7_2.1.12-stable-9build1_s390x.deb ... 190s Unpacking libevent-core-2.1-7:s390x (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 190s Preparing to unpack .../68-libldap-common_2.6.7+dfsg-1~exp1ubuntu6_all.deb ... 190s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 190s Selecting previously unselected package linux-modules-6.8.0-20-generic. 190s Preparing to unpack .../69-linux-modules-6.8.0-20-generic_6.8.0-20.20_s390x.deb ... 190s Unpacking linux-modules-6.8.0-20-generic (6.8.0-20.20) ... 190s Selecting previously unselected package linux-image-6.8.0-20-generic. 190s Preparing to unpack .../70-linux-image-6.8.0-20-generic_6.8.0-20.20_s390x.deb ... 190s Unpacking linux-image-6.8.0-20-generic (6.8.0-20.20) ... 190s Selecting previously unselected package linux-modules-extra-6.8.0-20-generic. 190s Preparing to unpack .../71-linux-modules-extra-6.8.0-20-generic_6.8.0-20.20_s390x.deb ... 190s Unpacking linux-modules-extra-6.8.0-20-generic (6.8.0-20.20) ... 190s Preparing to unpack .../72-linux-generic_6.8.0-20.20+1_s390x.deb ... 190s Unpacking linux-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 190s Preparing to unpack .../73-linux-image-generic_6.8.0-20.20+1_s390x.deb ... 190s Unpacking linux-image-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 190s Preparing to unpack .../74-linux-virtual_6.8.0-20.20+1_s390x.deb ... 190s Unpacking linux-virtual (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 190s Preparing to unpack .../75-linux-image-virtual_6.8.0-20.20+1_s390x.deb ... 190s Unpacking linux-image-virtual (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 190s Preparing to unpack .../76-linux-headers-virtual_6.8.0-20.20+1_s390x.deb ... 190s Unpacking linux-headers-virtual (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 190s Selecting previously unselected package linux-headers-6.8.0-20. 190s Preparing to unpack .../77-linux-headers-6.8.0-20_6.8.0-20.20_all.deb ... 190s Unpacking linux-headers-6.8.0-20 (6.8.0-20.20) ... 192s Selecting previously unselected package linux-headers-6.8.0-20-generic. 192s Preparing to unpack .../78-linux-headers-6.8.0-20-generic_6.8.0-20.20_s390x.deb ... 192s Unpacking linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 193s Preparing to unpack .../79-linux-headers-generic_6.8.0-20.20+1_s390x.deb ... 193s Unpacking linux-headers-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 193s Selecting previously unselected package linux-tools-common. 193s Preparing to unpack .../80-linux-tools-common_6.8.0-20.20_all.deb ... 193s Unpacking linux-tools-common (6.8.0-20.20) ... 193s Selecting previously unselected package linux-tools-6.8.0-20. 193s Preparing to unpack .../81-linux-tools-6.8.0-20_6.8.0-20.20_s390x.deb ... 193s Unpacking linux-tools-6.8.0-20 (6.8.0-20.20) ... 193s Selecting previously unselected package linux-tools-6.8.0-20-generic. 193s Preparing to unpack .../82-linux-tools-6.8.0-20-generic_6.8.0-20.20_s390x.deb ... 193s Unpacking linux-tools-6.8.0-20-generic (6.8.0-20.20) ... 193s Selecting previously unselected package manpages-dev. 193s Preparing to unpack .../83-manpages-dev_6.05.01-1_all.deb ... 193s Unpacking manpages-dev (6.05.01-1) ... 193s Preparing to unpack .../84-python3-distutils_3.12.2-3ubuntu1.1_all.deb ... 193s Unpacking python3-distutils (3.12.2-3ubuntu1.1) over (3.11.5-1) ... 193s Preparing to unpack .../85-python3-lib2to3_3.12.2-3ubuntu1.1_all.deb ... 193s Unpacking python3-lib2to3 (3.12.2-3ubuntu1.1) over (3.11.5-1) ... 193s Preparing to unpack .../86-python3-pyrsistent_0.20.0-1build1_s390x.deb ... 193s Unpacking python3-pyrsistent:s390x (0.20.0-1build1) over (0.20.0-1) ... 193s Preparing to unpack .../87-python3-typing-extensions_4.10.0-1_all.deb ... 194s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ... 194s Preparing to unpack .../88-s390-tools-data_2.31.0-0ubuntu3_all.deb ... 194s Unpacking s390-tools-data (2.31.0-0ubuntu3) over (2.31.0-0ubuntu1) ... 194s Selecting previously unselected package ubuntu-kernel-accessories. 194s Preparing to unpack .../89-ubuntu-kernel-accessories_1.536build1_s390x.deb ... 194s Unpacking ubuntu-kernel-accessories (1.536build1) ... 194s Preparing to unpack .../90-kpartx_0.9.4-5ubuntu6_s390x.deb ... 194s Unpacking kpartx (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ... 194s Setting up pinentry-curses (1.2.1-3ubuntu4) ... 194s Setting up motd-news-config (13ubuntu8) ... 194s Setting up libtext-iconv-perl:s390x (1.7-8build2) ... 194s Setting up libtext-charwidth-perl:s390x (0.04-11build2) ... 194s Setting up libsharpyuv0:s390x (1.3.2-0.4build2) ... 194s Setting up liburcu8t64:s390x (0.14.0-3.1) ... 194s Setting up tcpdump (4.99.4-3ubuntu2) ... 194s Setting up libibverbs1:s390x (50.0-2build1) ... 194s Setting up ubuntu-kernel-accessories (1.536build1) ... 194s Setting up libapparmor1:s390x (4.0.0-beta3-0ubuntu2) ... 194s Setting up libatm1t64:s390x (1:2.5.1-5.1) ... 194s Setting up libgdbm6t64:s390x (1.23-5.1) ... 194s Setting up bsdextrautils (2.39.3-9ubuntu2) ... 194s Setting up libxpm4:s390x (1:3.5.17-1build1) ... 194s Setting up libgdbm-compat4t64:s390x (1.23-5.1) ... 194s Setting up xdg-user-dirs (0.18-1) ... 194s Setting up ibverbs-providers:s390x (50.0-2build1) ... 194s Setting up linux-headers-6.8.0-20 (6.8.0-20.20) ... 194s Setting up libmagic-mgc (1:5.45-3) ... 194s Setting up gawk (1:5.2.1-2build2) ... 194s Setting up manpages (6.05.01-1) ... 194s Setting up libtirpc-common (1.3.4+ds-1.1) ... 194s Setting up libbrotli1:s390x (1.1.0-2build1) ... 194s Setting up libsqlite3-0:s390x (3.45.1-1ubuntu1) ... 194s Setting up libsasl2-modules:s390x (2.1.28+dfsg1-5ubuntu1) ... 194s Setting up libuv1t64:s390x (1.48.0-1.1) ... 194s Setting up libmagic1t64:s390x (1:5.45-3) ... 194s Setting up rsyslog (8.2312.0-3ubuntu7) ... 194s info: The user `syslog' is already a member of `adm'. 195s Setting up libpsl5t64:s390x (0.21.2-1.1) ... 195s Setting up libnghttp2-14:s390x (1.59.0-1build1) ... 195s Setting up libdeflate0:s390x (1.19-1) ... 195s Setting up linux-libc-dev:s390x (6.8.0-20.20) ... 195s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ... 195s Setting up systemd-dev (255.4-1ubuntu5) ... 195s Setting up libparted2t64:s390x (3.6-3.1build2) ... 195s Setting up krb5-locales (1.20.1-6ubuntu1) ... 195s Setting up file (1:5.45-3) ... 195s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ... 195s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ... 195s Setting up libprotobuf-c1:s390x (1.4.1-1ubuntu3) ... 195s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ... 195s Setting up xxd (2:9.1.0016-1ubuntu6) ... 195s Setting up libelf1t64:s390x (0.190-1.1build2) ... 195s Setting up libkrb5support0:s390x (1.20.1-6ubuntu1) ... 195s Setting up libdw1t64:s390x (0.190-1.1build2) ... 195s Setting up linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 195s Setting up eject (2.39.3-9ubuntu2) ... 195s Setting up apparmor (4.0.0-beta3-0ubuntu2) ... 195s Installing new version of config file /etc/apparmor.d/abstractions/authentication ... 195s Installing new version of config file /etc/apparmor.d/abstractions/crypto ... 195s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ... 195s Installing new version of config file /etc/apparmor.d/abstractions/openssl ... 195s Installing new version of config file /etc/apparmor.d/code ... 195s Installing new version of config file /etc/apparmor.d/firefox ... 196s Reloading AppArmor profiles 196s Setting up libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ... 196s No schema files found: doing nothing. 196s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 196s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 196s Setting up vim-common (2:9.1.0016-1ubuntu6) ... 196s Setting up libqrtr-glib0:s390x (1.2.2-1ubuntu3) ... 196s Setting up libslang2:s390x (2.3.3-3build1) ... 196s Setting up libnvme1t64 (1.8-3) ... 196s Setting up mtr-tiny (0.95-1.1build1) ... 196s Setting up gnupg-l10n (2.4.4-2ubuntu15) ... 196s Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build6) ... 196s Setting up libdbus-1-3:s390x (1.14.10-4ubuntu2) ... 196s Setting up xz-utils (5.6.0-0.2) ... 196s Setting up perl-modules-5.38 (5.38.2-3.2) ... 196s Setting up libproc2-0:s390x (2:4.0.4-4ubuntu2) ... 196s Setting up fonts-dejavu-mono (2.37-8) ... 196s Setting up libpng16-16t64:s390x (1.6.43-3) ... 196s Setting up libevent-core-2.1-7:s390x (2.1.12-stable-9build1) ... 196s Setting up libss2:s390x (1.47.0-2.4~exp1ubuntu2) ... 196s Setting up usb.ids (2024.03.18-1) ... 196s Setting up sudo (1.9.15p5-3ubuntu3) ... 196s Setting up fonts-dejavu-core (2.37-8) ... 196s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ... 196s Setting up gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) ... 196s Setting up libk5crypto3:s390x (1.20.1-6ubuntu1) ... 196s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 196s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ... 196s Setting up libwebp7:s390x (1.3.2-0.4build2) ... 196s Setting up libfdisk1:s390x (2.39.3-9ubuntu2) ... 196s Setting up libdb5.3t64:s390x (5.3.28+dfsg2-6) ... 196s Setting up libaio1t64:s390x (0.3.113-6) ... 196s Setting up python-apt-common (2.7.7) ... 196s Setting up mount (2.39.3-9ubuntu2) ... 196s Setting up uuid-runtime (2.39.3-9ubuntu2) ... 197s uuidd.service is a disabled or a static unit not running, not starting it. 197s Setting up libmm-glib0:s390x (1.23.4-0ubuntu1) ... 197s Setting up groff-base (1.23.0-3build1) ... 197s Setting up libcrypt-dev:s390x (1:4.4.36-4) ... 197s Setting up libplymouth5:s390x (24.004.60-1ubuntu6) ... 197s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ... 197s Setting up procps (2:4.0.4-4ubuntu2) ... 198s Setting up gpgconf (2.4.4-2ubuntu15) ... 198s Setting up libcryptsetup12:s390x (2:2.7.0-1ubuntu2) ... 198s Setting up libgirepository-1.0-1:s390x (1.79.1-1ubuntu6) ... 198s Setting up libjson-glib-1.0-common (1.8.0-2build1) ... 198s Setting up libkrb5-3:s390x (1.20.1-6ubuntu1) ... 198s Setting up libpython3.11-minimal:s390x (3.11.8-1build4) ... 198s Setting up libperl5.38t64:s390x (5.38.2-3.2) ... 198s Setting up tnftp (20230507-2build1) ... 198s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ... 198s Setting up libfido2-1:s390x (1.14.0-1build1) ... 198s Setting up libc-dev-bin (2.39-0ubuntu6) ... 198s Setting up openssl (3.0.13-0ubuntu2) ... 198s Setting up linux-modules-6.8.0-20-generic (6.8.0-20.20) ... 198s Setting up readline-common (8.2-4) ... 198s Setting up libxml2:s390x (2.9.14+dfsg-1.3ubuntu2) ... 198s Setting up libxmuu1:s390x (2:1.1.3-3build1) ... 198s Setting up dbus-bin (1.14.10-4ubuntu2) ... 198s Setting up info (7.1-3build1) ... 198s Setting up liblocale-gettext-perl (1.07-6ubuntu4) ... 198s Setting up gpg (2.4.4-2ubuntu15) ... 198s Setting up libgudev-1.0-0:s390x (1:238-3ubuntu2) ... 198s Setting up libpolkit-gobject-1-0:s390x (124-1ubuntu1) ... 198s Setting up libbpf1:s390x (1:1.3.0-2build1) ... 198s Setting up libmbim-glib4:s390x (1.31.2-0ubuntu2) ... 198s Setting up rsync (3.2.7-1build1) ... 199s rsync.service is a disabled or a static unit not running, not starting it. 199s Setting up libudisks2-0:s390x (2.10.1-6) ... 199s Setting up libkmod2:s390x (31+20240202-2ubuntu4) ... 199s Setting up bolt (0.9.6-2build1) ... 199s bolt.service is a disabled or a static unit not running, not starting it. 199s Setting up s390-tools-data (2.31.0-0ubuntu3) ... 199s Setting up libllvm18:s390x (1:18.1.2-1ubuntu2) ... 199s Setting up gnupg-utils (2.4.4-2ubuntu15) ... 199s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 199s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ... 199s Setting up python3.11-minimal (3.11.8-1build4) ... 200s Setting up libclang1-18 (1:18.1.2-1ubuntu2) ... 200s Setting up manpages-dev (6.05.01-1) ... 200s Setting up linux-modules-extra-6.8.0-20-generic (6.8.0-20.20) ... 200s Setting up apt-utils (2.7.14) ... 200s Setting up gpg-agent (2.4.4-2ubuntu15) ... 201s Setting up libpython3.12-stdlib:s390x (3.12.2-4build3) ... 201s Setting up wget (1.21.4-1ubuntu2) ... 201s Setting up fontconfig-config (2.15.0-1.1ubuntu1) ... 201s Setting up libxmlb2:s390x (0.3.15-1build1) ... 201s Setting up btrfs-progs (6.6.3-1.1build1) ... 201s Setting up libpython3.11-stdlib:s390x (3.11.8-1build4) ... 201s Setting up python3.12 (3.12.2-4build3) ... 202s Setting up gpgsm (2.4.4-2ubuntu15) ... 202s Setting up inetutils-telnet (2:2.5-3ubuntu3) ... 202s Setting up parted (3.6-3.1build2) ... 202s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ... 202s update-initramfs: deferring update (trigger activated) 203s e2scrub_all.service is a disabled or a static unit not running, not starting it. 203s Setting up linux-headers-generic (6.8.0-20.20+1) ... 203s Setting up dbus-daemon (1.14.10-4ubuntu2) ... 203s Setting up libmbim-proxy (1.31.2-0ubuntu2) ... 203s Setting up vim-tiny (2:9.1.0016-1ubuntu6) ... 203s Setting up kmod (31+20240202-2ubuntu4) ... 203s Setting up libnetplan1:s390x (1.0-1) ... 203s Setting up man-db (2.12.0-3build4) ... 203s Updating database of manual pages ... 205s man-db.service is a disabled or a static unit not running, not starting it. 205s Setting up fdisk (2.39.3-9ubuntu2) ... 205s Setting up libjson-glib-1.0-0:s390x (1.8.0-2build1) ... 205s Setting up libsasl2-modules-db:s390x (2.1.28+dfsg1-5ubuntu1) ... 205s Setting up hwdata (0.379-1) ... 205s Setting up perl (5.38.2-3.2) ... 205s Setting up libfreetype6:s390x (2.13.2+dfsg-1build2) ... 205s Setting up gir1.2-girepository-2.0:s390x (1.79.1-1ubuntu6) ... 205s Setting up dbus (1.14.10-4ubuntu2) ... 205s A reboot is required to replace the running dbus-daemon. 205s Please reboot the system when convenient. 205s Setting up shared-mime-info (2.4-1build1) ... 206s Setting up libblockdev-utils3:s390x (3.1.0-1build1) ... 206s Setting up libgssapi-krb5-2:s390x (1.20.1-6ubuntu1) ... 206s Setting up libsystemd-shared:s390x (255.4-1ubuntu5) ... 206s Setting up ftp (20230507-2build1) ... 206s Setting up keyboxd (2.4.4-2ubuntu15) ... 206s Setting up libdpkg-perl (1.22.6ubuntu5) ... 206s Setting up libsasl2-2:s390x (2.1.28+dfsg1-5ubuntu1) ... 206s Setting up libssh-4:s390x (0.10.6-2build1) ... 206s Setting up libblockdev-nvme3:s390x (3.1.0-1build1) ... 206s Setting up libblockdev-fs3:s390x (3.1.0-1build1) ... 206s Setting up ieee-data (20220827.1) ... 206s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu1) ... 206s Setting up libpolkit-agent-1-0:s390x (124-1ubuntu1) ... 206s Setting up libc6-dev:s390x (2.39-0ubuntu6) ... 206s Setting up libgpgme11t64:s390x (1.18.0-4.1ubuntu3) ... 206s Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu1) ... 206s Setting up libclang-cpp18 (1:18.1.2-1ubuntu2) ... 206s Setting up libbpfcc:s390x (0.29.1+ds-1ubuntu4) ... 206s Setting up linux-tools-common (6.8.0-20.20) ... 206s Setting up libarchive13t64:s390x (3.7.2-1.1ubuntu2) ... 206s Setting up libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu6) ... 206s Setting up libpython3-stdlib:s390x (3.12.2-0ubuntu1) ... 206s Setting up python3.11 (3.11.8-1build4) ... 207s Setting up telnet (0.17+2.5-3ubuntu3) ... 207s Setting up libblockdev-mdraid3:s390x (3.1.0-1build1) ... 207s Setting up linux-headers-virtual (6.8.0-20.20+1) ... 207s Setting up libcurl4t64:s390x (8.5.0-2ubuntu8) ... 207s Setting up bpftrace (0.20.2-1ubuntu1) ... 207s Setting up bind9-libs:s390x (1:9.18.24-0ubuntu3) ... 207s Setting up linux-image-6.8.0-20-generic (6.8.0-20.20) ... 207s I: /boot/vmlinuz is now a symlink to vmlinuz-6.8.0-20-generic 207s I: /boot/initrd.img is now a symlink to initrd.img-6.8.0-20-generic 207s Setting up libtirpc3t64:s390x (1.3.4+ds-1.1) ... 207s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ... 207s Setting up libblockdev-swap3:s390x (3.1.0-1build1) ... 207s Setting up iproute2 (6.1.0-1ubuntu5) ... 208s Setting up openssh-client (1:9.6p1-3ubuntu11) ... 208s Setting up libgusb2:s390x (0.4.8-1build1) ... 208s Setting up libblockdev-loop3:s390x (3.1.0-1build1) ... 208s Setting up libcurl3t64-gnutls:s390x (8.5.0-2ubuntu8) ... 208s Setting up libqmi-glib5:s390x (1.35.2-0ubuntu1) ... 208s Setting up linux-tools-6.8.0-20 (6.8.0-20.20) ... 208s Setting up python3 (3.12.2-0ubuntu1) ... 208s Setting up systemd (255.4-1ubuntu5) ... 209s Setting up libblockdev3:s390x (3.1.0-1build1) ... 209s Setting up libjcat1:s390x (0.2.0-2build2) ... 209s Setting up dpkg-dev (1.22.6ubuntu5) ... 209s Setting up libblockdev-part3:s390x (3.1.0-1build1) ... 209s Setting up dirmngr (2.4.4-2ubuntu15) ... 209s Setting up linux-tools-6.8.0-20-generic (6.8.0-20.20) ... 209s Setting up python3-cryptography (41.0.7-4build2) ... 209s Setting up python3-gi (3.47.0-3build1) ... 209s Setting up libgd3:s390x (2.3.3-9ubuntu3) ... 209s Setting up systemd-timesyncd (255.4-1ubuntu5) ... 210s Setting up udev (255.4-1ubuntu5) ... 210s Setting up python3-typing-extensions (4.10.0-1) ... 211s Setting up lsof (4.95.0-1build2) ... 211s Setting up python3-pyrsistent:s390x (0.20.0-1build1) ... 211s Setting up python3-netaddr (0.8.0-2ubuntu1) ... 211s Setting up kpartx (0.9.4-5ubuntu6) ... 211s Setting up libnsl2:s390x (1.3.0-3build2) ... 211s Setting up gnupg (2.4.4-2ubuntu15) ... 211s Setting up python3-netplan (1.0-1) ... 211s Setting up curl (8.5.0-2ubuntu8) ... 211s Setting up libvolume-key1:s390x (0.3.12-7build1) ... 211s Setting up linux-image-virtual (6.8.0-20.20+1) ... 211s Setting up netplan-generator (1.0-1) ... 211s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 211s Setting up bind9-host (1:9.18.24-0ubuntu3) ... 211s Setting up python3-lib2to3 (3.12.2-3ubuntu1.1) ... 211s Setting up python3-bpfcc (0.29.1+ds-1ubuntu4) ... 211s Setting up libc-devtools (2.39-0ubuntu6) ... 211s Setting up systemd-resolved (255.4-1ubuntu5) ... 212s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... 212s Setting up python3-distutils (3.12.2-3ubuntu1.1) ... 212s python3.12: can't get files for byte-compilation 212s Setting up openssh-sftp-server (1:9.6p1-3ubuntu11) ... 212s Setting up linux-image-generic (6.8.0-20.20+1) ... 212s Setting up systemd-sysv (255.4-1ubuntu5) ... 212s Setting up python3-dbus (1.3.2-5build2) ... 212s Setting up python3-setuptools (68.1.2-2ubuntu1) ... 213s Setting up gpg-wks-client (2.4.4-2ubuntu15) ... 213s Setting up openssh-server (1:9.6p1-3ubuntu11) ... 213s Replacing config file /etc/ssh/sshd_config with new version 215s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket. 216s Setting up linux-generic (6.8.0-20.20+1) ... 216s Setting up libblockdev-crypto3:s390x (3.1.0-1build1) ... 216s Setting up python3-gdbm:s390x (3.12.2-3ubuntu1.1) ... 216s Setting up plymouth (24.004.60-1ubuntu6) ... 216s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 216s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 220s Not invoking zipl: initrd doesn't exist yet 220s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 220s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 220s Setting up python3-apt (2.7.7) ... 221s Setting up libfwupd2:s390x (1.9.15-2) ... 221s Setting up libnss-systemd:s390x (255.4-1ubuntu5) ... 221s Setting up python3-yaml (6.0.1-2build1) ... 221s Setting up libqmi-proxy (1.35.2-0ubuntu1) ... 221s Setting up multipath-tools (0.9.4-5ubuntu6) ... 221s Setting up netplan.io (1.0-1) ... 221s Setting up linux-virtual (6.8.0-20.20+1) ... 221s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) ... 221s update-initramfs: deferring update (trigger activated) 221s Setting up bpfcc-tools (0.29.1+ds-1ubuntu4) ... 221s Setting up libpam-systemd:s390x (255.4-1ubuntu5) ... 222s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ... 222s Setting up ubuntu-pro-client (31.2.2) ... 223s Setting up fwupd (1.9.15-2) ... 223s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 223s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 223s fwupd.service is a disabled or a static unit not running, not starting it. 224s Setting up ubuntu-pro-client-l10n (31.2.2) ... 224s Setting up udisks2 (2.10.1-6) ... 224s Setting up dbus-user-session (1.14.10-4ubuntu2) ... 224s Processing triggers for install-info (7.1-3build1) ... 224s Processing triggers for initramfs-tools (0.142ubuntu23) ... 224s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 224s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 228s Not invoking zipl: initrd doesn't exist yet 228s Processing triggers for libc-bin (2.39-0ubuntu6) ... 228s Processing triggers for ufw (0.36.2-5) ... 228s Processing triggers for debianutils (5.17) ... 228s Processing triggers for linux-image-6.8.0-20-generic (6.8.0-20.20) ... 228s /etc/kernel/postinst.d/initramfs-tools: 228s update-initramfs: Generating /boot/initrd.img-6.8.0-20-generic 228s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 231s Using config file '/etc/zipl.conf' 231s Building bootmap in '/boot' 231s Adding IPL section 'ubuntu' (default) 231s Preparing boot device for LD-IPL: vda (0000). 231s Done. 231s /etc/kernel/postinst.d/zz-zipl: 231s Using config file '/etc/zipl.conf' 231s Building bootmap in '/boot' 231s Adding IPL section 'ubuntu' (default) 231s Preparing boot device for LD-IPL: vda (0000). 231s Done. 233s Reading package lists... 233s Building dependency tree... 233s Reading state information... 233s The following packages will be REMOVED: 233s libaio1* libnetplan0* python3-distutils* python3-lib2to3* 233s 0 upgraded, 0 newly installed, 4 to remove and 1 not upgraded. 233s After this operation, 1445 kB disk space will be freed. 234s (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 ... 81786 files and directories currently installed.) 234s Removing libaio1:s390x (0.3.113-5) ... 234s Removing libnetplan0:s390x (0.107.1-3) ... 234s Removing python3-distutils (3.12.2-3ubuntu1.1) ... 234s Removing python3-lib2to3 (3.12.2-3ubuntu1.1) ... 234s Processing triggers for libc-bin (2.39-0ubuntu6) ... 234s autopkgtest [01:28:20]: rebooting testbed after setup commands that affected boot 266s autopkgtest [01:28:52]: testbed running kernel: Linux 6.8.0-20-generic #20-Ubuntu SMP Mon Mar 18 10:49:25 UTC 2024 269s autopkgtest [01:28:55]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-pscbs 274s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-pscbs 0.66.0-2 (dsc) [2361 B] 274s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-pscbs 0.66.0-2 (tar) [3692 kB] 274s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-pscbs 0.66.0-2 (diff) [3744 B] 274s gpgv: Signature made Mon Nov 1 20:33:04 2021 UTC 274s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 274s gpgv: issuer "nilesh@debian.org" 274s gpgv: Can't check signature: No public key 274s dpkg-source: warning: cannot verify inline signature for ./r-cran-pscbs_0.66.0-2.dsc: no acceptable signature found 274s autopkgtest [01:29:00]: testing package r-cran-pscbs version 0.66.0-2 274s autopkgtest [01:29:00]: build not needed 284s autopkgtest [01:29:10]: test run-unit-test: preparing testbed 287s Reading package lists... 287s Building dependency tree... 287s Reading state information... 287s Starting pkgProblemResolver with broken count: 0 287s Starting 2 pkgProblemResolver with broken count: 0 287s Done 287s The following additional packages will be installed: 287s fontconfig fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax 287s javascript-common libblas3 libcairo2 libdatrie1 libgfortran5 libgomp1 287s libgraphite2-3 libharfbuzz0b libice6 libjs-bootstrap libjs-bootstrap4 287s libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery 287s libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json 287s libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js 287s libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 287s liblua5.4-0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 287s libpaper-utils libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data 287s libthai0 libtk8.6 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 287s libxt6t64 littler node-bootstrap-sass node-html5shiv node-normalize.css 287s pandoc pandoc-data r-base-core r-bioc-aroma.light r-bioc-biocgenerics 287s r-bioc-dnacopy r-cran-acepack r-cran-backports r-cran-base64enc r-cran-bslib 287s r-cran-cachem r-cran-checkmate r-cran-chron r-cran-cli r-cran-cluster 287s r-cran-codetools r-cran-colorspace r-cran-commonmark r-cran-cpp11 287s r-cran-crayon r-cran-data.table r-cran-deldir r-cran-digest r-cran-dplyr 287s r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap 287s r-cran-fontawesome r-cran-foreign r-cran-formula r-cran-fs r-cran-future 287s r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gridextra 287s r-cran-gtable r-cran-highr r-cran-hmisc r-cran-htmltable r-cran-htmltools 287s r-cran-htmlwidgets r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg 287s r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later 287s r-cran-lattice r-cran-latticeextra r-cran-lifecycle r-cran-listenv 287s r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats 287s r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme 287s r-cran-nnet r-cran-parallelly r-cran-pillar r-cran-pkgconfig 287s r-cran-pkgkitten r-cran-png r-cran-promises r-cran-pscbs r-cran-purrr 287s r-cran-r.cache r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 287s r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen 287s r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass 287s r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr 287s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex 287s r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr 287s r-cran-xfun r-cran-xtable r-cran-yaml unzip x11-common xdg-utils zip 287s Suggested packages: 287s apache2 | lighttpd | httpd libjs-jquery-ui-docs fonts-mathjax-extras 287s fonts-stix libjs-mathjax-doc tcl8.6 tk8.6 nodejs texlive-latex-recommended 287s texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context 287s wkhtmltopdf librsvg2-bin groff ghc php python ruby libjs-katex 287s citation-style-language-styles elpa-ess r-doc-info | r-doc-pdf r-mathlib 287s r-base-html r-cran-princurve r-bioc-biobase r-bioc-s4vectors r-bioc-iranges 287s r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools 287s r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-runit 287s r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shinyjs 287s r-cran-polyclip r-cran-covr r-cran-markdown r-cran-sp r-cran-scatterplot3d 287s r-cran-magick r-cran-sf r-cran-testthat r-cran-getopt r-cran-httr 287s r-cran-bit64 r-cran-dbi r-cran-formattable r-cran-nanotime 287s r-cran-palmerpenguins r-cran-units r-cran-vdiffr r-cran-roxygen2 287s r-cran-inline r-cran-bench r-cran-blob r-cran-brio r-cran-callr r-cran-here 287s r-cran-hms r-cran-pkgbuild r-cran-pkgload r-cran-plm r-cran-zoo 287s Recommended packages: 287s node-jquery r-recommended r-base-dev r-doc-html r-cran-curl r-cran-testthat 287s r-cran-thematic r-cran-fastmatch r-cran-devtools r-cran-tinytest 287s r-cran-callr r-cran-covr r-cran-mockery r-cran-processx r-cran-ps 287s r-cran-rprojroot r-cran-whoami r-cran-xml2 r-cran-bench r-cran-brio 287s r-cran-decor r-cran-desc r-cran-lobstr r-cran-progress r-cran-bit64 287s r-cran-bit r-cran-xts r-cran-nanotime r-cran-zoo r-cran-broom r-cran-dbi 287s r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite 287s r-cran-unitizer r-cran-rsvg r-cran-spelling r-cran-rhpcblasctl r-cran-r.rsp 287s r-cran-markdown r-cran-pkgload r-cran-hexbin r-cran-mapproj r-cran-maps 287s r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-sf 287s r-cran-svglite r-cran-vdiffr r-cran-waldo r-cran-testit r-cran-cairo 287s r-cran-httr r-cran-formatr r-cran-gridsvg r-cran-magick r-cran-reticulate 287s r-cran-rgl r-cran-tikzdevice r-cran-webshot node-highlight.js r-cran-lintr 287s r-cran-tidyverse r-cran-r.devices r-cran-lubridate r-cran-usethis 287s r-cran-dygraphs r-cran-rsconnect r-cran-downlit r-cran-dichromat r-cran-hms 287s r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot 287s r-cran-remotes r-cran-renv r-cran-runit libfile-mimeinfo-perl 287s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 287s The following NEW packages will be installed: 288s autopkgtest-satdep fontconfig fonts-font-awesome fonts-glyphicons-halflings 288s fonts-mathjax javascript-common libblas3 libcairo2 libdatrie1 libgfortran5 288s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjs-bootstrap 288s libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery 288s libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json 288s libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js 288s libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 288s liblua5.4-0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 288s libpaper-utils libpaper1 libpixman-1-0 libsm6 libtcl8.6 libthai-data 288s libthai0 libtk8.6 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 288s libxt6t64 littler node-bootstrap-sass node-html5shiv node-normalize.css 288s pandoc pandoc-data r-base-core r-bioc-aroma.light r-bioc-biocgenerics 288s r-bioc-dnacopy r-cran-acepack r-cran-backports r-cran-base64enc r-cran-bslib 288s r-cran-cachem r-cran-checkmate r-cran-chron r-cran-cli r-cran-cluster 288s r-cran-codetools r-cran-colorspace r-cran-commonmark r-cran-cpp11 288s r-cran-crayon r-cran-data.table r-cran-deldir r-cran-digest r-cran-dplyr 288s r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap 288s r-cran-fontawesome r-cran-foreign r-cran-formula r-cran-fs r-cran-future 288s r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gridextra 288s r-cran-gtable r-cran-highr r-cran-hmisc r-cran-htmltable r-cran-htmltools 288s r-cran-htmlwidgets r-cran-httpuv r-cran-interp r-cran-isoband r-cran-jpeg 288s r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-later 288s r-cran-lattice r-cran-latticeextra r-cran-lifecycle r-cran-listenv 288s r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats 288s r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme 288s r-cran-nnet r-cran-parallelly r-cran-pillar r-cran-pkgconfig 288s r-cran-pkgkitten r-cran-png r-cran-promises r-cran-pscbs r-cran-purrr 288s r-cran-r.cache r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 288s r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen 288s r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstudioapi r-cran-sass 288s r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr 288s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex 288s r-cran-utf8 r-cran-vctrs r-cran-viridis r-cran-viridislite r-cran-withr 288s r-cran-xfun r-cran-xtable r-cran-yaml unzip x11-common xdg-utils zip 288s 0 upgraded, 167 newly installed, 0 to remove and 1 not upgraded. 288s Need to get 176 MB/176 MB of archives. 288s After this operation, 608 MB of additional disk space will be used. 288s Get:1 /tmp/autopkgtest.iuHVDJ/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [748 B] 288s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig s390x 2.15.0-1.1ubuntu1 [191 kB] 288s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 288s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 288s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 290s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x javascript-common all 11+nmu1 [5936 B] 290s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 290s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 290s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 290s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 290s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 290s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcairo2 s390x 1.18.0-1ubuntu1 [589 kB] 290s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libdatrie1 s390x 0.2.13-3 [22.6 kB] 290s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240315-1ubuntu1 [600 kB] 291s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240315-1ubuntu1 [151 kB] 291s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 291s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libharfbuzz0b s390x 8.3.0-2build1 [515 kB] 291s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] 291s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libice6 s390x 2:1.0.10-1build2 [40.8 kB] 291s Get:20 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 292s Get:21 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-popper.js all 1.16.1+ds-6 [54.1 kB] 292s Get:22 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB] 292s Get:23 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-d3 all 3.5.17-4 [132 kB] 292s Get:24 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-es5-shim all 4.6.7-2 [39.8 kB] 292s Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 292s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 293s Get:27 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 293s Get:28 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 293s Get:29 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B] 293s Get:30 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 293s Get:31 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 293s Get:32 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-json all 0~20221030+~1.0.8-1 [20.6 kB] 293s Get:33 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB] 293s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 295s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblua5.4-0 s390x 5.4.6-3build1 [179 kB] 296s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libthai-data all 0.1.29-2 [158 kB] 296s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libthai0 s390x 0.1.29-2 [20.6 kB] 296s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpango-1.0-0 s390x 1.52.1+ds-1 [242 kB] 296s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpangoft2-1.0-0 s390x 1.52.1+ds-1 [44.2 kB] 296s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpangocairo-1.0-0 s390x 1.52.1+ds-1 [28.7 kB] 296s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libpaper1 s390x 1.1.29 [13.3 kB] 296s Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libpaper-utils s390x 1.1.29 [8452 B] 296s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libsm6 s390x 2:1.2.3-1build2 [16.9 kB] 296s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtcl8.6 s390x 8.6.14+dfsg-1 [1037 kB] 297s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libxft2 s390x 2.3.6-1 [44.3 kB] 297s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libxss1 s390x 1:1.2.3-1build2 [8192 B] 297s Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libtk8.6 s390x 8.6.14-1 [833 kB] 298s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxt6t64 s390x 1:1.2.1-1.2 [184 kB] 298s Get:49 http://ftpmaster.internal/ubuntu noble/main s390x zip s390x 3.0-13 [175 kB] 298s Get:50 http://ftpmaster.internal/ubuntu noble/main s390x unzip s390x 6.0-28ubuntu3 [180 kB] 299s Get:51 http://ftpmaster.internal/ubuntu noble/main s390x xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 299s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x r-base-core s390x 4.3.3-2build1 [27.1 MB] 317s Get:53 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-littler s390x 0.3.19-1 [93.0 kB] 318s Get:54 http://ftpmaster.internal/ubuntu noble/universe s390x littler all 0.3.19-1 [2472 B] 318s Get:55 http://ftpmaster.internal/ubuntu noble/universe s390x node-bootstrap-sass all 3.4.3-2 [187 kB] 318s Get:56 http://ftpmaster.internal/ubuntu noble/universe s390x node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 318s Get:57 http://ftpmaster.internal/ubuntu noble/universe s390x node-normalize.css all 8.0.1-5 [10.8 kB] 318s Get:58 http://ftpmaster.internal/ubuntu noble/universe s390x pandoc-data all 3.1.3-1 [92.4 kB] 318s Get:59 http://ftpmaster.internal/ubuntu noble/universe s390x pandoc s390x 3.1.3+ds-2 [41.5 MB] 345s Get:60 http://ftpmaster.internal/ubuntu noble/universe s390x r-bioc-biocgenerics all 0.48.1-2 [595 kB] 345s Get:61 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 345s Get:62 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-r.oo all 1.26.0-1 [955 kB] 346s Get:63 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-r.utils all 2.12.3-1 [1386 kB] 347s Get:64 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-matrixstats s390x 1.2.0-1 [513 kB] 348s Get:65 http://ftpmaster.internal/ubuntu noble/universe s390x r-bioc-aroma.light all 3.32.0-1 [576 kB] 348s Get:66 http://ftpmaster.internal/ubuntu noble/universe s390x r-bioc-dnacopy s390x 1.76.0-1 [384 kB] 348s Get:67 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-acepack s390x 1.4.2-1 [68.3 kB] 348s Get:68 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-backports s390x 1.4.1-1 [101 kB] 348s Get:69 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-base64enc s390x 0.1-3-3 [28.0 kB] 348s Get:70 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rlang s390x 1.1.3-1 [1672 kB] 350s Get:71 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-fastmap s390x 1.1.1-1 [69.1 kB] 350s Get:72 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-cachem s390x 1.0.8-1 [72.1 kB] 350s Get:73 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-digest s390x 0.6.34-1 [187 kB] 350s Get:74 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-ellipsis s390x 0.3.2-2 [35.4 kB] 350s Get:75 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-htmltools s390x 0.5.7-1 [368 kB] 350s Get:76 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB] 350s Get:77 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-jsonlite s390x 1.8.8+dfsg-1 [444 kB] 351s Get:78 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-cli s390x 3.6.2-1 [1382 kB] 352s Get:79 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-glue s390x 1.7.0-1 [154 kB] 352s Get:80 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 352s Get:81 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-memoise all 2.0.1-1 [53.9 kB] 352s Get:82 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mime s390x 0.12-1 [35.7 kB] 352s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x r-cran-fs s390x 1.6.3+dfsg-1build1 [229 kB] 352s Get:84 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-r6 all 2.5.1-1 [99.0 kB] 352s Get:85 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rappdirs s390x 0.3.3-1 [47.5 kB] 353s Get:86 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-sass s390x 0.4.8+dfsg-1 [1025 kB] 353s Get:87 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-bslib all 0.6.1+dfsg-1 [5138 kB] 357s Get:88 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-checkmate s390x 2.3.1-1 [716 kB] 357s Get:89 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-chron s390x 2.3-61-2 [186 kB] 357s Get:90 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-cluster s390x 2.1.6-1 [562 kB] 358s Get:91 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-codetools all 0.2-19-1 [90.5 kB] 358s Get:92 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-colorspace s390x 2.1-0+dfsg-1 [1540 kB] 359s Get:93 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-commonmark s390x 1.9.1-1 [142 kB] 359s Get:94 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-cpp11 all 0.4.7-1 [266 kB] 359s Get:95 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-crayon all 1.5.2-1 [164 kB] 359s Get:96 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-data.table s390x 1.14.10+dfsg-1 [1880 kB] 361s Get:97 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-deldir s390x 2.0-4-1 [271 kB] 361s Get:98 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-generics all 0.1.3-1 [81.3 kB] 361s Get:99 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-magrittr s390x 2.0.3-1 [154 kB] 362s Get:100 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-fansi s390x 1.0.5-1 [615 kB] 362s Get:101 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-utf8 s390x 1.2.4-1 [143 kB] 362s Get:102 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-vctrs s390x 0.6.5-1 [1448 kB] 364s Get:103 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 364s Get:104 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 364s Get:105 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-tibble s390x 3.2.1+dfsg-2 [415 kB] 365s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x r-cran-withr all 3.0.0+dfsg-1 [228 kB] 365s Get:107 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-tidyselect s390x 1.2.0+dfsg-1 [218 kB] 365s Get:108 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-dplyr s390x 1.1.4-1 [1515 kB] 366s Get:109 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-evaluate all 0.23-1 [90.2 kB] 366s Get:110 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-farver s390x 2.1.1-1 [1347 kB] 366s Get:111 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-fontawesome all 0.5.2-1 [1300 kB] 366s Get:112 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-foreign s390x 0.8.86-1 [247 kB] 366s Get:113 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-formula all 1.2-5-1 [158 kB] 366s Get:114 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-globals all 0.16.2-1 [117 kB] 366s Get:115 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 366s Get:116 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-parallelly s390x 1.37.1-1 [365 kB] 367s Get:117 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-future all 1.33.1+dfsg-1 [634 kB] 367s Get:118 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 367s Get:119 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-isoband s390x 0.2.7-1 [1481 kB] 367s Get:120 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mass s390x 7.3-60.0.1-1 [1122 kB] 367s Get:121 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-lattice s390x 0.22-5-1 [1341 kB] 367s Get:122 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-nlme s390x 3.1.164-1 [2268 kB] 368s Get:123 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-matrix s390x 1.6-5-1 [3983 kB] 369s Get:124 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB] 370s Get:125 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-labeling all 0.4.3-1 [62.1 kB] 370s Get:126 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-munsell all 0.5.0-2build1 [208 kB] 370s Get:127 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 370s Get:128 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-viridislite all 0.4.2-2 [1088 kB] 370s Get:129 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-scales all 1.3.0-1 [603 kB] 370s Get:130 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 371s Get:131 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-gridextra all 2.3-3build1 [1024 kB] 371s Get:132 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-xfun s390x 0.41+dfsg-1 [415 kB] 372s Get:133 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-highr all 0.10+dfsg-1 [38.3 kB] 372s Get:134 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-survival s390x 3.5-8-1 [6161 kB] 374s Get:135 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rpart s390x 4.1.23-1 [667 kB] 374s Get:136 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-nnet s390x 7.3-19-2 [112 kB] 374s Get:137 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-stringi s390x 1.8.3-1 [885 kB] 374s Get:138 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-stringr all 1.5.1-1 [290 kB] 375s Get:139 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-yaml s390x 2.3.8-1 [127 kB] 375s Get:140 http://ftpmaster.internal/ubuntu noble/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 378s Get:141 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-knitr all 1.45+dfsg-1 [917 kB] 378s Get:142 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-tinytex all 0.49-1 [141 kB] 378s Get:143 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-modernizr all 2.6.2+ds1-5 [48.3 kB] 378s Get:144 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 378s Get:145 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rcpp s390x 1.0.12-1 [1985 kB] 379s Get:146 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-later s390x 1.3.2+dfsg-1 [126 kB] 379s Get:147 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-promises s390x 1.2.1+dfsg-1 [285 kB] 379s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x r-cran-httpuv s390x 1.6.14+dfsg-1build1 [518 kB] 380s Get:149 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-xtable all 1:1.8-4-2 [689 kB] 380s Get:150 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-sourcetools s390x 0.1.7-1-1 [47.1 kB] 380s Get:151 http://ftpmaster.internal/ubuntu noble/universe s390x libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 380s Get:152 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-shiny all 1.8.0+dfsg-1 [2762 kB] 382s Get:153 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rmarkdown all 2.25+dfsg-3 [1481 kB] 382s Get:154 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] 383s Get:155 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rstudioapi all 0.15.0-1 [277 kB] 383s Get:156 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-purrr s390x 1.0.2-1 [501 kB] 383s Get:157 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-tidyr s390x 1.3.1-1 [1157 kB] 384s Get:158 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-htmltable all 2.4.2-1 [381 kB] 384s Get:159 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-viridis all 0.6.5-1 [2770 kB] 385s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x r-cran-png s390x 0.1-8-1build1 [41.6 kB] 385s Get:161 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-jpeg s390x 0.1-10-1 [31.3 kB] 385s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x r-cran-rcppeigen s390x 0.3.4.0.0-1 [1428 kB] 387s Get:163 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-interp s390x 1.1-6-1 [1465 kB] 387s Get:164 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-latticeextra all 0.6-30-1 [2198 kB] 388s Get:165 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-hmisc s390x 5.1-1-1 [3488 kB] 390s Get:166 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-r.cache all 0.16.0-1 [113 kB] 390s Get:167 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-pscbs all 0.66.0-2 [4345 kB] 393s Preconfiguring packages ... 393s Fetched 176 MB in 1min 45s (1672 kB/s) 393s Selecting previously unselected package fontconfig. 394s (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 ... 81562 files and directories currently installed.) 394s Preparing to unpack .../000-fontconfig_2.15.0-1.1ubuntu1_s390x.deb ... 394s Unpacking fontconfig (2.15.0-1.1ubuntu1) ... 394s Selecting previously unselected package fonts-font-awesome. 394s Preparing to unpack .../001-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 394s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 394s Selecting previously unselected package fonts-glyphicons-halflings. 394s Preparing to unpack .../002-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 394s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 394s Selecting previously unselected package fonts-mathjax. 394s Preparing to unpack .../003-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 394s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 394s Selecting previously unselected package javascript-common. 394s Preparing to unpack .../004-javascript-common_11+nmu1_all.deb ... 394s Unpacking javascript-common (11+nmu1) ... 394s Selecting previously unselected package libblas3:s390x. 394s Preparing to unpack .../005-libblas3_3.12.0-3_s390x.deb ... 394s Unpacking libblas3:s390x (3.12.0-3) ... 394s Selecting previously unselected package libpixman-1-0:s390x. 394s Preparing to unpack .../006-libpixman-1-0_0.42.2-1_s390x.deb ... 394s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 394s Selecting previously unselected package libxcb-render0:s390x. 394s Preparing to unpack .../007-libxcb-render0_1.15-1_s390x.deb ... 394s Unpacking libxcb-render0:s390x (1.15-1) ... 394s Selecting previously unselected package libxcb-shm0:s390x. 394s Preparing to unpack .../008-libxcb-shm0_1.15-1_s390x.deb ... 394s Unpacking libxcb-shm0:s390x (1.15-1) ... 394s Selecting previously unselected package libxrender1:s390x. 394s Preparing to unpack .../009-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 394s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 394s Selecting previously unselected package libcairo2:s390x. 394s Preparing to unpack .../010-libcairo2_1.18.0-1ubuntu1_s390x.deb ... 394s Unpacking libcairo2:s390x (1.18.0-1ubuntu1) ... 394s Selecting previously unselected package libdatrie1:s390x. 394s Preparing to unpack .../011-libdatrie1_0.2.13-3_s390x.deb ... 394s Unpacking libdatrie1:s390x (0.2.13-3) ... 394s Selecting previously unselected package libgfortran5:s390x. 394s Preparing to unpack .../012-libgfortran5_14-20240315-1ubuntu1_s390x.deb ... 394s Unpacking libgfortran5:s390x (14-20240315-1ubuntu1) ... 394s Selecting previously unselected package libgomp1:s390x. 394s Preparing to unpack .../013-libgomp1_14-20240315-1ubuntu1_s390x.deb ... 394s Unpacking libgomp1:s390x (14-20240315-1ubuntu1) ... 394s Selecting previously unselected package libgraphite2-3:s390x. 394s Preparing to unpack .../014-libgraphite2-3_1.3.14-2_s390x.deb ... 394s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 394s Selecting previously unselected package libharfbuzz0b:s390x. 394s Preparing to unpack .../015-libharfbuzz0b_8.3.0-2build1_s390x.deb ... 394s Unpacking libharfbuzz0b:s390x (8.3.0-2build1) ... 394s Selecting previously unselected package x11-common. 394s Preparing to unpack .../016-x11-common_1%3a7.7+23ubuntu2_all.deb ... 394s Unpacking x11-common (1:7.7+23ubuntu2) ... 394s Selecting previously unselected package libice6:s390x. 394s Preparing to unpack .../017-libice6_2%3a1.0.10-1build2_s390x.deb ... 394s Unpacking libice6:s390x (2:1.0.10-1build2) ... 394s Selecting previously unselected package libjs-bootstrap. 394s Preparing to unpack .../018-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 394s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 394s Selecting previously unselected package libjs-popper.js. 394s Preparing to unpack .../019-libjs-popper.js_1.16.1+ds-6_all.deb ... 394s Unpacking libjs-popper.js (1.16.1+ds-6) ... 394s Selecting previously unselected package libjs-bootstrap4. 394s Preparing to unpack .../020-libjs-bootstrap4_4.6.1+dfsg1-4_all.deb ... 394s Unpacking libjs-bootstrap4 (4.6.1+dfsg1-4) ... 394s Selecting previously unselected package libjs-d3. 394s Preparing to unpack .../021-libjs-d3_3.5.17-4_all.deb ... 394s Unpacking libjs-d3 (3.5.17-4) ... 394s Selecting previously unselected package libjs-es5-shim. 394s Preparing to unpack .../022-libjs-es5-shim_4.6.7-2_all.deb ... 394s Unpacking libjs-es5-shim (4.6.7-2) ... 394s Selecting previously unselected package libjs-highlight.js. 394s Preparing to unpack .../023-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 394s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 394s Selecting previously unselected package libjs-jquery. 394s Preparing to unpack .../024-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 394s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 394s Selecting previously unselected package libjs-jquery-datatables. 394s Preparing to unpack .../025-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 394s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 394s Selecting previously unselected package libjs-sifter.js. 394s Preparing to unpack .../026-libjs-sifter.js_0.6.0+dfsg-3_all.deb ... 394s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ... 394s Selecting previously unselected package libjs-microplugin.js. 394s Preparing to unpack .../027-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ... 394s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ... 394s Selecting previously unselected package libjs-jquery-selectize.js. 394s Preparing to unpack .../028-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ... 394s Unpacking libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 394s Selecting previously unselected package libjs-jquery-ui. 394s Preparing to unpack .../029-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 394s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 395s Selecting previously unselected package libjs-json. 395s Preparing to unpack .../030-libjs-json_0~20221030+~1.0.8-1_all.deb ... 395s Unpacking libjs-json (0~20221030+~1.0.8-1) ... 395s Selecting previously unselected package libjs-prettify. 395s Preparing to unpack .../031-libjs-prettify_2015.12.04+dfsg-1.1_all.deb ... 395s Unpacking libjs-prettify (2015.12.04+dfsg-1.1) ... 395s Selecting previously unselected package liblapack3:s390x. 395s Preparing to unpack .../032-liblapack3_3.12.0-3_s390x.deb ... 395s Unpacking liblapack3:s390x (3.12.0-3) ... 395s Selecting previously unselected package liblua5.4-0:s390x. 395s Preparing to unpack .../033-liblua5.4-0_5.4.6-3build1_s390x.deb ... 395s Unpacking liblua5.4-0:s390x (5.4.6-3build1) ... 395s Selecting previously unselected package libthai-data. 395s Preparing to unpack .../034-libthai-data_0.1.29-2_all.deb ... 395s Unpacking libthai-data (0.1.29-2) ... 395s Selecting previously unselected package libthai0:s390x. 395s Preparing to unpack .../035-libthai0_0.1.29-2_s390x.deb ... 395s Unpacking libthai0:s390x (0.1.29-2) ... 395s Selecting previously unselected package libpango-1.0-0:s390x. 395s Preparing to unpack .../036-libpango-1.0-0_1.52.1+ds-1_s390x.deb ... 395s Unpacking libpango-1.0-0:s390x (1.52.1+ds-1) ... 395s Selecting previously unselected package libpangoft2-1.0-0:s390x. 395s Preparing to unpack .../037-libpangoft2-1.0-0_1.52.1+ds-1_s390x.deb ... 395s Unpacking libpangoft2-1.0-0:s390x (1.52.1+ds-1) ... 395s Selecting previously unselected package libpangocairo-1.0-0:s390x. 395s Preparing to unpack .../038-libpangocairo-1.0-0_1.52.1+ds-1_s390x.deb ... 395s Unpacking libpangocairo-1.0-0:s390x (1.52.1+ds-1) ... 395s Selecting previously unselected package libpaper1:s390x. 395s Preparing to unpack .../039-libpaper1_1.1.29_s390x.deb ... 395s Unpacking libpaper1:s390x (1.1.29) ... 395s Selecting previously unselected package libpaper-utils. 395s Preparing to unpack .../040-libpaper-utils_1.1.29_s390x.deb ... 395s Unpacking libpaper-utils (1.1.29) ... 395s Selecting previously unselected package libsm6:s390x. 395s Preparing to unpack .../041-libsm6_2%3a1.2.3-1build2_s390x.deb ... 395s Unpacking libsm6:s390x (2:1.2.3-1build2) ... 395s Selecting previously unselected package libtcl8.6:s390x. 395s Preparing to unpack .../042-libtcl8.6_8.6.14+dfsg-1_s390x.deb ... 395s Unpacking libtcl8.6:s390x (8.6.14+dfsg-1) ... 395s Selecting previously unselected package libxft2:s390x. 395s Preparing to unpack .../043-libxft2_2.3.6-1_s390x.deb ... 395s Unpacking libxft2:s390x (2.3.6-1) ... 395s Selecting previously unselected package libxss1:s390x. 395s Preparing to unpack .../044-libxss1_1%3a1.2.3-1build2_s390x.deb ... 395s Unpacking libxss1:s390x (1:1.2.3-1build2) ... 395s Selecting previously unselected package libtk8.6:s390x. 395s Preparing to unpack .../045-libtk8.6_8.6.14-1_s390x.deb ... 395s Unpacking libtk8.6:s390x (8.6.14-1) ... 395s Selecting previously unselected package libxt6t64:s390x. 395s Preparing to unpack .../046-libxt6t64_1%3a1.2.1-1.2_s390x.deb ... 395s Unpacking libxt6t64:s390x (1:1.2.1-1.2) ... 395s Selecting previously unselected package zip. 395s Preparing to unpack .../047-zip_3.0-13_s390x.deb ... 395s Unpacking zip (3.0-13) ... 395s Selecting previously unselected package unzip. 395s Preparing to unpack .../048-unzip_6.0-28ubuntu3_s390x.deb ... 395s Unpacking unzip (6.0-28ubuntu3) ... 395s Selecting previously unselected package xdg-utils. 395s Preparing to unpack .../049-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 395s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 395s Selecting previously unselected package r-base-core. 395s Preparing to unpack .../050-r-base-core_4.3.3-2build1_s390x.deb ... 395s Unpacking r-base-core (4.3.3-2build1) ... 395s Selecting previously unselected package r-cran-littler. 395s Preparing to unpack .../051-r-cran-littler_0.3.19-1_s390x.deb ... 395s Unpacking r-cran-littler (0.3.19-1) ... 395s Selecting previously unselected package littler. 395s Preparing to unpack .../052-littler_0.3.19-1_all.deb ... 395s Unpacking littler (0.3.19-1) ... 395s Selecting previously unselected package node-bootstrap-sass. 395s Preparing to unpack .../053-node-bootstrap-sass_3.4.3-2_all.deb ... 395s Unpacking node-bootstrap-sass (3.4.3-2) ... 395s Selecting previously unselected package node-html5shiv. 395s Preparing to unpack .../054-node-html5shiv_3.7.3+dfsg-5_all.deb ... 395s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 395s Selecting previously unselected package node-normalize.css. 395s Preparing to unpack .../055-node-normalize.css_8.0.1-5_all.deb ... 395s Unpacking node-normalize.css (8.0.1-5) ... 395s Selecting previously unselected package pandoc-data. 395s Preparing to unpack .../056-pandoc-data_3.1.3-1_all.deb ... 395s Unpacking pandoc-data (3.1.3-1) ... 396s Selecting previously unselected package pandoc. 396s Preparing to unpack .../057-pandoc_3.1.3+ds-2_s390x.deb ... 396s Unpacking pandoc (3.1.3+ds-2) ... 397s Selecting previously unselected package r-bioc-biocgenerics. 397s Preparing to unpack .../058-r-bioc-biocgenerics_0.48.1-2_all.deb ... 397s Unpacking r-bioc-biocgenerics (0.48.1-2) ... 397s Selecting previously unselected package r-cran-r.methodss3. 397s Preparing to unpack .../059-r-cran-r.methodss3_1.8.2-1_all.deb ... 397s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 397s Selecting previously unselected package r-cran-r.oo. 397s Preparing to unpack .../060-r-cran-r.oo_1.26.0-1_all.deb ... 397s Unpacking r-cran-r.oo (1.26.0-1) ... 397s Selecting previously unselected package r-cran-r.utils. 397s Preparing to unpack .../061-r-cran-r.utils_2.12.3-1_all.deb ... 397s Unpacking r-cran-r.utils (2.12.3-1) ... 397s Selecting previously unselected package r-cran-matrixstats. 397s Preparing to unpack .../062-r-cran-matrixstats_1.2.0-1_s390x.deb ... 397s Unpacking r-cran-matrixstats (1.2.0-1) ... 397s Selecting previously unselected package r-bioc-aroma.light. 397s Preparing to unpack .../063-r-bioc-aroma.light_3.32.0-1_all.deb ... 397s Unpacking r-bioc-aroma.light (3.32.0-1) ... 398s Selecting previously unselected package r-bioc-dnacopy. 398s Preparing to unpack .../064-r-bioc-dnacopy_1.76.0-1_s390x.deb ... 398s Unpacking r-bioc-dnacopy (1.76.0-1) ... 398s Selecting previously unselected package r-cran-acepack. 398s Preparing to unpack .../065-r-cran-acepack_1.4.2-1_s390x.deb ... 398s Unpacking r-cran-acepack (1.4.2-1) ... 398s Selecting previously unselected package r-cran-backports. 398s Preparing to unpack .../066-r-cran-backports_1.4.1-1_s390x.deb ... 398s Unpacking r-cran-backports (1.4.1-1) ... 398s Selecting previously unselected package r-cran-base64enc. 398s Preparing to unpack .../067-r-cran-base64enc_0.1-3-3_s390x.deb ... 398s Unpacking r-cran-base64enc (0.1-3-3) ... 398s Selecting previously unselected package r-cran-rlang. 398s Preparing to unpack .../068-r-cran-rlang_1.1.3-1_s390x.deb ... 398s Unpacking r-cran-rlang (1.1.3-1) ... 398s Selecting previously unselected package r-cran-fastmap. 398s Preparing to unpack .../069-r-cran-fastmap_1.1.1-1_s390x.deb ... 398s Unpacking r-cran-fastmap (1.1.1-1) ... 398s Selecting previously unselected package r-cran-cachem. 398s Preparing to unpack .../070-r-cran-cachem_1.0.8-1_s390x.deb ... 398s Unpacking r-cran-cachem (1.0.8-1) ... 398s Selecting previously unselected package r-cran-digest. 398s Preparing to unpack .../071-r-cran-digest_0.6.34-1_s390x.deb ... 398s Unpacking r-cran-digest (0.6.34-1) ... 398s Selecting previously unselected package r-cran-ellipsis. 398s Preparing to unpack .../072-r-cran-ellipsis_0.3.2-2_s390x.deb ... 398s Unpacking r-cran-ellipsis (0.3.2-2) ... 398s Selecting previously unselected package r-cran-htmltools. 398s Preparing to unpack .../073-r-cran-htmltools_0.5.7-1_s390x.deb ... 398s Unpacking r-cran-htmltools (0.5.7-1) ... 398s Selecting previously unselected package r-cran-jquerylib. 398s Preparing to unpack .../074-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ... 398s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ... 398s Selecting previously unselected package r-cran-jsonlite. 398s Preparing to unpack .../075-r-cran-jsonlite_1.8.8+dfsg-1_s390x.deb ... 398s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 398s Selecting previously unselected package r-cran-cli. 398s Preparing to unpack .../076-r-cran-cli_3.6.2-1_s390x.deb ... 398s Unpacking r-cran-cli (3.6.2-1) ... 398s Selecting previously unselected package r-cran-glue. 398s Preparing to unpack .../077-r-cran-glue_1.7.0-1_s390x.deb ... 398s Unpacking r-cran-glue (1.7.0-1) ... 398s Selecting previously unselected package r-cran-lifecycle. 398s Preparing to unpack .../078-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 398s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 398s Selecting previously unselected package r-cran-memoise. 398s Preparing to unpack .../079-r-cran-memoise_2.0.1-1_all.deb ... 398s Unpacking r-cran-memoise (2.0.1-1) ... 398s Selecting previously unselected package r-cran-mime. 398s Preparing to unpack .../080-r-cran-mime_0.12-1_s390x.deb ... 398s Unpacking r-cran-mime (0.12-1) ... 398s Selecting previously unselected package r-cran-fs. 398s Preparing to unpack .../081-r-cran-fs_1.6.3+dfsg-1build1_s390x.deb ... 398s Unpacking r-cran-fs (1.6.3+dfsg-1build1) ... 398s Selecting previously unselected package r-cran-r6. 398s Preparing to unpack .../082-r-cran-r6_2.5.1-1_all.deb ... 398s Unpacking r-cran-r6 (2.5.1-1) ... 398s Selecting previously unselected package r-cran-rappdirs. 398s Preparing to unpack .../083-r-cran-rappdirs_0.3.3-1_s390x.deb ... 398s Unpacking r-cran-rappdirs (0.3.3-1) ... 398s Selecting previously unselected package r-cran-sass. 398s Preparing to unpack .../084-r-cran-sass_0.4.8+dfsg-1_s390x.deb ... 398s Unpacking r-cran-sass (0.4.8+dfsg-1) ... 398s Selecting previously unselected package r-cran-bslib. 398s Preparing to unpack .../085-r-cran-bslib_0.6.1+dfsg-1_all.deb ... 398s Unpacking r-cran-bslib (0.6.1+dfsg-1) ... 398s Selecting previously unselected package r-cran-checkmate. 398s Preparing to unpack .../086-r-cran-checkmate_2.3.1-1_s390x.deb ... 398s Unpacking r-cran-checkmate (2.3.1-1) ... 398s Selecting previously unselected package r-cran-chron. 398s Preparing to unpack .../087-r-cran-chron_2.3-61-2_s390x.deb ... 398s Unpacking r-cran-chron (2.3-61-2) ... 398s Selecting previously unselected package r-cran-cluster. 398s Preparing to unpack .../088-r-cran-cluster_2.1.6-1_s390x.deb ... 398s Unpacking r-cran-cluster (2.1.6-1) ... 398s Selecting previously unselected package r-cran-codetools. 398s Preparing to unpack .../089-r-cran-codetools_0.2-19-1_all.deb ... 398s Unpacking r-cran-codetools (0.2-19-1) ... 398s Selecting previously unselected package r-cran-colorspace. 398s Preparing to unpack .../090-r-cran-colorspace_2.1-0+dfsg-1_s390x.deb ... 398s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 398s Selecting previously unselected package r-cran-commonmark. 398s Preparing to unpack .../091-r-cran-commonmark_1.9.1-1_s390x.deb ... 398s Unpacking r-cran-commonmark (1.9.1-1) ... 398s Selecting previously unselected package r-cran-cpp11. 398s Preparing to unpack .../092-r-cran-cpp11_0.4.7-1_all.deb ... 398s Unpacking r-cran-cpp11 (0.4.7-1) ... 398s Selecting previously unselected package r-cran-crayon. 398s Preparing to unpack .../093-r-cran-crayon_1.5.2-1_all.deb ... 398s Unpacking r-cran-crayon (1.5.2-1) ... 398s Selecting previously unselected package r-cran-data.table. 398s Preparing to unpack .../094-r-cran-data.table_1.14.10+dfsg-1_s390x.deb ... 398s Unpacking r-cran-data.table (1.14.10+dfsg-1) ... 398s Selecting previously unselected package r-cran-deldir. 398s Preparing to unpack .../095-r-cran-deldir_2.0-4-1_s390x.deb ... 398s Unpacking r-cran-deldir (2.0-4-1) ... 398s Selecting previously unselected package r-cran-generics. 398s Preparing to unpack .../096-r-cran-generics_0.1.3-1_all.deb ... 398s Unpacking r-cran-generics (0.1.3-1) ... 398s Selecting previously unselected package r-cran-magrittr. 398s Preparing to unpack .../097-r-cran-magrittr_2.0.3-1_s390x.deb ... 398s Unpacking r-cran-magrittr (2.0.3-1) ... 398s Selecting previously unselected package r-cran-fansi. 398s Preparing to unpack .../098-r-cran-fansi_1.0.5-1_s390x.deb ... 398s Unpacking r-cran-fansi (1.0.5-1) ... 399s Selecting previously unselected package r-cran-utf8. 399s Preparing to unpack .../099-r-cran-utf8_1.2.4-1_s390x.deb ... 399s Unpacking r-cran-utf8 (1.2.4-1) ... 399s Selecting previously unselected package r-cran-vctrs. 399s Preparing to unpack .../100-r-cran-vctrs_0.6.5-1_s390x.deb ... 399s Unpacking r-cran-vctrs (0.6.5-1) ... 399s Selecting previously unselected package r-cran-pillar. 399s Preparing to unpack .../101-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 399s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 399s Selecting previously unselected package r-cran-pkgconfig. 399s Preparing to unpack .../102-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 399s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 399s Selecting previously unselected package r-cran-tibble. 399s Preparing to unpack .../103-r-cran-tibble_3.2.1+dfsg-2_s390x.deb ... 399s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 399s Selecting previously unselected package r-cran-withr. 399s Preparing to unpack .../104-r-cran-withr_3.0.0+dfsg-1_all.deb ... 399s Unpacking r-cran-withr (3.0.0+dfsg-1) ... 399s Selecting previously unselected package r-cran-tidyselect. 399s Preparing to unpack .../105-r-cran-tidyselect_1.2.0+dfsg-1_s390x.deb ... 399s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 399s Selecting previously unselected package r-cran-dplyr. 399s Preparing to unpack .../106-r-cran-dplyr_1.1.4-1_s390x.deb ... 399s Unpacking r-cran-dplyr (1.1.4-1) ... 399s Selecting previously unselected package r-cran-evaluate. 399s Preparing to unpack .../107-r-cran-evaluate_0.23-1_all.deb ... 399s Unpacking r-cran-evaluate (0.23-1) ... 399s Selecting previously unselected package r-cran-farver. 399s Preparing to unpack .../108-r-cran-farver_2.1.1-1_s390x.deb ... 399s Unpacking r-cran-farver (2.1.1-1) ... 399s Selecting previously unselected package r-cran-fontawesome. 399s Preparing to unpack .../109-r-cran-fontawesome_0.5.2-1_all.deb ... 399s Unpacking r-cran-fontawesome (0.5.2-1) ... 399s Selecting previously unselected package r-cran-foreign. 399s Preparing to unpack .../110-r-cran-foreign_0.8.86-1_s390x.deb ... 399s Unpacking r-cran-foreign (0.8.86-1) ... 399s Selecting previously unselected package r-cran-formula. 399s Preparing to unpack .../111-r-cran-formula_1.2-5-1_all.deb ... 399s Unpacking r-cran-formula (1.2-5-1) ... 399s Selecting previously unselected package r-cran-globals. 399s Preparing to unpack .../112-r-cran-globals_0.16.2-1_all.deb ... 399s Unpacking r-cran-globals (0.16.2-1) ... 399s Selecting previously unselected package r-cran-listenv. 399s Preparing to unpack .../113-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 399s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 399s Selecting previously unselected package r-cran-parallelly. 399s Preparing to unpack .../114-r-cran-parallelly_1.37.1-1_s390x.deb ... 399s Unpacking r-cran-parallelly (1.37.1-1) ... 399s Selecting previously unselected package r-cran-future. 399s Preparing to unpack .../115-r-cran-future_1.33.1+dfsg-1_all.deb ... 399s Unpacking r-cran-future (1.33.1+dfsg-1) ... 399s Selecting previously unselected package r-cran-gtable. 399s Preparing to unpack .../116-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 399s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 399s Selecting previously unselected package r-cran-isoband. 399s Preparing to unpack .../117-r-cran-isoband_0.2.7-1_s390x.deb ... 399s Unpacking r-cran-isoband (0.2.7-1) ... 399s Selecting previously unselected package r-cran-mass. 399s Preparing to unpack .../118-r-cran-mass_7.3-60.0.1-1_s390x.deb ... 399s Unpacking r-cran-mass (7.3-60.0.1-1) ... 399s Selecting previously unselected package r-cran-lattice. 399s Preparing to unpack .../119-r-cran-lattice_0.22-5-1_s390x.deb ... 399s Unpacking r-cran-lattice (0.22-5-1) ... 399s Selecting previously unselected package r-cran-nlme. 399s Preparing to unpack .../120-r-cran-nlme_3.1.164-1_s390x.deb ... 399s Unpacking r-cran-nlme (3.1.164-1) ... 399s Selecting previously unselected package r-cran-matrix. 399s Preparing to unpack .../121-r-cran-matrix_1.6-5-1_s390x.deb ... 399s Unpacking r-cran-matrix (1.6-5-1) ... 399s Selecting previously unselected package r-cran-mgcv. 399s Preparing to unpack .../122-r-cran-mgcv_1.9-1-1_s390x.deb ... 399s Unpacking r-cran-mgcv (1.9-1-1) ... 399s Selecting previously unselected package r-cran-labeling. 399s Preparing to unpack .../123-r-cran-labeling_0.4.3-1_all.deb ... 399s Unpacking r-cran-labeling (0.4.3-1) ... 399s Selecting previously unselected package r-cran-munsell. 399s Preparing to unpack .../124-r-cran-munsell_0.5.0-2build1_all.deb ... 399s Unpacking r-cran-munsell (0.5.0-2build1) ... 399s Selecting previously unselected package r-cran-rcolorbrewer. 399s Preparing to unpack .../125-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 399s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 399s Selecting previously unselected package r-cran-viridislite. 399s Preparing to unpack .../126-r-cran-viridislite_0.4.2-2_all.deb ... 399s Unpacking r-cran-viridislite (0.4.2-2) ... 399s Selecting previously unselected package r-cran-scales. 399s Preparing to unpack .../127-r-cran-scales_1.3.0-1_all.deb ... 399s Unpacking r-cran-scales (1.3.0-1) ... 399s Selecting previously unselected package r-cran-ggplot2. 399s Preparing to unpack .../128-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 399s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 400s Selecting previously unselected package r-cran-gridextra. 400s Preparing to unpack .../129-r-cran-gridextra_2.3-3build1_all.deb ... 400s Unpacking r-cran-gridextra (2.3-3build1) ... 400s Selecting previously unselected package r-cran-xfun. 400s Preparing to unpack .../130-r-cran-xfun_0.41+dfsg-1_s390x.deb ... 400s Unpacking r-cran-xfun (0.41+dfsg-1) ... 400s Selecting previously unselected package r-cran-highr. 400s Preparing to unpack .../131-r-cran-highr_0.10+dfsg-1_all.deb ... 400s Unpacking r-cran-highr (0.10+dfsg-1) ... 400s Selecting previously unselected package r-cran-survival. 400s Preparing to unpack .../132-r-cran-survival_3.5-8-1_s390x.deb ... 400s Unpacking r-cran-survival (3.5-8-1) ... 400s Selecting previously unselected package r-cran-rpart. 400s Preparing to unpack .../133-r-cran-rpart_4.1.23-1_s390x.deb ... 400s Unpacking r-cran-rpart (4.1.23-1) ... 400s Selecting previously unselected package r-cran-nnet. 400s Preparing to unpack .../134-r-cran-nnet_7.3-19-2_s390x.deb ... 400s Unpacking r-cran-nnet (7.3-19-2) ... 400s Selecting previously unselected package r-cran-stringi. 400s Preparing to unpack .../135-r-cran-stringi_1.8.3-1_s390x.deb ... 400s Unpacking r-cran-stringi (1.8.3-1) ... 400s Selecting previously unselected package r-cran-stringr. 400s Preparing to unpack .../136-r-cran-stringr_1.5.1-1_all.deb ... 400s Unpacking r-cran-stringr (1.5.1-1) ... 400s Selecting previously unselected package r-cran-yaml. 400s Preparing to unpack .../137-r-cran-yaml_2.3.8-1_s390x.deb ... 400s Unpacking r-cran-yaml (2.3.8-1) ... 400s Selecting previously unselected package libjs-mathjax. 400s Preparing to unpack .../138-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 400s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 401s Selecting previously unselected package r-cran-knitr. 401s Preparing to unpack .../139-r-cran-knitr_1.45+dfsg-1_all.deb ... 401s Unpacking r-cran-knitr (1.45+dfsg-1) ... 401s Selecting previously unselected package r-cran-tinytex. 401s Preparing to unpack .../140-r-cran-tinytex_0.49-1_all.deb ... 401s Unpacking r-cran-tinytex (0.49-1) ... 401s Selecting previously unselected package libjs-modernizr. 401s Preparing to unpack .../141-libjs-modernizr_2.6.2+ds1-5_all.deb ... 401s Unpacking libjs-modernizr (2.6.2+ds1-5) ... 401s Selecting previously unselected package r-cran-pkgkitten. 401s Preparing to unpack .../142-r-cran-pkgkitten_0.2.3-1_all.deb ... 401s Unpacking r-cran-pkgkitten (0.2.3-1) ... 401s Selecting previously unselected package r-cran-rcpp. 401s Preparing to unpack .../143-r-cran-rcpp_1.0.12-1_s390x.deb ... 401s Unpacking r-cran-rcpp (1.0.12-1) ... 401s Selecting previously unselected package r-cran-later. 401s Preparing to unpack .../144-r-cran-later_1.3.2+dfsg-1_s390x.deb ... 401s Unpacking r-cran-later (1.3.2+dfsg-1) ... 401s Selecting previously unselected package r-cran-promises. 401s Preparing to unpack .../145-r-cran-promises_1.2.1+dfsg-1_s390x.deb ... 401s Unpacking r-cran-promises (1.2.1+dfsg-1) ... 401s Selecting previously unselected package r-cran-httpuv. 401s Preparing to unpack .../146-r-cran-httpuv_1.6.14+dfsg-1build1_s390x.deb ... 401s Unpacking r-cran-httpuv (1.6.14+dfsg-1build1) ... 401s Selecting previously unselected package r-cran-xtable. 401s Preparing to unpack .../147-r-cran-xtable_1%3a1.8-4-2_all.deb ... 401s Unpacking r-cran-xtable (1:1.8-4-2) ... 401s Selecting previously unselected package r-cran-sourcetools. 401s Preparing to unpack .../148-r-cran-sourcetools_0.1.7-1-1_s390x.deb ... 401s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 401s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 401s Preparing to unpack .../149-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 401s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 401s Selecting previously unselected package r-cran-shiny. 401s Preparing to unpack .../150-r-cran-shiny_1.8.0+dfsg-1_all.deb ... 401s Unpacking r-cran-shiny (1.8.0+dfsg-1) ... 401s Selecting previously unselected package r-cran-rmarkdown. 401s Preparing to unpack .../151-r-cran-rmarkdown_2.25+dfsg-3_all.deb ... 401s Unpacking r-cran-rmarkdown (2.25+dfsg-3) ... 402s Selecting previously unselected package r-cran-htmlwidgets. 402s Preparing to unpack .../152-r-cran-htmlwidgets_1.6.4+dfsg-1_all.deb ... 402s Unpacking r-cran-htmlwidgets (1.6.4+dfsg-1) ... 402s Selecting previously unselected package r-cran-rstudioapi. 402s Preparing to unpack .../153-r-cran-rstudioapi_0.15.0-1_all.deb ... 402s Unpacking r-cran-rstudioapi (0.15.0-1) ... 402s Selecting previously unselected package r-cran-purrr. 402s Preparing to unpack .../154-r-cran-purrr_1.0.2-1_s390x.deb ... 402s Unpacking r-cran-purrr (1.0.2-1) ... 402s Selecting previously unselected package r-cran-tidyr. 402s Preparing to unpack .../155-r-cran-tidyr_1.3.1-1_s390x.deb ... 402s Unpacking r-cran-tidyr (1.3.1-1) ... 402s Selecting previously unselected package r-cran-htmltable. 402s Preparing to unpack .../156-r-cran-htmltable_2.4.2-1_all.deb ... 402s Unpacking r-cran-htmltable (2.4.2-1) ... 402s Selecting previously unselected package r-cran-viridis. 402s Preparing to unpack .../157-r-cran-viridis_0.6.5-1_all.deb ... 402s Unpacking r-cran-viridis (0.6.5-1) ... 402s Selecting previously unselected package r-cran-png. 402s Preparing to unpack .../158-r-cran-png_0.1-8-1build1_s390x.deb ... 402s Unpacking r-cran-png (0.1-8-1build1) ... 402s Selecting previously unselected package r-cran-jpeg. 402s Preparing to unpack .../159-r-cran-jpeg_0.1-10-1_s390x.deb ... 402s Unpacking r-cran-jpeg (0.1-10-1) ... 402s Selecting previously unselected package r-cran-rcppeigen. 402s Preparing to unpack .../160-r-cran-rcppeigen_0.3.4.0.0-1_s390x.deb ... 402s Unpacking r-cran-rcppeigen (0.3.4.0.0-1) ... 402s Selecting previously unselected package r-cran-interp. 402s Preparing to unpack .../161-r-cran-interp_1.1-6-1_s390x.deb ... 402s Unpacking r-cran-interp (1.1-6-1) ... 402s Selecting previously unselected package r-cran-latticeextra. 402s Preparing to unpack .../162-r-cran-latticeextra_0.6-30-1_all.deb ... 402s Unpacking r-cran-latticeextra (0.6-30-1) ... 402s Selecting previously unselected package r-cran-hmisc. 402s Preparing to unpack .../163-r-cran-hmisc_5.1-1-1_s390x.deb ... 402s Unpacking r-cran-hmisc (5.1-1-1) ... 402s Selecting previously unselected package r-cran-r.cache. 402s Preparing to unpack .../164-r-cran-r.cache_0.16.0-1_all.deb ... 402s Unpacking r-cran-r.cache (0.16.0-1) ... 402s Selecting previously unselected package r-cran-pscbs. 402s Preparing to unpack .../165-r-cran-pscbs_0.66.0-2_all.deb ... 402s Unpacking r-cran-pscbs (0.66.0-2) ... 402s Selecting previously unselected package autopkgtest-satdep. 402s Preparing to unpack .../166-1-autopkgtest-satdep.deb ... 402s Unpacking autopkgtest-satdep (0) ... 402s Setting up libjs-json (0~20221030+~1.0.8-1) ... 402s Setting up javascript-common (11+nmu1) ... 402s Setting up libgraphite2-3:s390x (1.3.14-2) ... 402s Setting up libpixman-1-0:s390x (0.42.2-1) ... 402s Setting up libpaper1:s390x (1.1.29) ... 402s 402s Creating config file /etc/papersize with new version 402s Setting up fontconfig (2.15.0-1.1ubuntu1) ... 404s Regenerating fonts cache... done. 404s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 404s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 404s Setting up libxrender1:s390x (1:0.9.10-1.1) ... 404s Setting up libdatrie1:s390x (0.2.13-3) ... 404s Setting up libjs-popper.js (1.16.1+ds-6) ... 404s Setting up libxcb-render0:s390x (1.15-1) ... 404s Setting up libjs-sifter.js (0.6.0+dfsg-3) ... 404s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 404s Setting up unzip (6.0-28ubuntu3) ... 404s Setting up x11-common (1:7.7+23ubuntu2) ... 405s Setting up node-html5shiv (3.7.3+dfsg-5) ... 405s Setting up libjs-microplugin.js (0.0.3+dfsg-1.1) ... 405s Setting up libxcb-shm0:s390x (1.15-1) ... 405s Setting up libpaper-utils (1.1.29) ... 405s Setting up libgomp1:s390x (14-20240315-1ubuntu1) ... 405s Setting up libjs-modernizr (2.6.2+ds1-5) ... 405s Setting up libcairo2:s390x (1.18.0-1ubuntu1) ... 405s Setting up libjs-es5-shim (4.6.7-2) ... 405s Setting up zip (3.0-13) ... 405s Setting up libblas3:s390x (3.12.0-3) ... 405s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 405s Setting up libjs-d3 (3.5.17-4) ... 405s Setting up libtcl8.6:s390x (8.6.14+dfsg-1) ... 405s Setting up libgfortran5:s390x (14-20240315-1ubuntu1) ... 405s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ... 405s Setting up liblua5.4-0:s390x (5.4.6-3build1) ... 405s Setting up libharfbuzz0b:s390x (8.3.0-2build1) ... 405s Setting up libthai-data (0.1.29-2) ... 405s Setting up node-bootstrap-sass (3.4.3-2) ... 405s Setting up libjs-prettify (2015.12.04+dfsg-1.1) ... 405s Setting up libxss1:s390x (1:1.2.3-1build2) ... 405s Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ... 405s Setting up pandoc-data (3.1.3-1) ... 405s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 405s Setting up node-normalize.css (8.0.1-5) ... 405s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 405s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 405s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 405s Setting up libjs-bootstrap (3.4.1+dfsg-3) ... 405s Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 405s Setting up libice6:s390x (2:1.0.10-1build2) ... 405s Setting up liblapack3:s390x (3.12.0-3) ... 405s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 405s Setting up libxft2:s390x (2.3.6-1) ... 405s Setting up libtk8.6:s390x (8.6.14-1) ... 405s Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 405s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... 405s Setting up libthai0:s390x (0.1.29-2) ... 405s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 405s Setting up pandoc (3.1.3+ds-2) ... 405s Setting up libsm6:s390x (2:1.2.3-1build2) ... 405s Setting up libpango-1.0-0:s390x (1.52.1+ds-1) ... 405s Setting up libxt6t64:s390x (1:1.2.1-1.2) ... 405s Setting up libpangoft2-1.0-0:s390x (1.52.1+ds-1) ... 405s Setting up libpangocairo-1.0-0:s390x (1.52.1+ds-1) ... 405s Setting up r-base-core (4.3.3-2build1) ... 405s 405s Creating config file /etc/R/Renviron with new version 405s Setting up r-cran-crayon (1.5.2-1) ... 405s Setting up r-cran-labeling (0.4.3-1) ... 405s Setting up r-cran-sourcetools (0.1.7-1-1) ... 405s Setting up r-cran-lattice (0.22-5-1) ... 405s Setting up r-cran-nlme (3.1.164-1) ... 405s Setting up r-cran-farver (2.1.1-1) ... 405s Setting up r-cran-formula (1.2-5-1) ... 405s Setting up r-cran-viridislite (0.4.2-2) ... 405s Setting up r-cran-cluster (2.1.6-1) ... 405s Setting up r-cran-nnet (7.3-19-2) ... 405s Setting up r-cran-commonmark (1.9.1-1) ... 405s Setting up r-cran-r6 (2.5.1-1) ... 405s Setting up r-cran-pkgkitten (0.2.3-1) ... 405s Setting up r-cran-jpeg (0.1-10-1) ... 405s Setting up r-cran-chron (2.3-61-2) ... 405s Setting up r-cran-magrittr (2.0.3-1) ... 405s Setting up r-cran-rappdirs (0.3.3-1) ... 405s Setting up r-cran-littler (0.3.19-1) ... 405s Setting up r-cran-fs (1.6.3+dfsg-1build1) ... 405s Setting up r-cran-rcpp (1.0.12-1) ... 405s Setting up r-cran-codetools (0.2-19-1) ... 405s Setting up r-bioc-biocgenerics (0.48.1-2) ... 405s Setting up r-cran-rlang (1.1.3-1) ... 405s Setting up r-cran-matrixstats (1.2.0-1) ... 405s Setting up r-cran-listenv (0.9.1+dfsg-1) ... 405s Setting up littler (0.3.19-1) ... 405s Setting up r-cran-xfun (0.41+dfsg-1) ... 405s Setting up r-cran-withr (3.0.0+dfsg-1) ... 405s Setting up r-cran-backports (1.4.1-1) ... 405s Setting up r-cran-mime (0.12-1) ... 405s Setting up r-cran-generics (0.1.3-1) ... 405s Setting up r-cran-base64enc (0.1-3-3) ... 405s Setting up r-cran-digest (0.6.34-1) ... 405s Setting up r-cran-yaml (2.3.8-1) ... 405s Setting up r-cran-evaluate (0.23-1) ... 405s Setting up r-cran-highr (0.10+dfsg-1) ... 405s Setting up r-cran-fansi (1.0.5-1) ... 405s Setting up r-cran-mass (7.3-60.0.1-1) ... 405s Setting up r-cran-checkmate (2.3.1-1) ... 405s Setting up r-cran-acepack (1.4.2-1) ... 405s Setting up r-cran-data.table (1.14.10+dfsg-1) ... 405s Setting up r-cran-glue (1.7.0-1) ... 405s Setting up r-cran-foreign (0.8.86-1) ... 405s Setting up r-cran-xtable (1:1.8-4-2) ... 405s Setting up r-cran-cli (3.6.2-1) ... 405s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 405s Setting up r-cran-deldir (2.0-4-1) ... 405s Setting up r-cran-fastmap (1.1.1-1) ... 405s Setting up r-cran-png (0.1-8-1build1) ... 405s Setting up r-cran-r.methodss3 (1.8.2-1) ... 405s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... 405s Setting up r-cran-rstudioapi (0.15.0-1) ... 405s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 405s Setting up r-cran-utf8 (1.2.4-1) ... 405s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 405s Setting up r-cran-parallelly (1.37.1-1) ... 405s Setting up r-cran-stringi (1.8.3-1) ... 405s Setting up r-cran-cpp11 (0.4.7-1) ... 405s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 405s Setting up r-cran-isoband (0.2.7-1) ... 405s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 405s Setting up r-cran-later (1.3.2+dfsg-1) ... 405s Setting up r-cran-matrix (1.6-5-1) ... 405s Setting up r-cran-tinytex (0.49-1) ... 405s Setting up r-cran-knitr (1.45+dfsg-1) ... 405s Setting up r-cran-mgcv (1.9-1-1) ... 405s Setting up r-bioc-dnacopy (1.76.0-1) ... 405s Setting up r-cran-cachem (1.0.8-1) ... 405s Setting up r-cran-globals (0.16.2-1) ... 405s Setting up r-cran-vctrs (0.6.5-1) ... 405s Setting up r-cran-rcppeigen (0.3.4.0.0-1) ... 405s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 405s Setting up r-cran-ellipsis (0.3.2-2) ... 405s Setting up r-cran-stringr (1.5.1-1) ... 405s Setting up r-cran-munsell (0.5.0-2build1) ... 405s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 405s Setting up r-cran-survival (3.5-8-1) ... 405s Setting up r-cran-r.oo (1.26.0-1) ... 405s Setting up r-cran-future (1.33.1+dfsg-1) ... 405s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 405s Setting up r-cran-interp (1.1-6-1) ... 405s Setting up r-cran-gridextra (2.3-3build1) ... 405s Setting up r-cran-scales (1.3.0-1) ... 405s Setting up r-cran-memoise (2.0.1-1) ... 405s Setting up r-cran-promises (1.2.1+dfsg-1) ... 405s Setting up r-cran-purrr (1.0.2-1) ... 405s Setting up r-cran-htmltools (0.5.7-1) ... 405s Setting up r-cran-sass (0.4.8+dfsg-1) ... 405s Setting up r-cran-dplyr (1.1.4-1) ... 405s Setting up r-cran-r.utils (2.12.3-1) ... 405s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 405s Setting up r-cran-httpuv (1.6.14+dfsg-1build1) ... 405s Setting up r-cran-rpart (4.1.23-1) ... 405s Setting up r-cran-fontawesome (0.5.2-1) ... 405s Setting up r-cran-latticeextra (0.6-30-1) ... 405s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... 405s Setting up r-cran-viridis (0.6.5-1) ... 405s Setting up r-cran-bslib (0.6.1+dfsg-1) ... 405s Setting up r-cran-tidyr (1.3.1-1) ... 405s Setting up r-bioc-aroma.light (3.32.0-1) ... 405s Setting up r-cran-r.cache (0.16.0-1) ... 405s Setting up r-cran-shiny (1.8.0+dfsg-1) ... 405s Setting up r-cran-pscbs (0.66.0-2) ... 405s Setting up r-cran-rmarkdown (2.25+dfsg-3) ... 405s Setting up r-cran-htmlwidgets (1.6.4+dfsg-1) ... 405s Setting up r-cran-htmltable (2.4.2-1) ... 405s Setting up r-cran-hmisc (5.1-1-1) ... 405s Setting up autopkgtest-satdep (0) ... 405s Processing triggers for man-db (2.12.0-3build4) ... 406s Processing triggers for install-info (7.1-3build1) ... 406s Processing triggers for libc-bin (2.39-0ubuntu6) ... 412s (Reading database ... 100485 files and directories currently installed.) 412s Removing autopkgtest-satdep (0) ... 413s autopkgtest [01:31:19]: test run-unit-test: [----------------------- 413s + pkg=r-cran-pscbs 413s + [ /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp = ] 413s + cd /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp 413s + 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.iuHVDJ/autopkgtest_tmp 413s + find . -name *.gz -exec gunzip {} ; 413s + export LC_ALL=C 413s + dpkg-architecture -qDEB_HOST_ARCH 413s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 413s + hostarch=s390x 413s + [ s390x = armhf ] 413s + ls PairedPSCBS,boot.R findLargeGaps.R randomSeed.R segmentByCBS,calls.R segmentByCBS,futures.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,futures.R segmentByPairedPSCBS,noNormalBAFs.R segmentByPairedPSCBS,report.R segmentByPairedPSCBS,seqOfSegmentsByDP.R segmentByPairedPSCBS.R weightedQuantile.R 413s + sed s/\.R$// 413s + echo Begin test PairedPSCBS,boot 413s + exitcode=0 413s + R CMD BATCH PairedPSCBS,boot.R 413s Begin test PairedPSCBS,boot 417s + cat PairedPSCBS,boot.Rout 417s 417s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 417s Copyright (C) 2024 The R Foundation for Statistical Computing 417s Platform: s390x-ibm-linux-gnu (64-bit) 417s 417s R is free software and comes with ABSOLUTELY NO WARRANTY. 417s You are welcome to redistribute it under certain conditions. 417s Type 'license()' or 'licence()' for distribution details. 417s 417s R is a collaborative project with many contributors. 417s Type 'contributors()' for more information and 417s 'citation()' on how to cite R or R packages in publications. 417s 417s Type 'demo()' for some demos, 'help()' for on-line help, or 417s 'help.start()' for an HTML browser interface to help. 417s Type 'q()' to quit R. 417s 417s > ########################################################### 417s > # This tests: 417s > # - Bootstrapping for PairedPSCBS objects 417s > ########################################################### 417s > library("PSCBS") 417s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 417s 417s Attaching package: 'PSCBS' 417s 417s The following objects are masked from 'package:base': 417s 417s append, load 417s 417s > 417s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 417s > # Load SNP microarray data 417s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 417s > data <- PSCBS::exampleData("paired.chr01") 417s > 417s > 417s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 417s > # Paired PSCBS segmentation 417s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 417s > # Drop single-locus outliers 417s > dataS <- dropSegmentationOutliers(data) 417s > dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 417s > nSegs <- 4L 417s > str(dataS) 417s 'data.frame': 14670 obs. of 6 variables: 417s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 417s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 417s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 417s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 417s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 417s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 417s > # Segment known regions 417s > knownSegments <- data.frame( 417s + chromosome = c( 1, 1, 1), 417s + start = c( -Inf, NA, 141510003), 417s + end = c(120992603, NA, +Inf) 417s + ) 417s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, avgDH="median", seed=0xBEEF) 417s > print(fit) 417s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 417s 1 1 1 1 554484 120992603 7586 1.385258 2108 417s 2 NA 2 1 NA NA NA NA 0 417s 3 1 3 1 141510003 185449813 2681 2.068861 777 417s 4 1 4 1 185449813 247137334 4391 2.634110 1311 417s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 417s 1 2108 2108 0.54551245 0.3147912 1.070467 417s 2 0 0 NA NA NA 417s 3 777 777 0.07132277 0.9606521 1.108209 417s 4 1311 1311 0.21663871 1.0317300 1.602380 417s > 417s > 417s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 417s > # Bootstrap 417s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 417s > B <- 1L 417s > seed <- 0xBEEF 417s > probs <- c(0.025, 0.05, 0.95, 0.975) 417s > 417s > sets <- getBootstrapLocusSets(fit, B=B, seed=seed) 417s > 417s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 417s > # Subset by first segment 417s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 417s > ss <- 1L 417s > 417s > fitT <- extractSegment(fit, ss) 417s > dataT <- getLocusData(fitT) 417s > segsT <- getSegments(fitT) 417s > 417s > # Truth 417s > bootT <- bootstrapSegmentsAndChangepoints(fitT, B=B, seed=seed) 417s > bootT1 <- bootT$segments[1L,,,drop=FALSE] 417s > types <- dimnames(bootT1)[[3L]] 417s > dim(bootT1) <- dim(bootT1)[-1L] 417s > colnames(bootT1) <- types 417s > sumsT <- apply(bootT1, MARGIN=2L, FUN=quantile, probs=probs) 417s > print(sumsT) 417s tcn dh c1 c2 417s 2.5% 1.383213 0.5466788 0.3135198 1.069693 417s 5% 1.383213 0.5466788 0.3135198 1.069693 417s 95% 1.383213 0.5466788 0.3135198 1.069693 417s 97.5% 1.383213 0.5466788 0.3135198 1.069693 417s > 417s > fitTB <- bootstrapTCNandDHByRegion(fitT, B=B, seed=seed) 417s > segsTB <- getSegments(fitTB) 417s > segsTB <- unlist(segsTB[,grep("_", colnames(segsTB))]) 417s > dim(segsTB) <- dim(sumsT) 417s > dimnames(segsTB) <- dimnames(sumsT) 417s > print(segsTB) 417s tcn dh c1 c2 417s 2.5% 1.383213 0.5466788 0.3135198 1.069693 417s 5% 1.383213 0.5466788 0.3135198 1.069693 417s 95% 1.383213 0.5466788 0.3135198 1.069693 417s 97.5% 1.383213 0.5466788 0.3135198 1.069693 417s > 417s > # Sanity check 417s > stopifnot(all.equal(segsTB, sumsT)) 417s > 417s > # Calculate summaries using the existing bootstrap samples 417s > fitTBp <- bootstrapTCNandDHByRegion(fitT, .boot=bootT) 417s > # Sanity check 417s > all.equal(fitTBp, fitTB) 417s [1] "Component \"tcn_2.5%\": Mean relative difference: 0.003070405" 417s [2] "Component \"tcn_5%\": Mean relative difference: 0.002241362" 417s [3] "Component \"tcn_95%\": Mean relative difference: 0.005458479" 417s [4] "Component \"tcn_97.5%\": Mean relative difference: 0.006030363" 417s [5] "Component \"dh_2.5%\": Mean relative difference: 0.02683423" 417s [6] "Component \"dh_5%\": Mean relative difference: 0.02409533" 417s [7] "Component \"dh_95%\": Mean relative difference: 0.0150081" 417s [8] "Component \"dh_97.5%\": Mean relative difference: 0.01826461" 417s [9] "Component \"c1_2.5%\": Mean relative difference: 0.02397349" 417s [10] "Component \"c1_5%\": Mean relative difference: 0.01800948" 417s [11] "Component \"c1_95%\": Mean relative difference: 0.0303456" 417s [12] "Component \"c1_97.5%\": Mean relative difference: 0.03420614" 417s [13] "Component \"c2_2.5%\": Mean relative difference: 0.008723378" 417s [14] "Component \"c2_5%\": Mean relative difference: 0.006834962" 417s [15] "Component \"c2_95%\": Mean relative difference: 0.00741949" 417s [16] "Component \"c2_97.5%\": Mean relative difference: 0.008743911" 417s attr(,"what") 417s [1] "getSegments()" 417s > 417s > 417s > # Bootstrap from scratch 417s > setsT <- getBootstrapLocusSets(fitT, B=B, seed=seed) 417s > lociT <- setsT$locusSet[[1L]]$bootstrap$loci 417s > idxs <- lociT$tcn 417s > tcnT <- array(dataT$CT[idxs], dim=dim(idxs)) 417s > tcnT <- apply(tcnT, MARGIN=2L, FUN=mean, na.rm=TRUE) 417s > idxs <- lociT$dh 417s > dhT <- array(dataT$rho[idxs], dim=dim(idxs)) 417s > dhT <- apply(dhT, MARGIN=2L, FUN=median, na.rm=TRUE) 417s > c1T <- (1-dhT) * tcnT / 2 417s > c2T <- tcnT - c1T 417s > bootT2 <- array(c(tcnT, dhT, c1T, c2T), dim=c(1L, 4L)) 417s > colnames(bootT2) <- colnames(bootT1) 417s > print(bootT2) 417s tcn dh c1 c2 417s [1,] 1.383213 0.5466788 0.3135198 1.069693 417s > 417s > # This comparison is only valid if B == 1L 417s > if (B == 1L) { 417s + # Sanity check 417s + stopifnot(all.equal(bootT2, bootT1)) 417s + } 417s > 417s > proc.time() 417s user system elapsed 417s 2.684 0.097 2.840 417s + Test PairedPSCBS,boot passed 417s 0 417s Begin test findLargeGaps 417s [ 0 != 0 ] 417s + echo Test PairedPSCBS,boot passed 417s + echo 0 417s + echo Begin test findLargeGaps 417s + exitcode=0 417s + R CMD BATCH findLargeGaps.R 418s + cat findLargeGaps.Rout 418s + [ 0 != 0 ] 418s + echo Test findLargeGaps passed 418s + echo 0 418s + echo Begin test randomSeed 418s + exitcode=0 418s + R CMD BATCH randomSeed.R 418s 418s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 418s Copyright (C) 2024 The R Foundation for Statistical Computing 418s Platform: s390x-ibm-linux-gnu (64-bit) 418s 418s R is free software and comes with ABSOLUTELY NO WARRANTY. 418s You are welcome to redistribute it under certain conditions. 418s Type 'license()' or 'licence()' for distribution details. 418s 418s R is a collaborative project with many contributors. 418s Type 'contributors()' for more information and 418s 'citation()' on how to cite R or R packages in publications. 418s 418s Type 'demo()' for some demos, 'help()' for on-line help, or 418s 'help.start()' for an HTML browser interface to help. 418s Type 'q()' to quit R. 418s 418s [Previously saved workspace restored] 418s 418s > library("PSCBS") 418s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 418s 418s Attaching package: 'PSCBS' 418s 418s The following objects are masked from 'package:base': 418s 418s append, load 418s 418s > 418s > # Simulating copy-number data 418s > set.seed(0xBEEF) 418s > 418s > # Simulate CN data 418s > J <- 1000 418s > mu <- double(J) 418s > mu[200:300] <- mu[200:300] + 1 418s > mu[350:400] <- NA # centromere 418s > mu[650:800] <- mu[650:800] - 1 418s > eps <- rnorm(J, sd=1/2) 418s > y <- mu + eps 418s > x <- seq(from=1, to=100e6, length.out=J) 418s > 418s > data <- data.frame(chromosome=0L, x=x) 418s > 418s > gaps <- findLargeGaps(x=x, minLength=1e6) 418s > print(gaps) 418s [1] start end length 418s <0 rows> (or 0-length row.names) 418s > stopifnot(is.data.frame(gaps)) 418s > stopifnot(nrow(gaps) == 0L) 418s > segs <- gapsToSegments(gaps) 418s > print(segs) 418s chromosome start end 418s 1 0 -Inf Inf 418s > stopifnot(is.data.frame(segs)) 418s > stopifnot(nrow(segs) == 1L) 418s > 418s > 418s > gaps <- findLargeGaps(data, minLength=1e6) 418s > print(gaps) 418s [1] chromosome start end 418s <0 rows> (or 0-length row.names) 418s > stopifnot(is.data.frame(gaps)) 418s > stopifnot(nrow(gaps) == 0L) 418s > segs <- gapsToSegments(gaps) 418s > print(segs) 418s chromosome start end 418s 1 0 -Inf Inf 418s > stopifnot(is.data.frame(segs)) 418s > stopifnot(nrow(segs) == 1L) 418s > 418s > 418s > ## Add missing values 418s > data2 <- data 418s > data$x[30e6 < x & x < 50e6] <- NA 418s > gaps <- findLargeGaps(data, minLength=1e6) 418s > print(gaps) 418s chromosome start end length 418s 1 0 29929932 50050050 20120118 418s > stopifnot(is.data.frame(gaps)) 418s > stopifnot(nrow(gaps) == 1L) 418s > segs <- gapsToSegments(gaps) 418s > print(segs) 418s chromosome start end length 418s 1 0 -Inf 29929931 Inf 418s 2 0 29929932 50050050 20120118 418s 3 0 50050051 Inf Inf 418s > stopifnot(is.data.frame(segs)) 418s > stopifnot(nrow(segs) == 3L) 418s > 418s > 418s > 418s > # BUG FIX: Issue #6 418s > gaps <- findLargeGaps(chromosome=rep(1,10), x=1:10, minLength=2) 418s > print(gaps) 418s [1] chromosome start end 418s <0 rows> (or 0-length row.names) 418s > stopifnot(is.data.frame(gaps)) 418s > stopifnot(nrow(gaps) == 0L) 418s > # BUG FIX: Issue #9 418s > segs <- gapsToSegments(gaps) 418s > print(segs) 418s chromosome start end 418s 1 0 -Inf Inf 418s > stopifnot(is.data.frame(segs)) 418s > stopifnot(nrow(segs) == 1L) 418s > 418s > 418s > # BUG FIX: PSCBS GitHub Issue #8 418s > gaps <- try({ 418s + findLargeGaps(chromosome=rep(1,3), x=as.numeric(1:3), minLength=1) 418s + }) 418s Error in findLargeGaps.default(chromosome = rep(1, 3), x = as.numeric(1:3), : 418s Cannot identify large gaps. Argument 'resolution' (=1) is not strictly smaller than 'minLength' (=1). 418s > stopifnot(inherits(gaps, "try-error")) 418s > 418s > proc.time() 418s user system elapsed 418s 0.425 0.053 0.480 418s Test findLargeGaps passed 418s 0 418s Begin test randomSeed 418s + cat randomSeed.Rout 418s 418s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 418s Copyright (C) 2024 The R Foundation for Statistical Computing 418s Platform: s390x-ibm-linux-gnu (64-bit) 418s 418s R is free software and comes with ABSOLUTELY NO WARRANTY. 418s You are welcome to redistribute it under certain conditions. 418s Type 'license()' or 'licence()' for distribution details. 418s 418s R is a collaborative project with many contributors. 418s Type 'contributors()' for more information and 418s 'citation()' on how to cite R or R packages in publications. 418s 418s Type 'demo()' for some demos, 'help()' for on-line help, or 418s 'help.start()' for an HTML browser interface to help. 418s Type 'q()' to quit R. 418s 418s [Previously saved workspace restored] 418s 418s > library("PSCBS") 418s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 418s 418s Attaching package: 'PSCBS' 418s 418s The following objects are masked from 'package:base': 418s 418s append, load 418s 418s > 418s > message("*** randomSeed() - setup ...") 418s *** randomSeed() - setup ... 418s > ovars <- ls(envir=globalenv()) 418s > genv <- globalenv() 418s > RNGkind("Mersenne-Twister") 418s > if (exists(".Random.seed", envir=genv, inherits=FALSE)) 418s + rm(list=".Random.seed", envir=genv, inherits=FALSE) 418s > seed0 <- genv$.Random.seed 418s > stopifnot(is.null(seed0)) 418s > okind0 <- RNGkind()[1L] 418s > 418s > sample1 <- function() { sample(0:9, size=1L) } 418s > message("*** randomSeed() - setup ... done") 418s *** randomSeed() - setup ... done 418s > 418s > 418s > message("*** randomSeed('get') ...") 418s *** randomSeed('get') ... 418s > ## Get random seed 418s > seed <- randomSeed("get") 418s > stopifnot(identical(seed, seed0)) 418s > 418s > ## Repeat after new sample 418s > y1 <- sample1() 418s > message(sprintf("Random number: %d", y1)) 418s Random number: 3 418s > seed1 <- randomSeed("get") 418s > stopifnot(!identical(seed1, seed0)) 418s > message("*** randomSeed('get') ... done") 418s *** randomSeed('get') ... done 418s > 418s > 418s > message("*** randomSeed('set', 42L) ...") 418s *** randomSeed('set', 42L) ... 418s > randomSeed("set", seed=42L) 418s > seed2 <- randomSeed("get") 418s > stopifnot(!identical(seed2, seed1)) 418s > 418s > y2 <- sample1() 418s > message(sprintf("Random number: %d (with random seed = 42L)", y2)) 418s Random number: 0 (with random seed = 42L) 418s > 418s > ## Reset to previous state 418s > randomSeed("reset") 418s > seed3 <- randomSeed("get") 418s > stopifnot(identical(seed3, seed1)) 418s > stopifnot(identical(RNGkind()[1L], okind0), 418s + identical(randomSeed("get"), seed1)) 418s > message("*** randomSeed('set', 42L) ... done") 418s *** randomSeed('set', 42L) ... done 418s > 418s > 418s > message("*** randomSeed('set', NULL) ...") 418s *** randomSeed('set', NULL) ... 418s > randomSeed("set", seed=NULL) 418s > seed4 <- randomSeed("get") 418s > stopifnot(is.null(seed4)) 418s > 418s > y3 <- sample1() 418s > message(sprintf("Random number: %d", y3)) 418s Random number: 4 418s > 418s > message("*** randomSeed('set', NULL) ... done") 418s *** randomSeed('set', NULL) ... done 418s > 418s > 418s > message("*** randomSeed('set', 42L) again ...") 418s *** randomSeed('set', 42L) again ... 418s > seed5 <- randomSeed("get") 418s > randomSeed("set", seed=42L) 418s > y4 <- sample1() 418s > message(sprintf("Random number: %d (with random seed = 42L)", y4)) 418s Random number: 0 (with random seed = 42L) 418s > stopifnot(identical(y4, y2)) 418s > 418s > randomSeed("reset") 418s > stopifnot(identical(RNGkind()[1L], okind0), 418s + identical(randomSeed("get"), seed5)) 418s > message("*** randomSeed('set', 42L) again ... done") 418s *** randomSeed('set', 42L) again ... done 418s > 418s > 418s > 418s > ## L'Ecuyer-CMRG: Random number generation for parallel processing 418s > message("*** randomSeed(): L'Ecuyer-CMRG stream ...") 418s *** randomSeed(): L'Ecuyer-CMRG stream ... 418s > 418s > okind <- RNGkind()[1L] 418s > stopifnot(identical(okind, okind0)) 418s > 418s > randomSeed("set", seed=NULL) 418s > oseed <- randomSeed("get") 418s > stopifnot(is.null(oseed)) 418s > 418s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 418s > oseed2 <- randomSeed("reset") 418s > str(oseed2) 418s NULL 418s > stopifnot(identical(oseed2, oseed)) 418s > stopifnot(identical(RNGkind()[1L], okind), 418s + identical(randomSeed("get"), oseed)) 418s > 418s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 418s > seed0 <- randomSeed("get") 418s > seeds0 <- lapply(1:10, FUN=function(i) randomSeed("advance")) 418s > oseed2 <- randomSeed("reset") 418s > stopifnot(identical(oseed2, oseed)) 418s > stopifnot(identical(RNGkind()[1L], okind), 418s + identical(randomSeed("get"), oseed)) 418s > 418s > 418s > ## Assert reproducible .Random.seed stream 418s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 418s > seed1 <- randomSeed("get") 418s > seeds1 <- lapply(1:10, FUN=function(i) randomSeed("advance")) 418s > stopifnot(identical(seed1, seed0)) 418s > stopifnot(identical(seeds1, seeds0)) 418s > 418s > randomSeed("reset") 418s > stopifnot(identical(RNGkind()[1L], okind), 418s + identical(randomSeed("get"), oseed)) 418s > 418s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 418s > seeds2 <- randomSeed("advance", n=10L) 418s > stopifnot(identical(seeds2, seeds0)) 418s > 418s > randomSeed("reset") 418s > stopifnot(identical(RNGkind()[1L], okind), 418s + identical(randomSeed("get"), oseed)) 418s > 418s > randomSeed("set", seed=seeds2[[1]], kind="L'Ecuyer-CMRG") 418s > randomSeed("reset") 418s > stopifnot(identical(RNGkind()[1L], okind), 418s + identical(randomSeed("get"), oseed)) 418s > 418s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 418s > y0 <- sapply(1:10, FUN=function(ii) { 418s + randomSeed("advance") 418s + sample1() 418s + }) 418s > print(y0) 418s [1] 6 9 6 9 9 9 0 7 6 5 418s > randomSeed("reset") 418s > 418s > randomSeed("set", seed=42L, kind="L'Ecuyer-CMRG") 418s > y1 <- sapply(1:10, FUN=function(ii) { 418s + randomSeed("advance") 418s + sample1() 418s + }) 418s > print(y1) 418s [1] 6 9 6 9 9 9 0 7 6 5 418s > stopifnot(identical(y1, y0)) 418s > randomSeed("reset") 418s > 418s > stopifnot(identical(RNGkind()[1L], okind)) 418s > 418s > message("*** randomSeed(): L'Ecuyer-CMRG stream ... done") 418s *** randomSeed(): L'Ecuyer-CMRG stream ... done 418s > 418s > 418s > ## Cleanup 418s > message("*** randomSeed() - cleanup ...") 418s *** randomSeed() - cleanup ... 418s > genv <- globalenv() 418s > RNGkind("Mersenne-Twister") 418s > if (exists(".Random.seed", envir=genv, inherits=FALSE)) 418s + rm(list=".Random.seed", envir=genv, inherits=FALSE) 418s > rm(list=ovars, envir=globalenv()) 418s > message("*** randomSeed() - cleanup ... done") 418s *** randomSeed() - cleanup ... done 418s > 418s > proc.time() 418s user system elapsed 418s 0.359 0.047 0.409 418s + [ 0 != 0 ] 418s + echo Test randomSeed passed 418s Test randomSeed passed 418s 0 418s Begin test segmentByCBS,calls 418s + echo 0 418s + echo Begin test segmentByCBS,calls 418s + exitcode=0 418s + R CMD BATCH segmentByCBS,calls.R 418s + cat segmentByCBS,calls.Rout 418s + 418s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 418s Copyright (C) 2024 The R Foundation for Statistical Computing 418s Platform: s390x-ibm-linux-gnu (64-bit) 418s 418s R is free software and comes with ABSOLUTELY NO WARRANTY. 418s You are welcome to redistribute it under certain conditions. 418s Type 'license()' or 'licence()' for distribution details. 418s 418s R is a collaborative project with many contributors. 418s Type 'contributors()' for more information and 418s 'citation()' on how to cite R or R packages in publications. 418s 418s Type 'demo()' for some demos, 'help()' for on-line help, or 418s 'help.start()' for an HTML browser interface to help. 418s Type 'q()' to quit R. 418s 418s [Previously saved workspace restored] 418s 418s > # This test script calls a report generator which requires 418s > # the 'ggplot2' package, which in turn will require packages 418s > # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'. 418s > 418s > # Only run this test in full testing mode 418s > if (Sys.getenv("_R_CHECK_FULL_") != "") { 418s + library("PSCBS") 418s + stext <- R.utils::stext 418s + 418s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 418s + # Load SNP microarray data 418s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 418s + data <- PSCBS::exampleData("paired.chr01") 418s + str(data) 418s + 418s + data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT) 418s + 418s + 418s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 418s + # CBS segmentation 418s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 418s + # Drop single-locus outliers 418s + dataS <- dropSegmentationOutliers(data) 418s + 418s + # Speed up example by segmenting fewer loci 418s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 418s + 418s + str(dataS) 418s + 418s + gaps <- findLargeGaps(dataS, minLength=2e6) 418s + knownSegments <- gapsToSegments(gaps) 418s + 418s + # CBS segmentation 418s + fit <- segmentByCBS(dataS, knownSegments=knownSegments, 418s + seed=0xBEEF, verbose=-10) 418s + signalType(fit) <- "ratio" 418s + plotTracks(fit) 418s + 418s + 418s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 418s + # Call using the UCSF MAD caller (not recommended) 418s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 418s + fitC <- callGainsAndLosses(fit) 418s + plotTracks(fitC) 418s + pars <- fitC$params$callGainsAndLosses 418s + stext(side=3, pos=1/2, line=-1, substitute(sigma==x, list(x=sprintf("%.2f", pars$sigmaMAD)))) 418s + mu <- pars$muR 418s + tau <- unlist(pars[c("tauLoss", "tauGain")], use.names=FALSE) 418s + abline(h=mu, lty=2, lwd=2) 418s + abline(h=tau, lwd=2) 418s + mtext(side=4, at=tau[1], expression(Delta[LOSS]), adj=-0.2, cex=0.7, las=2, xpd=TRUE) 418s + mtext(side=4, at=tau[2], expression(Delta[GAIN]), adj=-0.2, cex=0.7, las=2, xpd=TRUE) 418s + title(main="CN caller: \"ucsf-mad\"") 418s + 418s + 418s + # Caller to be implemented 418s + deltaCN <- estimateDeltaCN(fit) 418s + tau <- mu + 1/2*c(-1,+1)*deltaCN 418s + abline(h=tau, lty=2, lwd=1, col="red") 418s + 418s + 418s + 418s + } # if (Sys.getenv("_R_CHECK_FULL_")) 418s > 418s > proc.time() 418s user system elapsed 418s 0.156 0.029 0.186 418s [ 0 != 0Test segmentByCBS,calls passed 418s 0 418s Begin test segmentByCBS,futures 418s ] 418s + echo Test segmentByCBS,calls passed 418s + echo 0 418s + echo Begin test segmentByCBS,futures 418s + exitcode=0 418s + R CMD BATCH segmentByCBS,futures.R 420s + cat segmentByCBS,futures.Rout 420s + [ 0 != 0 ] 420s + echo Test segmentByCBS,futures passed 420s + echo 0 420s + echo Begin test segmentByCBS,median 420s + exitcode=0 420s + R CMD BATCH segmentByCBS,median.R 420s 420s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 420s Copyright (C) 2024 The R Foundation for Statistical Computing 420s Platform: s390x-ibm-linux-gnu (64-bit) 420s 420s R is free software and comes with ABSOLUTELY NO WARRANTY. 420s You are welcome to redistribute it under certain conditions. 420s Type 'license()' or 'licence()' for distribution details. 420s 420s R is a collaborative project with many contributors. 420s Type 'contributors()' for more information and 420s 'citation()' on how to cite R or R packages in publications. 420s 420s Type 'demo()' for some demos, 'help()' for on-line help, or 420s 'help.start()' for an HTML browser interface to help. 420s Type 'q()' to quit R. 420s 420s [Previously saved workspace restored] 420s 420s > library("PSCBS") 420s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 420s 420s Attaching package: 'PSCBS' 420s 420s The following objects are masked from 'package:base': 420s 420s append, load 420s 420s > 420s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 420s > # Simulating copy-number data 420s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 420s > set.seed(0xBEEF) 420s > 420s > # Number of loci 420s > J <- 1000 420s > 420s > mu <- double(J) 420s > mu[200:300] <- mu[200:300] + 1 420s > mu[350:400] <- NA # centromere 420s > mu[650:800] <- mu[650:800] - 1 420s > eps <- rnorm(J, sd=1/2) 420s > y <- mu + eps 420s > x <- sort(runif(length(y), max=length(y))) * 1e5 420s > w <- runif(J) 420s > w[650:800] <- 0.001 420s > 420s > ## Create multiple chromosomes 420s > data <- knownSegments <- list() 420s > for (cc in 1:3) { 420s + data[[cc]] <- data.frame(chromosome=cc, y=y, x=x) 420s + knownSegments[[cc]] <- data.frame( 420s + chromosome=c( cc, cc, cc), 420s + start =x[c( 1, 350, 401)], 420s + end =x[c(349, 400, J)] 420s + ) 420s + } 420s > data <- Reduce(rbind, data) 420s > str(data) 420s 'data.frame': 3000 obs. of 3 variables: 420s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 420s $ y : num 0.295 0.115 -0.194 -0.392 -0.518 ... 420s $ x : num 55168 593204 605649 630624 746896 ... 420s > knownSegments <- Reduce(rbind, knownSegments) 420s > str(knownSegments) 420s 'data.frame': 9 obs. of 3 variables: 420s $ chromosome: int 1 1 1 2 2 2 3 3 3 420s $ start : num 55168 34194740 41080533 55168 34194740 ... 420s $ end : num 34142178 41044125 99910827 34142178 41044125 ... 420s > 420s > message("*** segmentByCBS() via futures ...") 420s *** segmentByCBS() via futures ... 420s > 420s > 420s > message("*** segmentByCBS() via futures with 'future' attached ...") 420s *** segmentByCBS() via futures with 'future' attached ... 420s > library("future") 420s > oplan <- plan() 420s > 420s > strategies <- c("sequential", "multisession") 420s > 420s > ## Test 'future.batchtools' futures? 420s > pkg <- "future.batchtools" 420s > if (require(pkg, character.only=TRUE)) { 420s + strategies <- c(strategies, "batchtools_local") 420s + } 420s Loading required package: future.batchtools 420s Warning message: 420s In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : 420s there is no package called 'future.batchtools' 420s > 420s > message("Future strategies to test: ", paste(sQuote(strategies), collapse=", ")) 420s Future strategies to test: 'sequential', 'multisession' 420s > 420s > fits <- list() 420s > for (strategy in strategies) { 420s + message(sprintf("- segmentByCBS() using '%s' futures ...", strategy)) 420s + plan(strategy) 420s + fit <- segmentByCBS(data, seed=0xBEEF, verbose=TRUE) 420s + fits[[strategy]] <- fit 420s + stopifnot(all.equal(fit, fits[[1]])) 420s + } 420s - segmentByCBS() using 'sequential' futures ... 420s Segmenting by CBS... 420s Segmenting multiple chromosomes... 420s Number of chromosomes: 3 420s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 420s Produced 3 seeds from this stream for future usage 420s Chromosome #1 ('Chr01') of 3... 420s Segmenting by CBS... 420s Chromosome: 1 420s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 420s Segmenting by CBS...done 420s Chromosome #1 ('Chr01') of 3...done 420s Chromosome #2 ('Chr02') of 3... 420s Segmenting by CBS... 420s Chromosome: 2 420s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 420s Segmenting by CBS...done 420s Chromosome #2 ('Chr02') of 3...done 420s Chromosome #3 ('Chr03') of 3... 420s Segmenting by CBS... 420s Chromosome: 3 420s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 420s Segmenting by CBS...done 420s Chromosome #3 ('Chr03') of 3...done 420s Segmenting multiple chromosomes...done 420s Segmenting by CBS...done 420s list() 420s - segmentByCBS() using 'multisession' futures ... 420s Segmenting by CBS... 420s Segmenting multiple chromosomes... 420s Number of chromosomes: 3 420s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 420s Produced 3 seeds from this stream for future usage 420s Chromosome #1 ('Chr01') of 3... 420s Segmenting by CBS... 420s Chromosome: 1 420s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 420s Segmenting by CBS...done 420s Chromosome #1 ('Chr01') of 3...done 420s Chromosome #2 ('Chr02') of 3... 420s Segmenting by CBS... 420s Chromosome: 2 420s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 420s Segmenting by CBS...done 420s Chromosome #2 ('Chr02') of 3...done 420s Chromosome #3 ('Chr03') of 3... 420s Segmenting by CBS... 420s Chromosome: 3 420s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 420s Segmenting by CBS...done 420s Chromosome #3 ('Chr03') of 3...done 420s Segmenting multiple chromosomes...done 420s Segmenting by CBS...done 420s list() 420s > 420s > 420s > message("*** segmentByCBS() via futures with known segments ...") 420s *** segmentByCBS() via futures with known segments ... 420s > fits <- list() 420s > dataT <- subset(data, chromosome == 1) 420s > for (strategy in strategies) { 420s + message(sprintf("- segmentByCBS() w/ known segments using '%s' futures ...", strategy)) 420s + plan(strategy) 420s + fit <- segmentByCBS(dataT, knownSegments=knownSegments, seed=0xBEEF, verbose=TRUE) 420s + fits[[strategy]] <- fit 420s + stopifnot(all.equal(fit, fits[[1]])) 420s + } 420s - segmentByCBS() w/ known segments using 'sequential' futures ... 420s Segmenting by CBS... 420s Chromosome: 1 420s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 420s Produced 3 seeds from this stream for future usage 420s Segmenting by CBS...done 420s list() 420s - segmentByCBS() w/ known segments using 'multisession' futures ... 420s Segmenting by CBS... 420s Chromosome: 1 420s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 420s Produced 3 seeds from this stream for future usage 420s Segmenting by CBS...done 420s list() 420s > 420s > message("*** segmentByCBS() via futures ... DONE") 420s *** segmentByCBS() via futures ... DONE 420s > 420s > 420s > ## Cleanup 420s > plan(oplan) 420s > rm(list=c("fits", "dataT", "data", "fit")) 420s > 420s > 420s > proc.time() 420s user system elapsed 420s 1.851 0.074 1.942 420s Test segmentByCBS,futures passed 420s 0 420s Begin test segmentByCBS,median 422s + cat segmentByCBS,median.Rout 422s 422s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 422s Copyright (C) 2024 The R Foundation for Statistical Computing 422s Platform: s390x-ibm-linux-gnu (64-bit) 422s 422s R is free software and comes with ABSOLUTELY NO WARRANTY. 422s You are welcome to redistribute it under certain conditions. 422s Type 'license()' or 'licence()' for distribution details. 422s 422s R is a collaborative project with many contributors. 422s Type 'contributors()' for more information and 422s 'citation()' on how to cite R or R packages in publications. 422s 422s Type 'demo()' for some demos, 'help()' for on-line help, or 422s 'help.start()' for an HTML browser interface to help. 422s Type 'q()' to quit R. 422s 422s [Previously saved workspace restored] 422s 422s > library("PSCBS") 422s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 422s 422s Attaching package: 'PSCBS' 422s 422s The following objects are masked from 'package:base': 422s 422s append, load 422s 422s > 422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 422s > # Simulating copy-number data 422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 422s > set.seed(0xBEEF) 422s > 422s > # Number of loci 422s > J <- 1000 422s > 422s > x <- sort(runif(J, max=J)) * 1e5 422s > 422s > mu <- double(J) 422s > mu[200:300] <- mu[200:300] + 1 422s > mu[350:400] <- NA # centromere 422s > mu[650:800] <- mu[650:800] - 1 422s > eps <- rnorm(J, sd=1/2) 422s > y <- mu + eps 422s > 422s > outliers <- seq(from=1L, to=J, length.out=0.2*J) 422s > y[outliers] <- y[outliers] + 1.5 422s > 422s > w <- rep(1.0, times=J) 422s > w[outliers] <- 0.01 422s > 422s > data <- data.frame(chromosome=1L, x=x, y=y) 422s > dataW <- cbind(data, w=w) 422s > 422s > 422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 422s > # Single-chromosome segmentation 422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 422s > par(mar=c(2,3,0.2,1)+0.1) 422s > # Segment without weights 422s > fit <- segmentByCBS(data) 422s > sampleName(fit) <- "CBS_Example" 422s > print(fit) 422s sampleName chromosome start end nbrOfLoci mean 422s 1 CBS_Example 1 6.066868e+02 19076007 199 0.2622 422s 2 CBS_Example 1 1.907601e+07 29630949 99 1.4289 422s 3 CBS_Example 1 2.963095e+07 63224332 299 0.2854 422s 4 CBS_Example 1 6.322433e+07 78801707 153 -0.7408 422s 5 CBS_Example 1 7.880171e+07 99917418 199 0.3541 422s > plotTracks(fit) 422s Warning message: 422s In plotTracks.CBS(fit) : 422s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning. 422s > ## Highlight outliers (they pull up the mean levels) 422s > points(x[outliers]/1e6, y[outliers], col="purple") 422s > 422s > # Segment without weights but with median 422s > fitM <- segmentByCBS(data, avg="median") 422s > sampleName(fitM) <- "CBS_Example (median)" 422s > print(fitM) 422s sampleName chromosome start end nbrOfLoci mean 422s 1 CBS_Example (median) 1 6.066868e+02 19076007 199 0.1005418 422s 2 CBS_Example (median) 1 1.907601e+07 29630949 99 1.2720955 422s 3 CBS_Example (median) 1 2.963095e+07 63224332 299 0.1337148 422s 4 CBS_Example (median) 1 6.322433e+07 78801707 153 -0.8655254 422s 5 CBS_Example (median) 1 7.880171e+07 99917418 199 0.1718179 422s > drawLevels(fitM, col="magenta", lty=3) 422s NULL 422s > 422s > # Segment with weights 422s > fitW <- segmentByCBS(dataW, avg="median") 422s > sampleName(fitW) <- "CBS_Example (weighted)" 422s > print(fitW) 422s sampleName chromosome start end nbrOfLoci mean 422s 1 CBS_Example (weighted) 1 6.066868e+02 19076007 199 -0.08745973 422s 2 CBS_Example (weighted) 1 1.907601e+07 30126128 101 1.12968951 422s 3 CBS_Example (weighted) 1 3.012613e+07 63224332 297 -0.06074638 422s 4 CBS_Example (weighted) 1 6.322433e+07 78801707 153 -1.06373835 422s 5 CBS_Example (weighted) 1 7.880171e+07 99917418 199 0.04204744 422s > drawLevels(fitW, col="red") 422s NULL 422s > 422s > # Segment with weights and median 422s > fitWM <- segmentByCBS(dataW, avg="median") 422s > sampleName(fitWM) <- "CBS_Example (weighted median)" 422s > print(fitWM) 422s sampleName chromosome start end nbrOfLoci 422s 1 CBS_Example (weighted median) 1 6.066868e+02 19076007 199 422s 2 CBS_Example (weighted median) 1 1.907601e+07 30126128 101 422s 3 CBS_Example (weighted median) 1 3.012613e+07 63224332 297 422s 4 CBS_Example (weighted median) 1 6.322433e+07 78801707 153 422s 5 CBS_Example (weighted median) 1 7.880171e+07 99917418 199 422s mean 422s 1 -0.08745973 422s 2 1.12968951 422s 3 -0.06074638 422s 4 -1.06373835 422s 5 0.04204744 422s > drawLevels(fitWM, col="orange", lty=3) 422s NULL 422s > 422s > 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)) 422s > 422s > ## Assert that weighted segment means are less biased 422s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 422s > cat("Segment mean differences:\n") 422s Segment mean differences: 422s > print(dmean) 422s [1] 0.3496597 0.2992105 0.3461464 0.3229384 0.3120526 422s > stopifnot(all(dmean > 0, na.rm=TRUE)) 422s > 422s > dmean <- getSegments(fitM)$mean - getSegments(fitWM)$mean 422s > cat("Segment median differences:\n") 422s Segment median differences: 422s > print(dmean) 422s [1] 0.1880015 0.1424060 0.1944611 0.1982130 0.1297704 422s > stopifnot(all(dmean > 0, na.rm=TRUE)) 422s > 422s > 422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 422s > # Multi-chromosome segmentation 422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 422s > data2 <- data 422s > data2$chromosome <- 2L 422s > data <- rbind(data, data2) 422s > dataW <- cbind(data, w=w) 422s > 422s > par(mar=c(2,3,0.2,1)+0.1) 422s > # Segment without weights 422s > fit <- segmentByCBS(data) 422s > sampleName(fit) <- "CBS_Example" 422s > print(fit) 422s sampleName chromosome start end nbrOfLoci mean 422s 1 CBS_Example 1 6.066868e+02 19076007 199 0.2622 422s 2 CBS_Example 1 1.907601e+07 29630949 99 1.4289 422s 3 CBS_Example 1 2.963095e+07 63224332 299 0.2854 422s 4 CBS_Example 1 6.322433e+07 78801707 153 -0.7408 422s 5 CBS_Example 1 7.880171e+07 99917418 199 0.3541 422s 6 NA NA NA NA NA 422s 7 CBS_Example 2 6.066868e+02 19076007 199 0.2622 422s 8 CBS_Example 2 1.907601e+07 29630949 99 1.4289 422s 9 CBS_Example 2 2.963095e+07 63224332 299 0.2854 422s 10 CBS_Example 2 6.322433e+07 78801707 153 -0.7408 422s 11 CBS_Example 2 7.880171e+07 99917418 199 0.3541 422s > plotTracks(fit, Clim=c(-3,3)) 422s > 422s > # Segment without weights but with median 422s > fitM <- segmentByCBS(data, avg="median") 422s > sampleName(fitM) <- "CBS_Example (median)" 422s > print(fitM) 422s sampleName chromosome start end nbrOfLoci mean 422s 1 CBS_Example (median) 1 6.066868e+02 19076007 199 0.1005418 422s 2 CBS_Example (median) 1 1.907601e+07 29630949 99 1.2720955 422s 3 CBS_Example (median) 1 2.963095e+07 63224332 299 0.1337148 422s 4 CBS_Example (median) 1 6.322433e+07 78801707 153 -0.8655254 422s 5 CBS_Example (median) 1 7.880171e+07 99917418 199 0.1718179 422s 6 NA NA NA NA NA 422s 7 CBS_Example (median) 2 6.066868e+02 19076007 199 0.1005418 422s 8 CBS_Example (median) 2 1.907601e+07 29630949 99 1.2720955 422s 9 CBS_Example (median) 2 2.963095e+07 63224332 299 0.1337148 422s 10 CBS_Example (median) 2 6.322433e+07 78801707 153 -0.8655254 422s 11 CBS_Example (median) 2 7.880171e+07 99917418 199 0.1718179 422s > drawLevels(fitM, col="magenta", lty=3) 422s NULL 422s > 422s > # Segment with weights 422s > fitW <- segmentByCBS(dataW, avg="median") 422s > sampleName(fitW) <- "CBS_Example (weighted)" 422s > print(fitW) 422s sampleName chromosome start end nbrOfLoci 422s 1 CBS_Example (weighted) 1 6.066868e+02 19076007 199 422s 2 CBS_Example (weighted) 1 1.907601e+07 30126128 101 422s 3 CBS_Example (weighted) 1 3.012613e+07 63224332 297 422s 4 CBS_Example (weighted) 1 6.322433e+07 78801707 153 422s 5 CBS_Example (weighted) 1 7.880171e+07 99917418 199 422s 6 NA NA NA NA 422s 7 CBS_Example (weighted) 2 6.066868e+02 19076007 199 422s 8 CBS_Example (weighted) 2 1.907601e+07 30126128 101 422s 9 CBS_Example (weighted) 2 3.012613e+07 63224332 297 422s 10 CBS_Example (weighted) 2 6.322433e+07 78801707 153 422s 11 CBS_Example (weighted) 2 7.880171e+07 99917418 199 422s mean 422s 1 -0.08745973 422s 2 1.12968951 422s 3 -0.06074638 422s 4 -1.06373835 422s 5 0.04204744 422s 6 NA 422s 7 -0.08745973 422s 8 1.12968951 422s 9 -0.06074638 422s 10 -1.06373835 422s 11 0.04204744 422s > drawLevels(fitW, col="red") 422s NULL 422s > 422s > # Segment with weights and median 422s > fitWM <- segmentByCBS(dataW, avg="median") 422s > sampleName(fitWM) <- "CBS_Example (weighted median)" 422s > print(fitWM) 422s sampleName chromosome start end nbrOfLoci 422s 1 CBS_Example (weighted median) 1 6.066868e+02 19076007 199 422s 2 CBS_Example (weighted median) 1 1.907601e+07 30126128 101 422s 3 CBS_Example (weighted median) 1 3.012613e+07 63224332 297 422s 4 CBS_Example (weighted median) 1 6.322433e+07 78801707 153 422s 5 CBS_Example (weighted median) 1 7.880171e+07 99917418 199 422s 6 NA NA NA NA 422s 7 CBS_Example (weighted median) 2 6.066868e+02 19076007 199 422s 8 CBS_Example (weighted median) 2 1.907601e+07 30126128 101 422s 9 CBS_Example (weighted median) 2 3.012613e+07 63224332 297 422s 10 CBS_Example (weighted median) 2 6.322433e+07 78801707 153 422s 11 CBS_Example (weighted median) 2 7.880171e+07 99917418 199 422s mean 422s 1 -0.08745973 422s 2 1.12968951 422s 3 -0.06074638 422s 4 -1.06373835 422s 5 0.04204744 422s 6 NA 422s 7 -0.08745973 422s 8 1.12968951 422s 9 -0.06074638 422s 10 -1.06373835 422s 11 0.04204744 422s > drawLevels(fitWM, col="orange", lty=3) 422s NULL 422s > 422s > 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)) 422s > 422s > ## Assert that weighted segment means are less biased 422s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 422s > cat("Segment mean differences:\n") 422s Segment mean differences: 422s > print(dmean) 422s [1] 0.3496597 0.2992105 0.3461464 0.3229384 0.3120526 NA 0.3496597 422s [8] 0.2992105 0.3461464 0.3229384 0.3120526 422s > stopifnot(all(dmean > 0, na.rm=TRUE)) 422s > 422s > dmean <- getSegments(fitM)$mean - getSegments(fitWM)$mean 422s > cat("Segment median differences:\n") 422s Segment median differences: 422s > print(dmean) 422s [1] 0.1880015 0.1424060 0.1944611 0.1982130 0.1297704 NA 0.1880015 422s [8] 0.1424060 0.1944611 0.1982130 0.1297704 422s > stopifnot(all(dmean > 0, na.rm=TRUE)) 422s > 422s > proc.time() 422s user system elapsed 422s 1.343 0.060 1.417 422s Test segmentByCBS,median passed 422s 0 422s Begin test segmentByCBS,prune 422s + [ 0 != 0 ] 422s + echo Test segmentByCBS,median passed 422s + echo 0 422s + echo Begin test segmentByCBS,prune 422s + exitcode=0 422s + R CMD BATCH segmentByCBS,prune.R 424s + 424s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 424s Copyright (C) 2024 The R Foundation for Statistical Computing 424s Platform: s390x-ibm-linux-gnu (64-bit) 424s 424s R is free software and comes with ABSOLUTELY NO WARRANTY. 424s You are welcome to redistribute it under certain conditions. 424s Type 'license()' or 'licence()' for distribution details. 424s 424s R is a collaborative project with many contributors. 424s Type 'contributors()' for more information and 424s 'citation()' on how to cite R or R packages in publications. 424s 424s Type 'demo()' for some demos, 'help()' for on-line help, or 424s 'help.start()' for an HTML browser interface to help. 424s Type 'q()' to quit R. 424s 424s [Previously saved workspace restored] 424s 424s > library("PSCBS") 424s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 424s 424s Attaching package: 'PSCBS' 424s 424s The following objects are masked from 'package:base': 424s 424s append, load 424s 424s > 424s > ## Compare segments 424s > assertMatchingSegments <- function(fitM, fit) { 424s + chrs <- getChromosomes(fitM) 424s + segsM <- lapply(chrs, FUN=function(chr) { 424s + getSegments(extractChromosome(fitM, chr)) 424s + }) 424s + segs <- lapply(fit[chrs], FUN=getSegments) 424s + stopifnot(all.equal(segsM, segs, check.attributes=FALSE)) 424s + } 424s > 424s > ## Simulate data 424s > set.seed(0xBEEF) 424s > J <- 1000 424s > mu <- double(J) 424s > mu[200:300] <- mu[200:300] + 1 424s > mu[350:400] <- NA 424s > mu[650:800] <- mu[650:800] - 1 424s > eps <- rnorm(J, sd=1/2) 424s > y <- mu + eps 424s > x <- sort(runif(length(y), max=length(y))) * 1e5 424s > 424s > data <- list() 424s > for (chr in 1:2) { 424s + data[[chr]] <- data.frame(chromosome=chr, x=x, y=y) 424s + } 424s > data$M <- Reduce(rbind, data) 424s > 424s > ## Segment 424s > message("*** segmentByCBS()") 424s *** segmentByCBS() 424s > fit <- lapply(data, FUN=segmentByCBS) 424s > print(fit) 424s [[1]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 19648927 200 0.0109 424s 2 1 19648927.46 28239656 95 0.9529 424s 3 1 28239655.99 65697742 302 -0.0126 424s 4 1 65697742.20 79729368 153 -0.9534 424s 5 1 79729368.34 99819310 199 -0.0497 424s 424s [[2]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 2 65285.65 19648927 200 0.0109 424s 2 2 19648927.46 28239656 95 0.9529 424s 3 2 28239655.99 65697742 302 -0.0126 424s 4 2 65697742.20 79729368 153 -0.9534 424s 5 2 79729368.34 99819310 199 -0.0497 424s 424s $M 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 19648927 200 0.0109 424s 2 1 19648927.46 28239656 95 0.9529 424s 3 1 28239655.99 65697742 302 -0.0126 424s 4 1 65697742.20 79729368 153 -0.9534 424s 5 1 79729368.34 99819310 199 -0.0497 424s 6 NA NA NA NA NA 424s 7 2 65285.65 19648927 200 0.0109 424s 8 2 19648927.46 28239656 95 0.9529 424s 9 2 28239655.99 65697742 302 -0.0126 424s 10 2 65697742.20 79729368 153 -0.9534 424s 11 2 79729368.34 99819310 199 -0.0497 424s 424s > assertMatchingSegments(fit$M, fit) 424s > 424s > ## Join segments 424s > message("*** joinSegments()") 424s *** joinSegments() 424s > fitj <- lapply(fit, FUN=joinSegments) 424s > print(fitj) 424s [[1]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 19648927 200 0.0109 424s 2 1 19648927.46 28239656 95 0.9529 424s 3 1 28239655.99 65697742 302 -0.0126 424s 4 1 65697742.20 79729368 153 -0.9534 424s 5 1 79729368.34 99819310 199 -0.0497 424s 424s [[2]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 2 65285.65 19648927 200 0.0109 424s 2 2 19648927.46 28239656 95 0.9529 424s 3 2 28239655.99 65697742 302 -0.0126 424s 4 2 65697742.20 79729368 153 -0.9534 424s 5 2 79729368.34 99819310 199 -0.0497 424s 424s $M 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 19648927 200 0.0109 424s 2 1 19648927.46 28239656 95 0.9529 424s 3 1 28239655.99 65697742 302 -0.0126 424s 4 1 65697742.20 79729368 153 -0.9534 424s 5 1 79729368.34 99819310 199 -0.0497 424s 6 NA NA NA NA NA 424s 7 2 65285.65 19648927 200 0.0109 424s 8 2 19648927.46 28239656 95 0.9529 424s 9 2 28239655.99 65697742 302 -0.0126 424s 10 2 65697742.20 79729368 153 -0.9534 424s 11 2 79729368.34 99819310 199 -0.0497 424s 424s > assertMatchingSegments(fitj$M, fitj) 424s > 424s > ## Reset segments 424s > message("*** resetSegments()") 424s *** resetSegments() 424s > fitj <- lapply(fit, FUN=resetSegments) 424s > print(fitj) 424s [[1]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 19648927 200 0.0109 424s 2 1 19648927.46 28239656 95 0.9529 424s 3 1 28239655.99 65697742 302 -0.0126 424s 4 1 65697742.20 79729368 153 -0.9534 424s 5 1 79729368.34 99819310 199 -0.0497 424s 424s [[2]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 2 65285.65 19648927 200 0.0109 424s 2 2 19648927.46 28239656 95 0.9529 424s 3 2 28239655.99 65697742 302 -0.0126 424s 4 2 65697742.20 79729368 153 -0.9534 424s 5 2 79729368.34 99819310 199 -0.0497 424s 424s $M 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 19648927 200 0.0109 424s 2 1 19648927.46 28239656 95 0.9529 424s 3 1 28239655.99 65697742 302 -0.0126 424s 4 1 65697742.20 79729368 153 -0.9534 424s 5 1 79729368.34 99819310 199 -0.0497 424s 6 NA NA NA NA NA 424s 7 2 65285.65 19648927 200 0.0109 424s 8 2 19648927.46 28239656 95 0.9529 424s 9 2 28239655.99 65697742 302 -0.0126 424s 10 2 65697742.20 79729368 153 -0.9534 424s 11 2 79729368.34 99819310 199 -0.0497 424s 424s > assertMatchingSegments(fitj$M, fitj) 424s > 424s > ## Prune by SD undo 424s > message("*** pruneBySdUndo()") 424s *** pruneBySdUndo() 424s > fitp <- lapply(fit, FUN=pruneBySdUndo) 424s > print(fitp) 424s [[1]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 99819310 949 -0.07045097 424s 424s [[2]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 2 65285.65 99819310 949 -0.07045097 424s 424s $M 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 99819310 949 -0.07045097 424s 2 NA NA NA NA NA 424s 3 2 65285.65 99819310 949 -0.07045097 424s 424s > assertMatchingSegments(fitp$M, fitp) 424s > 424s > ## Prune by hierarchical clustering 424s > message("*** pruneByHClust()") 424s *** pruneByHClust() 424s > fitp <- lapply(fit, FUN=pruneByHClust, k=1L) 424s > print(fitp) 424s [[1]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 99819310 949 -0.07045097 424s 424s [[2]] 424s sampleName chromosome start end nbrOfLoci mean 424s 1 2 65285.65 99819310 949 -0.07045097 424s 424s $M 424s sampleName chromosome start end nbrOfLoci mean 424s 1 1 65285.65 99819310 949 -0.07045097 424s 6 NA NA NA NA NA 424s 7 2 65285.65 99819310 949 -0.07045097 424s 424s > assertMatchingSegments(fitp$M, fitp) 424s > 424s > proc.time() 424s user system elapsed 424s 0.847 0.052 0.903 424s Test segmentByCBS,prune passed 424s 0 424s Begin test segmentByCBS,report 424s cat segmentByCBS,prune.Rout 424s + [ 0 != 0 ] 424s + echo Test segmentByCBS,prune passed 424s + echo 0 424s + echo Begin test segmentByCBS,report 424s + exitcode=0 424s + R CMD BATCH segmentByCBS,report.R 424s + cat segmentByCBS,report.Rout 424s + [ 0 != 0 ] 424s + echo Test segmentByCBS,report passed 424s + echo 0 424s + echo Begin test segmentByCBS,shiftTCN 424s + exitcode=0 424s + R CMD BATCH segmentByCBS,shiftTCN.R 424s 424s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 424s Copyright (C) 2024 The R Foundation for Statistical Computing 424s Platform: s390x-ibm-linux-gnu (64-bit) 424s 424s R is free software and comes with ABSOLUTELY NO WARRANTY. 424s You are welcome to redistribute it under certain conditions. 424s Type 'license()' or 'licence()' for distribution details. 424s 424s R is a collaborative project with many contributors. 424s Type 'contributors()' for more information and 424s 'citation()' on how to cite R or R packages in publications. 424s 424s Type 'demo()' for some demos, 'help()' for on-line help, or 424s 'help.start()' for an HTML browser interface to help. 424s Type 'q()' to quit R. 424s 424s [Previously saved workspace restored] 424s 424s > # This test script calls a report generator which requires 424s > # the 'ggplot2' package, which in turn will require packages 424s > # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'. 424s > 424s > # Only run this test in full testing mode 424s > if (Sys.getenv("_R_CHECK_FULL_") != "") { 424s + library("PSCBS") 424s + 424s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 424s + # Load SNP microarray data 424s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 424s + data <- PSCBS::exampleData("paired.chr01") 424s + str(data) 424s + 424s + data <- data.frame(chromosome=data$chromosome, x=data$x, y=data$CT) 424s + 424s + 424s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 424s + # CBS segmentation 424s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 424s + # Drop single-locus outliers 424s + dataS <- dropSegmentationOutliers(data) 424s + 424s + # Speed up example by segmenting fewer loci 424s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 424s + 424s + str(dataS) 424s + 424s + gaps <- findLargeGaps(dataS, minLength=2e6) 424s + knownSegments <- gapsToSegments(gaps) 424s + 424s + # CBS segmentation 424s + fit <- segmentByCBS(dataS, knownSegments=knownSegments, 424s + seed=0xBEEF, verbose=-10) 424s + signalType(fit) <- "ratio" 424s + 424s + # Fake a multi-chromosome segmentation 424s + fit1 <- fit 424s + fit2 <- renameChromosomes(fit, from=1, to=2) 424s + fit <- c(fit1, fit2) 424s + 424s + report(fit, sampleName="CBS", studyName="CBS-Ex", verbose=-10) 424s + 424s + } # if (Sys.getenv("_R_CHECK_FULL_")) 424s > 424s > proc.time() 424s user system elapsed 424s 0.184 0.031 0.210 424s Test segmentByCBS,report passed 424s 0 424s Begin test segmentByCBS,shiftTCN 430s + cat segmentByCBS,shiftTCN.Rout 430s 430s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 430s Copyright (C) 2024 The R Foundation for Statistical Computing 430s Platform: s390x-ibm-linux-gnu (64-bit) 430s 430s R is free software and comes with ABSOLUTELY NO WARRANTY. 430s You are welcome to redistribute it under certain conditions. 430s Type 'license()' or 'licence()' for distribution details. 430s 430s R is a collaborative project with many contributors. 430s Type 'contributors()' for more information and 430s 'citation()' on how to cite R or R packages in publications. 430s 430s Type 'demo()' for some demos, 'help()' for on-line help, or 430s 'help.start()' for an HTML browser interface to help. 430s Type 'q()' to quit R. 430s 430s [Previously saved workspace restored] 430s 430s > library("PSCBS") 430s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 430s 430s Attaching package: 'PSCBS' 430s 430s The following objects are masked from 'package:base': 430s 430s append, load 430s 430s > subplots <- R.utils::subplots 430s > 430s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 430s > # Simulating copy-number data 430s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 430s > set.seed(0xBEEF) 430s > 430s > # Number of loci 430s > J <- 1000 430s > 430s > mu <- double(J) 430s > eps <- rnorm(J, sd=1/2) 430s > y <- mu + eps 430s > x <- sort(runif(length(y), max=length(y))) 430s > 430s > idxs <- which(200 <= x & x < 300) 430s > y[idxs] <- y[idxs] + 1 430s > idxs <- which(350 <= x & x < 400) 430s > y[idxs] <- NA # centromere 430s > x[idxs] <- NA # centromere 430s > idxs <- which(650 <= x & x < 800) 430s > y[idxs] <- y[idxs] - 1 430s > x <- x*1e5 430s > 430s > keep <- is.finite(x) 430s > x <- x[keep] 430s > y <- y[keep] 430s > 430s > data <- list() 430s > for (chr in 1:2) { 430s + data[[chr]] <- data.frame(chromosome=chr, y=y, x=x) 430s + } 430s > data <- Reduce(rbind, data) 430s > 430s > 430s > subplots(7, ncol=1) 430s > par(mar=c(1.7,1,0.2,1)+0.1) 430s > 430s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 430s > # Segmentation 430s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 430s > fit <- segmentByCBS(data) 430s > print(fit) 430s sampleName chromosome start end nbrOfLoci mean 430s 1 1 65285.65 20169684 205 0.0124 430s 2 1 20169684.05 29980147 103 0.9477 430s 3 1 29980147.36 64779929 287 -0.0299 430s 4 1 64779929.38 80010171 163 -0.9676 430s 5 1 80010171.14 99819310 196 -0.0484 430s 6 NA NA NA NA NA 430s 7 2 65285.65 20169684 205 0.0124 430s 8 2 20169684.05 29980147 103 0.9477 430s 9 2 29980147.36 64779929 287 -0.0299 430s 10 2 64779929.38 80010171 163 -0.9676 430s 11 2 80010171.14 99819310 196 -0.0484 430s > 430s > Clim <- c(-3,3) + c(0,10) 430s > plotTracks(fit, Clim=Clim) 430s > 430s > 430s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 430s > # Shifting every other chromosome 430s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 430s > fitList <- list() 430s > chrs <- getChromosomes(fit) 430s > for (kk in seq_along(chrs)) { 430s + chr <- chrs[kk] 430s + fitKK <- extractChromosome(fit, chr) 430s + if (kk %% 2 == 0) { 430s + fitKK <- shiftTCN(fitKK, shift=+10) 430s + } 430s + fitList[[kk]] <- fitKK 430s + } # for (kk ...) 430s > fitT <- do.call(c, fitList) 430s > # Sanity check 430s > stopifnot(nbrOfSegments(fitT) == nbrOfSegments(fit)) 430s > 430s > plotTracks(fitT, Clim=Clim) 430s > 430s > 430s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 430s > # Shifting every other known segment 430s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 430s > gaps <- findLargeGaps(data, minLength=40e5) 430s > knownSegments <- gapsToSegments(gaps, dropGaps=TRUE) 430s > fit <- segmentByCBS(data, knownSegments=knownSegments) 430s > 430s > subplots(2, ncol=1) 430s > plotTracks(fit, Clim=Clim) 430s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 430s > 430s > fitList <- list() 430s > for (kk in seq_len(nrow(knownSegments))) { 430s + seg <- knownSegments[kk,] 430s + start <- seg$start 430s + end <- seg$end 430s + fitKK <- extractChromosome(fit, seg$chromosome) 430s + segsKK <- getSegments(fitKK) 430s + idxStart <- min(which(segsKK$start >= start)) 430s + idxEnd <- max(which(segsKK$end <= end)) 430s + idxs <- idxStart:idxEnd 430s + fitKK <- extractSegments(fitKK, idxs) 430s + if (kk %% 2 == 0) { 430s + fitKK <- shiftTCN(fitKK, shift=+10) 430s + } 430s + fitList[[kk]] <- fitKK 430s + } # for (kk ...) 430s > fitT <- do.call(c, fitList) 430s > # Sanity check 430s > stopifnot(nbrOfSegments(fitT) == nbrOfSegments(fit)) 430s > 430s > plotTracks(fitT, Clim=Clim) 430s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 430s > 430s > 430s > segList <- seqOfSegmentsByDP(fit) 430s > K <- length(segList) 430s > subplots(K, ncol=2, byrow=FALSE) 430s > par(mar=c(2,1,1,1)) 430s > for (kk in 1:K) { 430s + knownSegments <- segList[[kk]] 430s + fitKK <- resegment(fit, knownSegments=knownSegments, undo=+Inf) 430s + plotTracks(fitKK, Clim=c(-3,3)) 430s + } # for (kk ...) 430s > 430s > proc.time() 430s user system elapsed 430s 6.823 0.078 6.919 431s + [Test segmentByCBS,shiftTCN passed 431s 0 431s Begin test segmentByCBS,weights 431s 0 != 0 ] 431s + echo Test segmentByCBS,shiftTCN passed 431s + echo 0 431s + echo Begin test segmentByCBS,weights 431s + exitcode=0 431s + R CMD BATCH segmentByCBS,weights.R 433s + cat segmentByCBS,weights.Rout 433s + [ 0 != 0 ] 433s + echo Test segmentByCBS,weights passed 433s + echo 0 433s + echo Begin test segmentByCBS 433s + exitcode=0 433s + R CMD BATCH segmentByCBS.R 433s 433s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 433s Copyright (C) 2024 The R Foundation for Statistical Computing 433s Platform: s390x-ibm-linux-gnu (64-bit) 433s 433s R is free software and comes with ABSOLUTELY NO WARRANTY. 433s You are welcome to redistribute it under certain conditions. 433s Type 'license()' or 'licence()' for distribution details. 433s 433s R is a collaborative project with many contributors. 433s Type 'contributors()' for more information and 433s 'citation()' on how to cite R or R packages in publications. 433s 433s Type 'demo()' for some demos, 'help()' for on-line help, or 433s 'help.start()' for an HTML browser interface to help. 433s Type 'q()' to quit R. 433s 433s [Previously saved workspace restored] 433s 433s > library("PSCBS") 433s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 433s 433s Attaching package: 'PSCBS' 433s 433s The following objects are masked from 'package:base': 433s 433s append, load 433s 433s > 433s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 433s > # Simulating copy-number data 433s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 433s > set.seed(0xBEEF) 433s > 433s > # Number of loci 433s > J <- 1000 433s > 433s > x <- sort(runif(J, max=J)) * 1e5 433s > 433s > mu <- double(J) 433s > mu[200:300] <- mu[200:300] + 1 433s > mu[350:400] <- NA # centromere 433s > mu[650:800] <- mu[650:800] - 1 433s > eps <- rnorm(J, sd=1/2) 433s > y <- mu + eps 433s > 433s > outliers <- seq(from=1L, to=J, length.out=0.2*J) 433s > y[outliers] <- y[outliers] + 1.5 433s > 433s > w <- rep(1.0, times=J) 433s > w[outliers] <- 0.01 433s > 433s > data <- data.frame(chromosome=1L, x=x, y=y) 433s > dataW <- cbind(data, w=w) 433s > 433s > 433s > par(mar=c(2,3,0.2,1)+0.1) 433s > 433s > 433s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 433s > # Single-chromosome segmentation 433s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 433s > # Segment without weights 433s > fit <- segmentByCBS(data) 433s > sampleName(fit) <- "CBS_Example" 433s > print(fit) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example 1 6.066868e+02 19076007 199 0.2622 433s 2 CBS_Example 1 1.907601e+07 29630949 99 1.4289 433s 3 CBS_Example 1 2.963095e+07 63224332 299 0.2854 433s 4 CBS_Example 1 6.322433e+07 78801707 153 -0.7408 433s 5 CBS_Example 1 7.880171e+07 99917418 199 0.3541 433s > plotTracks(fit) 433s Warning message: 433s In plotTracks.CBS(fit) : 433s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning. 433s > ## Highlight outliers (they pull up the mean levels) 433s > points(x[outliers]/1e6, y[outliers], col="purple") 433s > 433s > # Segment with weights 433s > fitW <- segmentByCBS(dataW) 433s > sampleName(fitW) <- "CBS_Example (weighted)" 433s > print(fitW) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example (weighted) 1 6.066868e+02 19076007 199 -0.0610 433s 2 CBS_Example (weighted) 1 1.907601e+07 30126128 101 1.1283 433s 3 CBS_Example (weighted) 1 3.012613e+07 63224332 297 -0.0298 433s 4 CBS_Example (weighted) 1 6.322433e+07 78801707 153 -1.0436 433s 5 CBS_Example (weighted) 1 7.880171e+07 99917418 199 0.0461 433s > drawLevels(fitW, col="red") 433s NULL 433s > 433s > 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)) 433s > 433s > ## Assert that weighted segment means are less biased 433s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 433s > cat("Segment mean differences:\n") 433s Segment mean differences: 433s > print(dmean) 433s [1] 0.3232 0.3006 0.3152 0.3028 0.3080 433s > stopifnot(all(dmean > 0, na.rm=TRUE)) 433s > 433s > 433s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 433s > # Segmentation with some known change points 433s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 433s > knownSegments <- data.frame( 433s + chromosome=c( 1, 1), 433s + start =x[c( 1, 401)], 433s + end =x[c(349, J)] 433s + ) 433s > fit2 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 433s Segmenting by CBS... 433s Chromosome: 1 433s Segmenting by CBS...done 433s > sampleName(fit2) <- "CBS_Example_2 (weighted)" 433s > print(fit2) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example_2 (weighted) 1 6.066868e+02 19076007 199 -0.0610 433s 2 CBS_Example_2 (weighted) 1 1.907601e+07 30126128 101 1.1283 433s 3 CBS_Example_2 (weighted) 1 3.012613e+07 35490554 49 -0.0832 433s 4 CBS_Example_2 (weighted) 1 3.987525e+07 63224332 248 -0.0192 433s 5 CBS_Example_2 (weighted) 1 6.322433e+07 78471531 152 -1.0480 433s 6 CBS_Example_2 (weighted) 1 7.847153e+07 99917418 200 0.0427 433s > plotTracks(fit2) 433s Warning message: 433s In plotTracks.CBS(fit2) : 433s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2) is unknown ('NA'). Use signalType(fit2) <- 'ratio' to avoid this warning. 433s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 433s > 433s > 433s > # Chromosome boundaries can be specified as -Inf and +Inf 433s > knownSegments <- data.frame( 433s + chromosome=c( 1, 1), 433s + start =c( -Inf, x[401]), 433s + end =c(x[349], +Inf) 433s + ) 433s > fit2b <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 433s Segmenting by CBS... 433s Chromosome: 1 433s Segmenting by CBS...done 433s > sampleName(fit2b) <- "CBS_Example_2b (weighted)" 433s > print(fit2b) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example_2b (weighted) 1 6.066868e+02 19076007 199 -0.0610 433s 2 CBS_Example_2b (weighted) 1 1.907601e+07 30126128 101 1.1283 433s 3 CBS_Example_2b (weighted) 1 3.012613e+07 35490554 49 -0.0832 433s 4 CBS_Example_2b (weighted) 1 3.987525e+07 63224332 248 -0.0192 433s 5 CBS_Example_2b (weighted) 1 6.322433e+07 78471531 152 -1.0480 433s 6 CBS_Example_2b (weighted) 1 7.847153e+07 99917418 200 0.0427 433s > plotTracks(fit2b) 433s Warning message: 433s In plotTracks.CBS(fit2b) : 433s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2b) is unknown ('NA'). Use signalType(fit2b) <- 'ratio' to avoid this warning. 433s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 433s > 433s > 433s > # As a proof of concept, it is possible to segment just the centromere, 433s > # which contains no data. All statistics will be NAs. 433s > knownSegments <- data.frame( 433s + chromosome=c( 1), 433s + start =x[c(350)], 433s + end =x[c(400)] 433s + ) 433s > fit3 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 433s Segmenting by CBS... 433s Chromosome: 1 433s Segmenting by CBS...done 433s > sampleName(fit3) <- "CBS_Example_3" 433s > print(fit3) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example_3 1 35661013 39852333 0 NA 433s > plotTracks(fit3, Clim=c(0,5), xlim=c(0,100)) 433s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 433s > 433s > 433s > # If one specify the (empty) centromere as a segment, then its 433s > # estimated statistics will be NAs, which becomes a natural 433s > # separator between the two "independent" arms. 433s > knownSegments <- data.frame( 433s + chromosome=c( 1, 1, 1), 433s + start =x[c( 1, 350, 401)], 433s + end =x[c(349, 400, J)] 433s + ) 433s > fit4 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 433s Segmenting by CBS... 433s Chromosome: 1 433s Segmenting by CBS...done 433s > sampleName(fit4) <- "CBS_Example_4" 433s > print(fit4) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example_4 1 6.066868e+02 19076007 199 -0.0610 433s 2 CBS_Example_4 1 1.907601e+07 30126128 101 1.1283 433s 3 CBS_Example_4 1 3.012613e+07 35490554 49 -0.0832 433s 4 CBS_Example_4 1 3.566101e+07 39852333 0 NA 433s 5 CBS_Example_4 1 3.987525e+07 63224332 248 -0.0192 433s 6 CBS_Example_4 1 6.322433e+07 78471531 152 -1.0480 433s 7 CBS_Example_4 1 7.847153e+07 99917418 200 0.0427 433s > plotTracks(fit4) 433s Warning message: 433s In plotTracks.CBS(fit4) : 433s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit4) is unknown ('NA'). Use signalType(fit4) <- 'ratio' to avoid this warning. 433s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 433s > 433s > 433s > fit5 <- segmentByCBS(dataW, knownSegments=knownSegments, undo=Inf, verbose=TRUE) 433s Segmenting by CBS... 433s Chromosome: 1 433s Segmenting by CBS...done 433s > sampleName(fit5) <- "CBS_Example_5" 433s > print(fit5) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example_5 1 6.066868e+02 35490554 349 0.59252133 433s 2 CBS_Example_5 1 3.566101e+07 39852333 0 NA 433s 3 CBS_Example_5 1 3.987525e+07 99917418 600 0.04882396 433s > plotTracks(fit5) 433s Warning message: 433s In plotTracks.CBS(fit5) : 433s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit5) is unknown ('NA'). Use signalType(fit5) <- 'ratio' to avoid this warning. 433s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 433s > stopifnot(nbrOfSegments(fit5) == nrow(knownSegments)) 433s > 433s > 433s > # One can also force a separator between two segments by setting 433s > # 'start' and 'end' to NAs ('chromosome' has to be given) 433s > knownSegments <- data.frame( 433s + chromosome=c( 1, 1, 1), 433s + start =x[c( 1, NA, 401)], 433s + end =x[c(349, NA, J)] 433s + ) 433s > fit6 <- segmentByCBS(dataW, knownSegments=knownSegments, verbose=TRUE) 433s Segmenting by CBS... 433s Chromosome: 1 433s Segmenting by CBS...done 433s > sampleName(fit6) <- "CBS_Example_6" 433s > print(fit6) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example_6 1 6.066868e+02 19076007 199 -0.0610 433s 2 CBS_Example_6 1 1.907601e+07 30126128 101 1.1283 433s 3 CBS_Example_6 1 3.012613e+07 35490554 49 -0.0832 433s 4 NA NA NA NA NA 433s 5 CBS_Example_6 1 3.987525e+07 63224332 248 -0.0192 433s 6 CBS_Example_6 1 6.322433e+07 78471531 152 -1.0480 433s 7 CBS_Example_6 1 7.847153e+07 99917418 200 0.0427 433s > plotTracks(fit6) 433s Warning message: 433s In plotTracks.CBS(fit6) : 433s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit6) is unknown ('NA'). Use signalType(fit6) <- 'ratio' to avoid this warning. 433s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 433s > 433s > 433s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 433s > # Multi-chromosome segmentation 433s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 433s > data2 <- data 433s > data2$chromosome <- 2L 433s > data <- rbind(data, data2) 433s > dataW <- cbind(data, w=w) 433s > 433s > par(mar=c(2,3,0.2,1)+0.1) 433s > # Segment without weights 433s > fit <- segmentByCBS(data) 433s > sampleName(fit) <- "CBS_Example" 433s > print(fit) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example 1 6.066868e+02 19076007 199 0.2622 433s 2 CBS_Example 1 1.907601e+07 29630949 99 1.4289 433s 3 CBS_Example 1 2.963095e+07 63224332 299 0.2854 433s 4 CBS_Example 1 6.322433e+07 78801707 153 -0.7408 433s 5 CBS_Example 1 7.880171e+07 99917418 199 0.3541 433s 6 NA NA NA NA NA 433s 7 CBS_Example 2 6.066868e+02 19076007 199 0.2622 433s 8 CBS_Example 2 1.907601e+07 29630949 99 1.4289 433s 9 CBS_Example 2 2.963095e+07 63224332 299 0.2854 433s 10 CBS_Example 2 6.322433e+07 78801707 153 -0.7408 433s 11 CBS_Example 2 7.880171e+07 99917418 199 0.3541 433s > plotTracks(fit, Clim=c(-3,3)) 433s > 433s > # Segment with weights 433s > fitW <- segmentByCBS(dataW) 433s > sampleName(fitW) <- "CBS_Example (weighted)" 433s > print(fitW) 433s sampleName chromosome start end nbrOfLoci mean 433s 1 CBS_Example (weighted) 1 6.066868e+02 19076007 199 -0.0610 433s 2 CBS_Example (weighted) 1 1.907601e+07 30126128 101 1.1283 433s 3 CBS_Example (weighted) 1 3.012613e+07 63224332 297 -0.0298 433s 4 CBS_Example (weighted) 1 6.322433e+07 78801707 153 -1.0436 433s 5 CBS_Example (weighted) 1 7.880171e+07 99917418 199 0.0461 433s 6 NA NA NA NA NA 433s 7 CBS_Example (weighted) 2 6.066868e+02 19076007 199 -0.0610 433s 8 CBS_Example (weighted) 2 1.907601e+07 30126128 101 1.1283 433s 9 CBS_Example (weighted) 2 3.012613e+07 63224332 297 -0.0298 433s 10 CBS_Example (weighted) 2 6.322433e+07 78801707 153 -1.0436 433s 11 CBS_Example (weighted) 2 7.880171e+07 99917418 199 0.0461 433s > drawLevels(fitW, col="red") 433s NULL 433s > 433s > 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)) 433s > 433s > ## Assert that weighted segment means are less biased 433s > dmean <- getSegments(fit)$mean - getSegments(fitW)$mean 433s > cat("Segment mean differences:\n") 433s Segment mean differences: 433s > print(dmean) 433s [1] 0.3232 0.3006 0.3152 0.3028 0.3080 NA 0.3232 0.3006 0.3152 0.3028 433s [11] 0.3080 433s > stopifnot(all(dmean > 0, na.rm=TRUE)) 433s > 433s > proc.time() 433s user system elapsed 433s 2.347 0.067 2.427 433s Test segmentByCBS,weights passed 433s 0 433s Begin test segmentByCBS 435s + cat segmentByCBS.Rout 436s 436s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 436s Copyright (C) 2024 The R Foundation for Statistical Computing 436s Platform: s390x-ibm-linux-gnu (64-bit) 436s 436s R is free software and comes with ABSOLUTELY NO WARRANTY. 436s You are welcome to redistribute it under certain conditions. 436s Type 'license()' or 'licence()' for distribution details. 436s 436s R is a collaborative project with many contributors. 436s Type 'contributors()' for more information and 436s 'citation()' on how to cite R or R packages in publications. 436s 436s Type 'demo()' for some demos, 'help()' for on-line help, or 436s 'help.start()' for an HTML browser interface to help. 436s Type 'q()' to quit R. 436s 436s [Previously saved workspace restored] 436s 436s > ########################################################### 436s > # This tests: 436s > # - segmentByCBS(...) 436s > # - segmentByCBS(..., knownSegments) 436s > # - tileChromosomes() 436s > # - plotTracks() 436s > ########################################################### 436s > library("PSCBS") 436s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 436s 436s Attaching package: 'PSCBS' 436s 436s The following objects are masked from 'package:base': 436s 436s append, load 436s 436s > subplots <- R.utils::subplots 436s > 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > # Simulating copy-number data 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > set.seed(0xBEEF) 436s > 436s > # Number of loci 436s > J <- 1000 436s > 436s > mu <- double(J) 436s > mu[200:300] <- mu[200:300] + 1 436s > mu[350:400] <- NA # centromere 436s > mu[650:800] <- mu[650:800] - 1 436s > eps <- rnorm(J, sd=1/2) 436s > y <- mu + eps 436s > x <- sort(runif(length(y), max=length(y))) * 1e5 436s > w <- runif(J) 436s > w[650:800] <- 0.001 436s > 436s > 436s > subplots(8, ncol=1L) 436s > par(mar=c(1.7,1,0.2,1)+0.1) 436s > 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > # Segmentation 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > fit <- segmentByCBS(y, x=x) 436s > sampleName(fit) <- "CBS_Example" 436s > print(fit) 436s sampleName chromosome start end nbrOfLoci mean 436s 1 CBS_Example 0 65285.65 19648927 200 0.0109 436s 2 CBS_Example 0 19648927.46 28239656 95 0.9529 436s 3 CBS_Example 0 28239655.99 65697742 302 -0.0126 436s 4 CBS_Example 0 65697742.20 79729368 153 -0.9534 436s 5 CBS_Example 0 79729368.34 99819310 199 -0.0497 436s > plotTracks(fit) 436s Warning message: 436s In plotTracks.CBS(fit) : 436s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit) is unknown ('NA'). Use signalType(fit) <- 'ratio' to avoid this warning. 436s > 436s > 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > # Segmentation with some known change points 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > knownSegments <- data.frame( 436s + chromosome=c( 0, 0), 436s + start =x[c( 1, 401)], 436s + end =x[c(349, J)] 436s + ) 436s > fit2 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 436s Segmenting by CBS... 436s Chromosome: 0 436s Segmenting by CBS...done 436s > sampleName(fit2) <- "CBS_Example_2" 436s > print(fit2) 436s sampleName chromosome start end nbrOfLoci mean 436s 1 CBS_Example_2 0 65285.65 19648927 200 0.0109 436s 2 CBS_Example_2 0 19648927.46 28239656 95 0.9529 436s 3 CBS_Example_2 0 28239655.99 33106633 54 0.1169 436s 4 CBS_Example_2 0 38076667.59 65697742 248 -0.0408 436s 5 CBS_Example_2 0 65697742.20 79729368 153 -0.9534 436s 6 CBS_Example_2 0 79729368.34 99819310 199 -0.0497 436s > plotTracks(fit2) 436s Warning message: 436s In plotTracks.CBS(fit2) : 436s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2) is unknown ('NA'). Use signalType(fit2) <- 'ratio' to avoid this warning. 436s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 436s > 436s > 436s > # Chromosome boundaries can be specified as -Inf and +Inf 436s > knownSegments <- data.frame( 436s + chromosome=c( 0, 0), 436s + start =c( -Inf, x[401]), 436s + end =c(x[349], +Inf) 436s + ) 436s > fit2b <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 436s Segmenting by CBS... 436s Chromosome: 0 436s Segmenting by CBS...done 436s > sampleName(fit2b) <- "CBS_Example_2b" 436s > print(fit2b) 436s sampleName chromosome start end nbrOfLoci mean 436s 1 CBS_Example_2b 0 65285.65 19648927 200 0.0109 436s 2 CBS_Example_2b 0 19648927.46 28239656 95 0.9529 436s 3 CBS_Example_2b 0 28239655.99 33106633 54 0.1169 436s 4 CBS_Example_2b 0 38076667.59 65697742 248 -0.0408 436s 5 CBS_Example_2b 0 65697742.20 79729368 153 -0.9534 436s 6 CBS_Example_2b 0 79729368.34 99819310 199 -0.0497 436s > plotTracks(fit2b) 436s Warning message: 436s In plotTracks.CBS(fit2b) : 436s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit2b) is unknown ('NA'). Use signalType(fit2b) <- 'ratio' to avoid this warning. 436s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 436s > 436s > 436s > # As a proof of concept, it is possible to segment just the centromere, 436s > # which contains no data. All statistics will be NAs. 436s > knownSegments <- data.frame( 436s + chromosome=c( 0), 436s + start =x[c(350)], 436s + end =x[c(400)] 436s + ) 436s > fit3 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 436s Segmenting by CBS... 436s Chromosome: 0 436s Segmenting by CBS...done 436s > sampleName(fit3) <- "CBS_Example_3" 436s > print(fit3) 436s sampleName chromosome start end nbrOfLoci mean 436s 1 CBS_Example_3 0 33248518 37640521 0 NA 436s > plotTracks(fit3, Clim=c(0,5), xlim=c(0,100)) 436s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 436s > 436s > 436s > 436s > # If one specify the (empty) centromere as a segment, then its 436s > # estimated statistics will be NAs, which becomes a natural 436s > # separator between the two "independent" arms. 436s > knownSegments <- data.frame( 436s + chromosome=c( 0, 0, 0), 436s + start =x[c( 1, 350, 401)], 436s + end =x[c(349, 400, J)] 436s + ) 436s > fit4 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 436s Segmenting by CBS... 436s Chromosome: 0 436s Segmenting by CBS...done 436s > sampleName(fit4) <- "CBS_Example_4" 436s > print(fit4) 436s sampleName chromosome start end nbrOfLoci mean 436s 1 CBS_Example_4 0 65285.65 19648927 200 0.0109 436s 2 CBS_Example_4 0 19648927.46 28239656 95 0.9529 436s 3 CBS_Example_4 0 28239655.99 33106633 54 0.1169 436s 4 CBS_Example_4 0 33248517.78 37640521 0 NA 436s 5 CBS_Example_4 0 38076667.59 65697742 248 -0.0408 436s 6 CBS_Example_4 0 65697742.20 79729368 153 -0.9534 436s 7 CBS_Example_4 0 79729368.34 99819310 199 -0.0497 436s > plotTracks(fit4) 436s Warning message: 436s In plotTracks.CBS(fit4) : 436s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit4) is unknown ('NA'). Use signalType(fit4) <- 'ratio' to avoid this warning. 436s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 436s > 436s > 436s > 436s > fit5 <- segmentByCBS(y, x=x, knownSegments=knownSegments, undo=Inf, verbose=TRUE) 436s Segmenting by CBS... 436s Chromosome: 0 436s Segmenting by CBS...done 436s > sampleName(fit5) <- "CBS_Example_5" 436s > print(fit5) 436s sampleName chromosome start end nbrOfLoci mean 436s 1 CBS_Example_5 0 65285.65 33106633 349 0.2836973 436s 2 CBS_Example_5 0 33248517.78 37640521 0 NA 436s 3 CBS_Example_5 0 38076667.59 99819310 600 -0.2764472 436s > plotTracks(fit5) 436s Warning message: 436s In plotTracks.CBS(fit5) : 436s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit5) is unknown ('NA'). Use signalType(fit5) <- 'ratio' to avoid this warning. 436s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 436s > stopifnot(nbrOfSegments(fit5) == nrow(knownSegments)) 436s > 436s > 436s > # One can also force a separator between two segments by setting 436s > # 'start' and 'end' to NAs ('chromosome' has to be given) 436s > knownSegments <- data.frame( 436s + chromosome=c( 0, 0, 0), 436s + start =x[c( 1, NA, 401)], 436s + end =x[c(349, NA, J)] 436s + ) 436s > fit6 <- segmentByCBS(y, x=x, knownSegments=knownSegments, verbose=TRUE) 436s Segmenting by CBS... 436s Chromosome: 0 436s Segmenting by CBS...done 436s > sampleName(fit6) <- "CBS_Example_6" 436s > print(fit6) 436s sampleName chromosome start end nbrOfLoci mean 436s 1 CBS_Example_6 0 65285.65 19648927 200 0.0109 436s 2 CBS_Example_6 0 19648927.46 28239656 95 0.9529 436s 3 CBS_Example_6 0 28239655.99 33106633 54 0.1169 436s 4 NA NA NA NA NA 436s 5 CBS_Example_6 0 38076667.59 65697742 248 -0.0408 436s 6 CBS_Example_6 0 65697742.20 79729368 153 -0.9534 436s 7 CBS_Example_6 0 79729368.34 99819310 199 -0.0497 436s > plotTracks(fit6) 436s Warning message: 436s In plotTracks.CBS(fit6) : 436s Setting default 'Clim' assuming the signal type is 'ratio' because signalType(fit6) is unknown ('NA'). Use signalType(fit6) <- 'ratio' to avoid this warning. 436s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 436s > 436s > 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > # Segment multiple chromosomes 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > # Simulate multiple chromosomes 436s > fit1 <- renameChromosomes(fit, from=0, to=1) 436s > fit2 <- renameChromosomes(fit, from=0, to=2) 436s > fitM <- c(fit1, fit2) 436s > fitM <- segmentByCBS(fitM) 436s > sampleName(fitM) <- "CBS_Example_M" 436s > print(fitM) 436s sampleName chromosome start end nbrOfLoci mean 436s 1 CBS_Example_M 1 65285.65 19648927 200 0.0109 436s 2 CBS_Example_M 1 19648927.46 28239656 95 0.9529 436s 3 CBS_Example_M 1 28239655.99 65697742 302 -0.0126 436s 4 CBS_Example_M 1 65697742.20 79729368 153 -0.9534 436s 5 CBS_Example_M 1 79729368.34 99819310 199 -0.0497 436s 6 NA NA NA NA NA 436s 7 CBS_Example_M 2 65285.65 19648927 200 0.0109 436s 8 CBS_Example_M 2 19648927.46 28239656 95 0.9529 436s 9 CBS_Example_M 2 28239655.99 65697742 302 -0.0126 436s 10 CBS_Example_M 2 65697742.20 79729368 153 -0.9534 436s 11 CBS_Example_M 2 79729368.34 99819310 199 -0.0497 436s > plotTracks(fitM, Clim=c(-3,3)) 436s > 436s > 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > # Tiling multiple chromosomes 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > # Tile chromosomes 436s > fitT <- tileChromosomes(fitM) 436s > fitTb <- tileChromosomes(fitT) 436s > stopifnot(identical(fitTb, fitT)) 436s > 436s > 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > # Write segmentation to file 436s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 436s > pathT <- tempdir() 436s > 436s > ## Tab-delimited file 436s > pathname <- writeSegments(fitM, path=pathT) 436s Warning message: 436s In write.table(file = pathnameT, data, append = TRUE, quote = FALSE, : 436s appending column names to file 436s > print(pathname) 436s [1] "/tmp/RtmpE1ubeb/CBS_Example_M.tsv" 436s > 436s > ## WIG file 436s > pathname <- writeWIG(fitM, path=pathT) 436s > print(pathname) 436s [1] "/tmp/RtmpE1ubeb/CBS_Example_M.wig" 436s > 436s > unlink(pathT, recursive=TRUE) 436s > 436s > proc.time() 436s user system elapsed 436s 2.186 0.063 2.251 436s Test segmentByCBS passed 436s 0 436s Begin test segmentByNonPairedPSCBS,medianDH 436s + [ 0 != 0 ] 436s + echo Test segmentByCBS passed 436s + echo 0 436s + echo Begin test segmentByNonPairedPSCBS,medianDH 436s + exitcode=0 436s + R CMD BATCH segmentByNonPairedPSCBS,medianDH.R 438s + cat segmentByNonPairedPSCBS,medianDH.Rout 438s + [ 0 != 0 ] 438s + echo Test segmentByNonPairedPSCBS,medianDH passed 438s + echo 0 438s + echo Begin test segmentByPairedPSCBS,DH 438s + exitcode=0 438s + R CMD BATCH segmentByPairedPSCBS,DH.R 438s 438s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 438s Copyright (C) 2024 The R Foundation for Statistical Computing 438s Platform: s390x-ibm-linux-gnu (64-bit) 438s 438s R is free software and comes with ABSOLUTELY NO WARRANTY. 438s You are welcome to redistribute it under certain conditions. 438s Type 'license()' or 'licence()' for distribution details. 438s 438s R is a collaborative project with many contributors. 438s Type 'contributors()' for more information and 438s 'citation()' on how to cite R or R packages in publications. 438s 438s Type 'demo()' for some demos, 'help()' for on-line help, or 438s 'help.start()' for an HTML browser interface to help. 438s Type 'q()' to quit R. 438s 438s [Previously saved workspace restored] 438s 438s > library("PSCBS") 438s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 438s 438s Attaching package: 'PSCBS' 438s 438s The following objects are masked from 'package:base': 438s 438s append, load 438s 438s > 438s > 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > # Load SNP microarray data 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > data <- PSCBS::exampleData("paired.chr01") 438s > str(data) 438s 'data.frame': 73346 obs. of 6 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 438s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 438s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 438s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 438s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 438s > 438s > # Non-paired / tumor-only data 438s > data <- data[,c("chromosome", "x", "CT", "betaT")] 438s > str(data) 438s 'data.frame': 73346 obs. of 4 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 438s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 438s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 438s > 438s > 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > # Paired PSCBS segmentation 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > # Drop single-locus outliers 438s > dataS <- dropSegmentationOutliers(data) 438s > 438s > # Speed up example by segmenting fewer loci 438s > dataS <- dataS[seq(from=1, to=nrow(data), by=20),] 438s > 438s > # Fake a second chromosome 438s > dataT <- dataS 438s > dataT$chromosome <- 2L 438s > dataS <- rbind(dataS, dataT) 438s > rm(dataT) 438s > str(dataS) 438s 'data.frame': 7336 obs. of 4 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : int 1145994 4276892 5034491 6266412 8418532 11211748 13928296 14370144 15014887 16589707 ... 438s $ CT : num 1.63 1.16 1.35 1.39 1.55 ... 438s $ betaT : num 0.7574 0.0576 0.8391 0.7917 0.8141 ... 438s > 438s > # Non-Paired PSCBS segmentation 438s > fit <- segmentByNonPairedPSCBS(dataS, avgDH="median", seed=0xBEEF, verbose=-10) 438s Segmenting non-paired tumor signals using Non-paired PSCBS... 438s Number of loci: 7336 438s Number of SNPs: 7336 438s Calling "genotypes" from tumor allele B fractions... 438s num [1:7336] 0.7574 0.0576 0.8391 0.7917 0.8141 ... 438s Upper quantile: 0.475631667925522 438s Symmetric lower quantile: 0.290517384533512 438s (tauA, tauB) estimates: (%g,%g)0.2094826154664880.790517384533512 438s Homozygous treshholds: 438s [1] 0.2094826 0.7905174 438s Inferred germline genotypes (via tumor): 438s num [1:7336] 0.5 0 1 1 1 0 0 0 0.5 1 ... 438s muNx 438s 0 0.5 1 438s 2230 2910 2196 438s Calling "genotypes" from tumor allele B fractions...done 438s Segmenting non-paired tumor signals using Non-paired PSCBS...done 438s Segment using Paired PSCBS... 438s Segmenting paired tumor-normal signals using Paired PSCBS... 438s Setup up data... 438s 'data.frame': 7336 obs. of 6 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : num 1145994 4276892 5034491 6266412 8418532 ... 438s $ CT : num 1.63 1.16 1.35 1.39 1.55 ... 438s $ betaT : num 0.7574 0.0576 0.8391 0.7917 0.8141 ... 438s $ betaTN : num 0.7574 0.0576 0.8391 0.7917 0.8141 ... 438s $ muN : num 0.5 0 1 1 1 0 0 0 0.5 1 ... 438s Setup up data...done 438s Dropping loci for which TCNs are missing... 438s Number of loci dropped: 12 438s Dropping loci for which TCNs are missing...done 438s Ordering data along genome... 438s 'data.frame': 7324 obs. of 6 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : num 554484 1031563 1087198 1145994 1176365 ... 438s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 438s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s Ordering data along genome...done 438s Segmenting multiple chromosomes... 438s Number of chromosomes: 2 438s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 438s Produced 2 seeds from this stream for future usage 438s Chromosome #1 ('Chr01') of 2... 438s 'data.frame': 3662 obs. of 7 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : num 554484 1031563 1087198 1145994 1176365 ... 438s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 438s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 438s Known segments: 438s [1] chromosome start end 438s <0 rows> (or 0-length row.names) 438s Segmenting paired tumor-normal signals using Paired PSCBS... 438s Setup up data... 438s 'data.frame': 3662 obs. of 6 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : num 554484 1031563 1087198 1145994 1176365 ... 438s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 438s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s Setup up data...done 438s Ordering data along genome... 438s 'data.frame': 3662 obs. of 6 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : num 554484 1031563 1087198 1145994 1176365 ... 438s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 438s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s Ordering data along genome...done 438s Keeping only current chromosome for 'knownSegments'... 438s Chromosome: 1 438s Known segments for this chromosome: 438s [1] chromosome start end 438s <0 rows> (or 0-length row.names) 438s Keeping only current chromosome for 'knownSegments'...done 438s alphaTCN: 0.009 438s alphaDH: 0.001 438s Number of loci: 3662 438s Calculating DHs... 438s Number of SNPs: 3662 438s Number of heterozygous SNPs: 1451 (39.62%) 438s Normalized DHs: 438s num [1:3662] NA 0.216 0.198 0.515 0.29 ... 438s Calculating DHs...done 438s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 438s Produced 2 seeds from this stream for future usage 438s Identification of change points by total copy numbers... 438s Segmenting by CBS... 438s Chromosome: 1 438s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 438s Segmenting by CBS...done 438s List of 4 438s $ data :'data.frame': 3662 obs. of 4 variables: 438s ..$ chromosome: int [1:3662] 1 1 1 1 1 1 1 1 1 1 ... 438s ..$ x : num [1:3662] 554484 1031563 1087198 1145994 1176365 ... 438s ..$ y : num [1:3662] 1.88 1.64 1.77 1.63 1.59 ... 438s ..$ index : int [1:3662] 1 2 3 4 5 6 7 8 9 10 ... 438s $ output :'data.frame': 3 obs. of 6 variables: 438s ..$ sampleName: chr [1:3] NA NA NA 438s ..$ chromosome: int [1:3] 1 1 1 438s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 438s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 438s ..$ nbrOfLoci : int [1:3] 1880 671 1111 438s ..$ mean : num [1:3] 1.39 2.09 2.65 438s $ segRows:'data.frame': 3 obs. of 2 variables: 438s ..$ startRow: int [1:3] 1 1881 2552 438s ..$ endRow : int [1:3] 1880 2551 3662 438s $ params :List of 5 438s ..$ alpha : num 0.009 438s ..$ undo : num 0 438s ..$ joinSegments : logi TRUE 438s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 438s .. ..$ chromosome: int 1 438s .. ..$ start : num -Inf 438s .. ..$ end : num Inf 438s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 438s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 438s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.09 0.001 0.091 0 0 438s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 438s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 438s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 438s Identification of change points by total copy numbers...done 438s Restructure TCN segmentation results... 438s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 438s 1 1 554484 143663981 1880 1.3916 438s 2 1 143663981 185240536 671 2.0925 438s 3 1 185240536 246679946 1111 2.6545 438s Number of TCN segments: 3 438s Restructure TCN segmentation results...done 438s TCN-only segmentation... 438s Total CN segment #1 ([ 554484,1.43664e+08]) of 3... 438s Number of TCN loci in segment: 1880 438s Locus data for TCN segment: 438s 'data.frame': 1880 obs. of 8 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : num 554484 1031563 1087198 1145994 1176365 ... 438s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 438s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 438s $ rho : num NA 0.216 0.198 0.515 0.29 ... 438s Number of loci: 1880 438s Number of SNPs: 765 (40.69%) 438s Number of heterozygous SNPs: 765 (100.00%) 438s Total CN segment #1 ([ 554484,1.43664e+08]) of 3...done 438s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3... 438s Number of TCN loci in segment: 671 438s Locus data for TCN segment: 438s 'data.frame': 671 obs. of 8 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 438s $ CT : num 2.26 2.1 2.1 1.89 1.97 ... 438s $ betaT : num 0.958 0.19 0.909 0.13 0.141 ... 438s $ betaTN : num 0.958 0.19 0.909 0.13 0.141 ... 438s $ muN : num 1 0 1 0 0 0 0 0.5 0 1 ... 438s $ index : int 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 438s $ rho : num NA NA NA NA NA ... 438s Number of loci: 671 438s Number of SNPs: 272 (40.54%) 438s Number of heterozygous SNPs: 272 (100.00%) 438s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3...done 438s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3... 438s Number of TCN loci in segment: 1111 438s Locus data for TCN segment: 438s 'data.frame': 1111 obs. of 8 variables: 438s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 438s $ x : num 1.85e+08 1.86e+08 1.86e+08 1.86e+08 1.86e+08 ... 438s $ CT : num 2.44 3 2.32 2.76 2.48 ... 438s $ betaT : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 438s $ betaTN : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 438s $ muN : num 0 0.5 0.5 1 0 1 0 1 1 0.5 ... 438s $ index : int 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 438s $ rho : num NA 0.369 0.535 NA NA ... 438s Number of loci: 1111 438s Number of SNPs: 414 (37.26%) 438s Number of heterozygous SNPs: 414 (100.00%) 438s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3...done 438s TCN-only segmentation...done 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.3916 765 438s 2 1 2 1 143663981 185240536 671 2.0925 272 438s 3 1 3 1 185240536 246679946 1111 2.6545 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean 438s 1 765 765 554484 143663981 0.3979122 438s 2 272 272 143663981 185240536 0.2306116 438s 3 414 414 185240536 246679946 0.2798120 438s Calculating (C1,C2) per segment... 438s Calculating (C1,C2) per segment...done 438s Number of segments: 3 438s Segmenting paired tumor-normal signals using Paired PSCBS...done 438s Updating mean level using different estimator... 438s TCN estimator: mean 438s DH estimator: median 438s Updating mean level using different estimator...done 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s Chromosome #1 ('Chr01') of 2...done 438s Chromosome #2 ('Chr02') of 2... 438s 'data.frame': 3662 obs. of 7 variables: 438s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 438s $ x : num 554484 1031563 1087198 1145994 1176365 ... 438s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 438s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s $ index : int 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 438s Known segments: 438s [1] chromosome start end 438s <0 rows> (or 0-length row.names) 438s Segmenting paired tumor-normal signals using Paired PSCBS... 438s Setup up data... 438s 'data.frame': 3662 obs. of 6 variables: 438s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 438s $ x : num 554484 1031563 1087198 1145994 1176365 ... 438s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 438s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s Setup up data...done 438s Ordering data along genome... 438s 'data.frame': 3662 obs. of 6 variables: 438s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 438s $ x : num 554484 1031563 1087198 1145994 1176365 ... 438s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 438s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s Ordering data along genome...done 438s Keeping only current chromosome for 'knownSegments'... 438s Chromosome: 2 438s Known segments for this chromosome: 438s [1] chromosome start end 438s <0 rows> (or 0-length row.names) 438s Keeping only current chromosome for 'knownSegments'...done 438s alphaTCN: 0.009 438s alphaDH: 0.001 438s Number of loci: 3662 438s Calculating DHs... 438s Number of SNPs: 3662 438s Number of heterozygous SNPs: 1451 (39.62%) 438s Normalized DHs: 438s num [1:3662] NA 0.216 0.198 0.515 0.29 ... 438s Calculating DHs...done 438s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 438s Produced 2 seeds from this stream for future usage 438s Identification of change points by total copy numbers... 438s Segmenting by CBS... 438s Chromosome: 2 438s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 438s Segmenting by CBS...done 438s List of 4 438s $ data :'data.frame': 3662 obs. of 4 variables: 438s ..$ chromosome: int [1:3662] 2 2 2 2 2 2 2 2 2 2 ... 438s ..$ x : num [1:3662] 554484 1031563 1087198 1145994 1176365 ... 438s ..$ y : num [1:3662] 1.88 1.64 1.77 1.63 1.59 ... 438s ..$ index : int [1:3662] 1 2 3 4 5 6 7 8 9 10 ... 438s $ output :'data.frame': 3 obs. of 6 variables: 438s ..$ sampleName: chr [1:3] NA NA NA 438s ..$ chromosome: int [1:3] 2 2 2 438s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 438s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 438s ..$ nbrOfLoci : int [1:3] 1880 671 1111 438s ..$ mean : num [1:3] 1.39 2.09 2.65 438s $ segRows:'data.frame': 3 obs. of 2 variables: 438s ..$ startRow: int [1:3] 1 1881 2552 438s ..$ endRow : int [1:3] 1880 2551 3662 438s $ params :List of 5 438s ..$ alpha : num 0.009 438s ..$ undo : num 0 438s ..$ joinSegments : logi TRUE 438s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 438s .. ..$ chromosome: int 2 438s .. ..$ start : num -Inf 438s .. ..$ end : num Inf 438s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 438s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 438s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.089 0 0.091 0 0 438s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 438s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 438s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 438s Identification of change points by total copy numbers...done 438s Restructure TCN segmentation results... 438s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 438s 1 2 554484 143663981 1880 1.3916 438s 2 2 143663981 185240536 671 2.0925 438s 3 2 185240536 246679946 1111 2.6545 438s Number of TCN segments: 3 438s Restructure TCN segmentation results...done 438s TCN-only segmentation... 438s Total CN segment #1 ([ 554484,1.43664e+08]) of 3... 438s Number of TCN loci in segment: 1880 438s Locus data for TCN segment: 438s 'data.frame': 1880 obs. of 8 variables: 438s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 438s $ x : num 554484 1031563 1087198 1145994 1176365 ... 438s $ CT : num 1.88 1.64 1.77 1.63 1.59 ... 438s $ betaT : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ betaTN : num 0.0646 0.6078 0.401 0.7574 0.645 ... 438s $ muN : num 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 438s $ rho : num NA 0.216 0.198 0.515 0.29 ... 438s Number of loci: 1880 438s Number of SNPs: 765 (40.69%) 438s Number of heterozygous SNPs: 765 (100.00%) 438s Total CN segment #1 ([ 554484,1.43664e+08]) of 3...done 438s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3... 438s Number of TCN loci in segment: 671 438s Locus data for TCN segment: 438s 'data.frame': 671 obs. of 8 variables: 438s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 438s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 438s $ CT : num 2.26 2.1 2.1 1.89 1.97 ... 438s $ betaT : num 0.958 0.19 0.909 0.13 0.141 ... 438s $ betaTN : num 0.958 0.19 0.909 0.13 0.141 ... 438s $ muN : num 1 0 1 0 0 0 0 0.5 0 1 ... 438s $ index : int 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 438s $ rho : num NA NA NA NA NA ... 438s Number of loci: 671 438s Number of SNPs: 272 (40.54%) 438s Number of heterozygous SNPs: 272 (100.00%) 438s Total CN segment #2 ([1.43664e+08,1.85241e+08]) of 3...done 438s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3... 438s Number of TCN loci in segment: 1111 438s Locus data for TCN segment: 438s 'data.frame': 1111 obs. of 8 variables: 438s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 438s $ x : num 1.85e+08 1.86e+08 1.86e+08 1.86e+08 1.86e+08 ... 438s $ CT : num 2.44 3 2.32 2.76 2.48 ... 438s $ betaT : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 438s $ betaTN : num 0.0727 0.6845 0.2327 0.8118 0.0746 ... 438s $ muN : num 0 0.5 0.5 1 0 1 0 1 1 0.5 ... 438s $ index : int 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 438s $ rho : num NA 0.369 0.535 NA NA ... 438s Number of loci: 1111 438s Number of SNPs: 414 (37.26%) 438s Number of heterozygous SNPs: 414 (100.00%) 438s Total CN segment #3 ([1.85241e+08,2.4668e+08]) of 3...done 438s TCN-only segmentation...done 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 2 1 1 554484 143663981 1880 1.3916 765 438s 2 2 2 1 143663981 185240536 671 2.0925 272 438s 3 2 3 1 185240536 246679946 1111 2.6545 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean 438s 1 765 765 554484 143663981 0.3979122 438s 2 272 272 143663981 185240536 0.2306116 438s 3 414 414 185240536 246679946 0.2798120 438s Calculating (C1,C2) per segment... 438s Calculating (C1,C2) per segment...done 438s Number of segments: 3 438s Segmenting paired tumor-normal signals using Paired PSCBS...done 438s Updating mean level using different estimator... 438s TCN estimator: mean 438s DH estimator: median 438s Updating mean level using different estimator...done 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 2 1 1 554484 143663981 1880 1.391608 765 438s 2 2 2 1 143663981 185240536 671 2.092452 272 438s 3 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 2 1 1 554484 143663981 1880 1.391608 765 438s 2 2 2 1 143663981 185240536 671 2.092452 272 438s 3 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 2 1 1 554484 143663981 1880 1.391608 765 438s 2 2 2 1 143663981 185240536 671 2.092452 272 438s 3 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 2 1 1 554484 143663981 1880 1.391608 765 438s 2 2 2 1 143663981 185240536 671 2.092452 272 438s 3 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s Chromosome #2 ('Chr02') of 2...done 438s Merging (independently) segmented chromosome... 438s List of 5 438s $ data :Classes 'PairedPSCNData' and 'data.frame': 7324 obs. of 7 variables: 438s ..$ chromosome: int [1:7324] 1 1 1 1 1 1 1 1 1 1 ... 438s ..$ x : num [1:7324] 554484 1031563 1087198 1145994 1176365 ... 438s ..$ CT : num [1:7324] 1.88 1.64 1.77 1.63 1.59 ... 438s ..$ betaT : num [1:7324] 0.0646 0.6078 0.401 0.7574 0.645 ... 438s ..$ betaTN : num [1:7324] 0.0646 0.6078 0.401 0.7574 0.645 ... 438s ..$ muN : num [1:7324] 0 0.5 0.5 0.5 0.5 0.5 1 0.5 0.5 0.5 ... 438s ..$ rho : num [1:7324] NA 0.216 0.198 0.515 0.29 ... 438s $ output :Classes 'PairedPSCNSegments' and 'data.frame': 7 obs. of 15 variables: 438s ..$ chromosome : int [1:7] 1 1 1 NA 2 2 2 438s ..$ tcnId : int [1:7] 1 2 3 NA 1 2 3 438s ..$ dhId : int [1:7] 1 1 1 NA 1 1 1 438s ..$ tcnStart : num [1:7] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 438s ..$ tcnEnd : num [1:7] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 438s ..$ tcnNbrOfLoci: int [1:7] 1880 671 1111 NA 1880 671 1111 438s ..$ tcnMean : num [1:7] 1.39 2.09 2.65 NA 1.39 ... 438s ..$ tcnNbrOfSNPs: int [1:7] 765 272 414 NA 765 272 414 438s ..$ tcnNbrOfHets: int [1:7] 765 272 414 NA 765 272 414 438s ..$ dhNbrOfLoci : int [1:7] 765 272 414 NA 765 272 414 438s ..$ dhStart : num [1:7] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 438s ..$ dhEnd : num [1:7] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 438s ..$ dhMean : num [1:7] 0.421 0.176 0.27 NA 0.421 ... 438s ..$ c1Mean : num [1:7] 0.403 0.862 0.969 NA 0.403 ... 438s ..$ c2Mean : num [1:7] 0.988 1.231 1.685 NA 0.988 ... 438s $ tcnSegRows:'data.frame': 7 obs. of 2 variables: 438s ..$ startRow: int [1:7] 1 1881 2552 NA 3663 5543 6214 438s ..$ endRow : int [1:7] 1880 2551 3662 NA 5542 6213 7324 438s $ dhSegRows :'data.frame': 7 obs. of 2 variables: 438s ..$ startRow: int [1:7] 2 1888 2553 NA 3664 5550 6215 438s ..$ endRow : int [1:7] 1876 2548 3659 NA 5538 6210 7321 438s $ params :List of 8 438s ..$ alphaTCN : num 0.009 438s ..$ alphaDH : num 0.001 438s ..$ flavor : chr "tcn" 438s ..$ tbn : logi FALSE 438s ..$ joinSegments : logi TRUE 438s ..$ knownSegments :'data.frame': 0 obs. of 3 variables: 438s .. ..$ chromosome: int(0) 438s .. ..$ start : int(0) 438s .. ..$ end : int(0) 438s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 438s ..$ meanEstimators:List of 2 438s .. ..$ tcn: chr "mean" 438s .. ..$ dh : chr "median" 438s - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" 438s Merging (independently) segmented chromosome...done 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s 4 NA NA NA NA NA NA NA NA 438s 5 2 1 1 554484 143663981 1880 1.391608 765 438s 6 2 2 1 143663981 185240536 671 2.092452 272 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s 4 NA NA NA NA NA NA NA 438s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s 4 NA NA NA NA NA NA NA NA 438s 5 2 1 1 554484 143663981 1880 1.391608 765 438s 6 2 2 1 143663981 185240536 671 2.092452 272 438s 7 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s 4 NA NA NA NA NA NA NA 438s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 7 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s Segmenting multiple chromosomes...done 438s Segmenting paired tumor-normal signals using Paired PSCBS...done 438s Segment using Paired PSCBS...done 438s Coercing to Non-Paired PSCBS results... 438s Coercing to Non-Paired PSCBS results...done 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s 4 NA NA NA NA NA NA NA NA 438s 5 2 1 1 554484 143663981 1880 1.391608 765 438s 6 2 2 1 143663981 185240536 671 2.092452 272 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s 4 NA NA NA NA NA NA NA 438s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s 4 NA NA NA NA NA NA NA NA 438s 5 2 1 1 554484 143663981 1880 1.391608 765 438s 6 2 2 1 143663981 185240536 671 2.092452 272 438s 7 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 2 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 3 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s 4 NA NA NA NA NA NA NA 438s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s 6 272 272 143663981 185240536 0.1762428 0.8618360 1.2306156 438s 7 414 414 185240536 246679946 0.2697420 0.9692395 1.6852728 438s > print(fit) 438s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s 4 NA NA NA NA NA NA NA NA 438s 5 2 1 1 554484 143663981 1880 1.391608 765 438s 6 2 2 1 143663981 185240536 671 2.092452 272 438s 7 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 438s 1 765 765 0.4206323 0.4031263 0.9884817 438s 2 272 272 0.1762428 0.8618360 1.2306156 438s 3 414 414 0.2697420 0.9692395 1.6852728 438s 4 NA NA NA NA NA 438s 5 765 765 0.4206323 0.4031263 0.9884817 438s 6 272 272 0.1762428 0.8618360 1.2306156 438s 7 414 414 0.2697420 0.9692395 1.6852728 438s > 438s > 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > # Bootstrap segment level estimates 438s > # (used by the AB caller, which, if skipped here, 438s > # will do it automatically) 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > fit <- bootstrapTCNandDHByRegion(fit, B=100, verbose=-10) 438s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 438s Already done? 438s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 438s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 438s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 438s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 438s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 438s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 438s Number of loci: 7324 438s Number of SNPs: 2902 438s Number of non-SNPs: 4422 438s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 438s num [1:7, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : NULL 438s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 438s Segment #1 (chr 1, tcnId=1, dhId=1) of 7... 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 1 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s Number of TCNs: 1880 438s Number of DHs: 765 438s int [1:1880] 1 2 3 4 5 6 7 8 9 10 ... 438s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 438s int [1:1880] 1 2 3 4 5 6 7 8 9 10 ... 438s Identify loci used to bootstrap DH means... 438s Heterozygous SNPs to resample for DH: 438s int [1:765] 2 3 4 5 6 8 9 10 11 12 ... 438s Identify loci used to bootstrap DH means...done 438s Identify loci used to bootstrap TCN means... 438s SNPs: 438s int [1:765] 2 3 4 5 6 8 9 10 11 12 ... 438s Non-polymorphic loci: 438s int [1:1115] 1 7 15 28 30 32 34 35 36 37 ... 438s Heterozygous SNPs to resample for TCN: 438s int [1:765] 2 3 4 5 6 8 9 10 11 12 ... 438s Homozygous SNPs to resample for TCN: 438s int(0) 438s Non-polymorphic loci to resample for TCN: 438s int [1:1115] 1 7 15 28 30 32 34 35 36 37 ... 438s Heterozygous SNPs with non-DH to resample for TCN: 438s int(0) 438s Loci to resample for TCN: 438s int [1:1880] 1 2 3 4 5 6 7 8 9 10 ... 438s Identify loci used to bootstrap TCN means...done 438s Number of (#hets, #homs, #nonSNPs): (765,0,1115) 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 438s Number of bootstrap samples: 100 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 438s Segment #1 (chr 1, tcnId=1, dhId=1) of 7...done 438s Segment #2 (chr 1, tcnId=2, dhId=1) of 7... 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 2 272 272 143663981 185240536 0.1762428 0.861836 1.230616 438s Number of TCNs: 671 438s Number of DHs: 272 438s int [1:671] 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 438s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 438s int [1:671] 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 438s Identify loci used to bootstrap DH means... 438s Heterozygous SNPs to resample for DH: 438s int [1:272] 1888 1893 1894 1895 1896 1897 1901 1903 1907 1908 ... 438s Identify loci used to bootstrap DH means...done 438s Identify loci used to bootstrap TCN means... 438s SNPs: 438s int [1:272] 1888 1893 1894 1895 1896 1897 1901 1903 1907 1908 ... 438s Non-polymorphic loci: 438s int [1:399] 1881 1882 1883 1884 1885 1886 1887 1889 1890 1891 ... 438s Heterozygous SNPs to resample for TCN: 438s int [1:272] 1888 1893 1894 1895 1896 1897 1901 1903 1907 1908 ... 438s Homozygous SNPs to resample for TCN: 438s int(0) 438s Non-polymorphic loci to resample for TCN: 438s int [1:399] 1881 1882 1883 1884 1885 1886 1887 1889 1890 1891 ... 438s Heterozygous SNPs with non-DH to resample for TCN: 438s int(0) 438s Loci to resample for TCN: 438s int [1:671] 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 ... 438s Identify loci used to bootstrap TCN means...done 438s Number of (#hets, #homs, #nonSNPs): (272,0,399) 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 438s Number of bootstrap samples: 100 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 438s Segment #2 (chr 1, tcnId=2, dhId=1) of 7...done 438s Segment #3 (chr 1, tcnId=3, dhId=1) of 7... 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 3 414 414 185240536 246679946 0.269742 0.9692395 1.685273 438s Number of TCNs: 1111 438s Number of DHs: 414 438s int [1:1111] 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 438s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 438s int [1:1111] 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 438s Identify loci used to bootstrap DH means... 438s Heterozygous SNPs to resample for DH: 438s int [1:414] 2553 2554 2561 2562 2563 2568 2569 2572 2573 2574 ... 438s Identify loci used to bootstrap DH means...done 438s Identify loci used to bootstrap TCN means... 438s SNPs: 438s int [1:414] 2553 2554 2561 2562 2563 2568 2569 2572 2573 2574 ... 438s Non-polymorphic loci: 438s int [1:697] 2552 2555 2556 2557 2558 2559 2560 2564 2565 2566 ... 438s Heterozygous SNPs to resample for TCN: 438s int [1:414] 2553 2554 2561 2562 2563 2568 2569 2572 2573 2574 ... 438s Homozygous SNPs to resample for TCN: 438s int(0) 438s Non-polymorphic loci to resample for TCN: 438s int [1:697] 2552 2555 2556 2557 2558 2559 2560 2564 2565 2566 ... 438s Heterozygous SNPs with non-DH to resample for TCN: 438s int(0) 438s Loci to resample for TCN: 438s int [1:1111] 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 ... 438s Identify loci used to bootstrap TCN means...done 438s Number of (#hets, #homs, #nonSNPs): (414,0,697) 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 438s Number of bootstrap samples: 100 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 438s Segment #3 (chr 1, tcnId=3, dhId=1) of 7...done 438s Segment #5 (chr 2, tcnId=1, dhId=1) of 7... 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 5 2 1 1 554484 143663981 1880 1.391608 765 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 5 765 765 554484 143663981 0.4206323 0.4031263 0.9884817 438s Number of TCNs: 1880 438s Number of DHs: 765 438s int [1:1880] 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 438s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 438s int [1:1880] 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 438s Identify loci used to bootstrap DH means... 438s Heterozygous SNPs to resample for DH: 438s int [1:765] 3664 3665 3666 3667 3668 3670 3671 3672 3673 3674 ... 438s Identify loci used to bootstrap DH means...done 438s Identify loci used to bootstrap TCN means... 438s SNPs: 438s int [1:765] 3664 3665 3666 3667 3668 3670 3671 3672 3673 3674 ... 438s Non-polymorphic loci: 438s int [1:1115] 3663 3669 3677 3690 3692 3694 3696 3697 3698 3699 ... 438s Heterozygous SNPs to resample for TCN: 438s int [1:765] 3664 3665 3666 3667 3668 3670 3671 3672 3673 3674 ... 438s Homozygous SNPs to resample for TCN: 438s int(0) 438s Non-polymorphic loci to resample for TCN: 438s int [1:1115] 3663 3669 3677 3690 3692 3694 3696 3697 3698 3699 ... 438s Heterozygous SNPs with non-DH to resample for TCN: 438s int(0) 438s Loci to resample for TCN: 438s int [1:1880] 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 ... 438s Identify loci used to bootstrap TCN means...done 438s Number of (#hets, #homs, #nonSNPs): (765,0,1115) 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 438s Number of bootstrap samples: 100 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 438s Segment #5 (chr 2, tcnId=1, dhId=1) of 7...done 438s Segment #6 (chr 2, tcnId=2, dhId=1) of 7... 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 6 2 2 1 143663981 185240536 671 2.092452 272 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 6 272 272 143663981 185240536 0.1762428 0.861836 1.230616 438s Number of TCNs: 671 438s Number of DHs: 272 438s int [1:671] 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 ... 438s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 438s int [1:671] 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 ... 438s Identify loci used to bootstrap DH means... 438s Heterozygous SNPs to resample for DH: 438s int [1:272] 5550 5555 5556 5557 5558 5559 5563 5565 5569 5570 ... 438s Identify loci used to bootstrap DH means...done 438s Identify loci used to bootstrap TCN means... 438s SNPs: 438s int [1:272] 5550 5555 5556 5557 5558 5559 5563 5565 5569 5570 ... 438s Non-polymorphic loci: 438s int [1:399] 5543 5544 5545 5546 5547 5548 5549 5551 5552 5553 ... 438s Heterozygous SNPs to resample for TCN: 438s int [1:272] 5550 5555 5556 5557 5558 5559 5563 5565 5569 5570 ... 438s Homozygous SNPs to resample for TCN: 438s int(0) 438s Non-polymorphic loci to resample for TCN: 438s int [1:399] 5543 5544 5545 5546 5547 5548 5549 5551 5552 5553 ... 438s Heterozygous SNPs with non-DH to resample for TCN: 438s int(0) 438s Loci to resample for TCN: 438s int [1:671] 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 ... 438s Identify loci used to bootstrap TCN means...done 438s Number of (#hets, #homs, #nonSNPs): (272,0,399) 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 438s Number of bootstrap samples: 100 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 438s Segment #6 (chr 2, tcnId=2, dhId=1) of 7...done 438s Segment #7 (chr 2, tcnId=3, dhId=1) of 7... 438s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 7 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhStart dhEnd dhMean c1Mean c2Mean 438s 7 414 414 185240536 246679946 0.269742 0.9692395 1.685273 438s Number of TCNs: 1111 438s Number of DHs: 414 438s int [1:1111] 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 ... 438s int [1:7324] 1 2 3 4 5 6 7 8 9 10 ... 438s int [1:1111] 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 ... 438s Identify loci used to bootstrap DH means... 438s Heterozygous SNPs to resample for DH: 438s int [1:414] 6215 6216 6223 6224 6225 6230 6231 6234 6235 6236 ... 438s Identify loci used to bootstrap DH means...done 438s Identify loci used to bootstrap TCN means... 438s SNPs: 438s int [1:414] 6215 6216 6223 6224 6225 6230 6231 6234 6235 6236 ... 438s Non-polymorphic loci: 438s int [1:697] 6214 6217 6218 6219 6220 6221 6222 6226 6227 6228 ... 438s Heterozygous SNPs to resample for TCN: 438s int [1:414] 6215 6216 6223 6224 6225 6230 6231 6234 6235 6236 ... 438s Homozygous SNPs to resample for TCN: 438s int(0) 438s Non-polymorphic loci to resample for TCN: 438s int [1:697] 6214 6217 6218 6219 6220 6221 6222 6226 6227 6228 ... 438s Heterozygous SNPs with non-DH to resample for TCN: 438s int(0) 438s Loci to resample for TCN: 438s int [1:1111] 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 ... 438s Identify loci used to bootstrap TCN means...done 438s Number of (#hets, #homs, #nonSNPs): (414,0,697) 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 438s Number of bootstrap samples: 100 438s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 438s Segment #7 (chr 2, tcnId=3, dhId=1) of 7...done 438s Bootstrapped segment mean levels 438s num [1:7, 1:100, 1:4] 1.4 2.09 2.64 NA 1.39 ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : NULL 438s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 438s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 438s num [1:7, 1:100, 1:4] 1.4 2.09 2.64 NA 1.39 ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : NULL 438s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 438s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 438s Calculating polar (alpha,radius,manhattan) for change points... 438s num [1:6, 1:100, 1:2] -0.448 -0.131 NA NA -0.477 ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : NULL 438s ..$ : chr [1:2] "c1" "c2" 438s Bootstrapped change points 438s num [1:6, 1:100, 1:5] -2.65 -1.87 NA NA -2.72 ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : NULL 438s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 438s Calculating polar (alpha,radius,manhattan) for change points...done 438s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 438s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 438s num [1:7, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 438s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 438s Field #1 ('tcn') of 4... 438s Segment #1 of 7... 438s Segment #1 of 7...done 438s Segment #2 of 7... 438s Segment #2 of 7...done 438s Segment #3 of 7... 438s Segment #3 of 7...done 438s Segment #4 of 7... 438s Segment #4 of 7...done 438s Segment #5 of 7... 438s Segment #5 of 7...done 438s Segment #6 of 7... 438s Segment #6 of 7...done 438s Segment #7 of 7... 438s Segment #7 of 7...done 438s Field #1 ('tcn') of 4...done 438s Field #2 ('dh') of 4... 438s Segment #1 of 7... 438s Segment #1 of 7...done 438s Segment #2 of 7... 438s Segment #2 of 7...done 438s Segment #3 of 7... 438s Segment #3 of 7...done 438s Segment #4 of 7... 438s Segment #4 of 7...done 438s Segment #5 of 7... 438s Segment #5 of 7...done 438s Segment #6 of 7... 438s Segment #6 of 7...done 438s Segment #7 of 7... 438s Segment #7 of 7...done 438s Field #2 ('dh') of 4...done 438s Field #3 ('c1') of 4... 438s Segment #1 of 7... 438s Segment #1 of 7...done 438s Segment #2 of 7... 438s Segment #2 of 7...done 438s Segment #3 of 7... 438s Segment #3 of 7...done 438s Segment #4 of 7... 438s Segment #4 of 7...done 438s Segment #5 of 7... 438s Segment #5 of 7...done 438s Segment #6 of 7... 438s Segment #6 of 7...done 438s Segment #7 of 7... 438s Segment #7 of 7...done 438s Field #3 ('c1') of 4...done 438s Field #4 ('c2') of 4... 438s Segment #1 of 7... 438s Segment #1 of 7...done 438s Segment #2 of 7... 438s Segment #2 of 7...done 438s Segment #3 of 7... 438s Segment #3 of 7...done 438s Segment #4 of 7... 438s Segment #4 of 7...done 438s Segment #5 of 7... 438s Segment #5 of 7...done 438s Segment #6 of 7... 438s Segment #6 of 7...done 438s Segment #7 of 7... 438s Segment #7 of 7...done 438s Field #4 ('c2') of 4...done 438s Bootstrap statistics 438s num [1:7, 1:4, 1:4] 1.38 2.07 2.63 NA 1.38 ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 438s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 438s Statistical sanity checks (iff B >= 100)... 438s Available summaries: 2.5%, 5%, 95%, 97.5% 438s Available quantiles: 0.025, 0.05, 0.95, 0.975 438s num [1:7, 1:4, 1:4] 1.38 2.07 2.63 NA 1.38 ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 438s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 438s Field #1 ('tcn') of 4... 438s Seg 1. mean=1.39161, range=[1.38025,1.40693], n=1880 438s Seg 2. mean=2.09245, range=[2.06856,2.1165], n=671 438s Seg 3. mean=2.65451, range=[2.62678,2.6834], n=1111 438s Seg 4. mean=NA, range=[NA,NA], n=NA 438s Seg 5. mean=1.39161, range=[1.37999,1.40474], n=1880 438s Seg 6. mean=2.09245, range=[2.06923,2.11747], n=671 438s Seg 7. mean=2.65451, range=[2.62867,2.68639], n=1111 438s Field #1 ('tcn') of 4...done 438s Field #2 ('dh') of 4... 438s Seg 1. mean=0.420632, range=[0.406983,0.437756], n=765 438s Seg 2. mean=0.176243, range=[0.141232,0.202975], n=272 438s Seg 3. mean=0.269742, range=[0.245337,0.292784], n=414 438s Seg 4. mean=NA, range=[NA,NA], n=NA 438s Seg 5. mean=0.420632, range=[0.406204,0.436189], n=765 438s Seg 6. mean=0.176243, range=[0.13696,0.212132], n=272 438s Seg 7. mean=0.269742, range=[0.230034,0.296763], n=414 438s Field #2 ('dh') of 4...done 438s Field #3 ('c1') of 4... 438s Seg 1. mean=0.403126, range=[0.391189,0.413437], n=765 438s Seg 2. mean=0.861836, range=[0.833296,0.900874], n=272 438s Seg 3. mean=0.969239, range=[0.937437,1.00659], n=414 438s Seg 4. mean=NA, range=[NA,NA], n=NA 438s Seg 5. mean=0.403126, range=[0.392112,0.414529], n=765 438s Seg 6. mean=0.861836, range=[0.823193,0.907577], n=272 438s Seg 7. mean=0.969239, range=[0.931951,1.01968], n=414 438s Field #3 ('c1') of 4...done 438s Field #4 ('c2') of 4... 438s Seg 1. mean=0.988482, range=[0.974501,1.00244], n=765 438s Seg 2. mean=1.23062, range=[1.18964,1.26157], n=272 438s Seg 3. mean=1.68527, range=[1.6481,1.72497], n=414 438s Seg 4. mean=NA, range=[NA,NA], n=NA 438s Seg 5. mean=0.988482, range=[0.9761,1.00076], n=765 438s Seg 6. mean=1.23062, range=[1.18936,1.26647], n=272 438s Seg 7. mean=1.68527, range=[1.63171,1.72526], n=414 438s Field #4 ('c2') of 4...done 438s Statistical sanity checks (iff B >= 100)...done 438s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 438s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 438s num [1:6, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 438s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 438s Field #1 ('alpha') of 5... 438s Changepoint #1 of 6... 438s Changepoint #1 of 6...done 438s Changepoint #2 of 6... 438s Changepoint #2 of 6...done 438s Changepoint #3 of 6... 438s Changepoint #3 of 6...done 438s Changepoint #4 of 6... 438s Changepoint #4 of 6...done 438s Changepoint #5 of 6... 438s Changepoint #5 of 6...done 438s Changepoint #6 of 6... 438s Changepoint #6 of 6...done 438s Field #1 ('alpha') of 5...done 438s Field #2 ('radius') of 5... 438s Changepoint #1 of 6... 438s Changepoint #1 of 6...done 438s Changepoint #2 of 6... 438s Changepoint #2 of 6...done 438s Changepoint #3 of 6... 438s Changepoint #3 of 6...done 438s Changepoint #4 of 6... 438s Changepoint #4 of 6...done 438s Changepoint #5 of 6... 438s Changepoint #5 of 6...done 438s Changepoint #6 of 6... 438s Changepoint #6 of 6...done 438s Field #2 ('radius') of 5...done 438s Field #3 ('manhattan') of 5... 438s Changepoint #1 of 6... 438s Changepoint #1 of 6...done 438s Changepoint #2 of 6... 438s Changepoint #2 of 6...done 438s Changepoint #3 of 6... 438s Changepoint #3 of 6...done 438s Changepoint #4 of 6... 438s Changepoint #4 of 6...done 438s Changepoint #5 of 6... 438s Changepoint #5 of 6...done 438s Changepoint #6 of 6... 438s Changepoint #6 of 6...done 438s Field #3 ('manhattan') of 5...done 438s Field #4 ('d1') of 5... 438s Changepoint #1 of 6... 438s Changepoint #1 of 6...done 438s Changepoint #2 of 6... 438s Changepoint #2 of 6...done 438s Changepoint #3 of 6... 438s Changepoint #3 of 6...done 438s Changepoint #4 of 6... 438s Changepoint #4 of 6...done 438s Changepoint #5 of 6... 438s Changepoint #5 of 6...done 438s Changepoint #6 of 6... 438s Changepoint #6 of 6...done 438s Field #4 ('d1') of 5...done 438s Field #5 ('d2') of 5... 438s Changepoint #1 of 6... 438s Changepoint #1 of 6...done 438s Changepoint #2 of 6... 438s Changepoint #2 of 6...done 438s Changepoint #3 of 6... 438s Changepoint #3 of 6...done 438s Changepoint #4 of 6... 438s Changepoint #4 of 6...done 438s Changepoint #5 of 6... 438s Changepoint #5 of 6...done 438s Changepoint #6 of 6... 438s Changepoint #6 of 6...done 438s Field #5 ('d2') of 5...done 438s Bootstrap statistics 438s num [1:6, 1:4, 1:5] -2.76 -1.91 NA NA -2.76 ... 438s - attr(*, "dimnames")=List of 3 438s ..$ : NULL 438s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 438s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 438s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 438s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 438s > print(fit) 438s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s 4 NA NA NA NA NA NA NA NA 438s 5 2 1 1 554484 143663981 1880 1.391608 765 438s 6 2 2 1 143663981 185240536 671 2.092452 272 438s 7 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 438s 1 765 765 0.4206323 0.4031263 0.9884817 438s 2 272 272 0.1762428 0.8618360 1.2306156 438s 3 414 414 0.2697420 0.9692395 1.6852728 438s 4 NA NA NA NA NA 438s 5 765 765 0.4206323 0.4031263 0.9884817 438s 6 272 272 0.1762428 0.8618360 1.2306156 438s 7 414 414 0.2697420 0.9692395 1.6852728 438s > 438s > 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > # Calling segments in allelic balance (AB) 438s > # NOTE: Ideally, this should be done on whole-genome data 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > # Explicitly estimate the threshold in DH for calling AB 438s > # (which be done by default by the caller, if skipped here) 438s > deltaAB <- estimateDeltaAB(fit, flavor="qq(DH)", verbose=-10) 438s Estimating DH threshold for calling allelic imbalances... 438s flavor: qq(DH) 438s scale: 1 438s Estimating DH threshold for AB caller... 438s quantile #1: 0.05 438s Symmetric quantile #2: 0.9 438s Number of segments: 6 438s Weighted 5% quantile of DH: 0.199618 438s Number of segments with small DH: 2 438s Number of data points: 1342 438s Number of finite data points: 544 438s Estimate of (1-0.9):th and 50% quantiles: (0.0289919,0.176243) 438s Estimate of 0.9:th "symmetric" quantile: 0.323494 438s Estimating DH threshold for AB caller...done 438s Estimated delta: 0.323 438s Estimating DH threshold for calling allelic imbalances...done 438s > print(deltaAB) 438s [1] 0.3234938 438s > 438s > fit <- callAB(fit, delta=deltaAB, verbose=-10) 438s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 438s delta (offset adjusting for bias in DH): 0.323493772175137 438s alpha (CI quantile; significance level): 0.05 438s Calling segments... 438s Number of segments called allelic balance (AB): 4 (57.14%) of 7 438s Calling segments...done 438s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 438s > print(fit) 438s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s 4 NA NA NA NA NA NA NA NA 438s 5 2 1 1 554484 143663981 1880 1.391608 765 438s 6 2 2 1 143663981 185240536 671 2.092452 272 438s 7 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall 438s 1 765 765 0.4206323 0.4031263 0.9884817 FALSE 438s 2 272 272 0.1762428 0.8618360 1.2306156 TRUE 438s 3 414 414 0.2697420 0.9692395 1.6852728 TRUE 438s 4 NA NA NA NA NA NA 438s 5 765 765 0.4206323 0.4031263 0.9884817 FALSE 438s 6 272 272 0.1762428 0.8618360 1.2306156 TRUE 438s 7 414 414 0.2697420 0.9692395 1.6852728 TRUE 438s > 438s > 438s > # Even if not explicitly specified, the estimated 438s > # threshold parameter is returned by the caller 438s > stopifnot(fit$params$deltaAB == deltaAB) 438s > 438s > 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > # Calling segments in loss-of-heterozygosity (LOH) 438s > # NOTE: Ideally, this should be done on whole-genome data 438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 438s > # Explicitly estimate the threshold in C1 for calling LOH 438s > # (which be done by default by the caller, if skipped here) 438s > deltaLOH <- estimateDeltaLOH(fit, flavor="minC1|nonAB", verbose=-10) 438s Estimating DH threshold for calling LOH... 438s flavor: minC1|nonAB 438s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1... 438s Argument 'midpoint': 0.5 438s Number of segments: 6 438s Number of segments in allelic balance: 4 (66.7%) of 6 438s Number of segments not in allelic balance: 2 (33.3%) of 6 438s Number of segments in allelic balance and TCN <= 3.00: 4 (66.7%) of 6 438s C: 2.09, 2.65, 2.09, 2.65 438s Corrected C1 (=C/2): 1.05, 1.33, 1.05, 1.33 438s Number of DHs: 272, 414, 272, 414 438s Weights: 0.198, 0.302, 0.198, 0.302 438s Weighted median of (corrected) C1 in allelic balance: 1.274 438s Smallest C1 among segments not in allelic balance: 0.403 438s There are 2 segments with in total 765 heterozygous SNPs with this level. 438s There are 2 segments with in total 765 heterozygous SNPs with this level. 438s Midpoint between the two: 0.839 438s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1...done 438s delta: 0.839 438s Estimating DH threshold for calling LOH...done 438s > print(deltaLOH) 438s [1] 0.838563 438s > 438s > fit <- callLOH(fit, delta=deltaLOH, verbose=-10) 438s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 438s delta (offset adjusting for bias in C1): 0.838562992888546 438s alpha (CI quantile; significance level): 0.05 438s Calling segments... 438s Number of segments called low C1 (LowC1, "LOH_C1"): 3 (42.86%) of 7 438s Calling segments...done 438s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 438s > print(fit) 438s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 438s 1 1 1 1 554484 143663981 1880 1.391608 765 438s 2 1 2 1 143663981 185240536 671 2.092452 272 438s 3 1 3 1 185240536 246679946 1111 2.654512 414 438s 4 NA NA NA NA NA NA NA NA 438s 5 2 1 1 554484 143663981 1880 1.391608 765 438s 6 2 2 1 143663981 185240536 671 2.092452 272 438s 7 2 3 1 185240536 246679946 1111 2.654512 414 438s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall lohCall 438s 1 765 765 0.4206323 0.4031263 0.9884817 FALSE TRUE 438s 2 272 272 0.1762428 0.8618360 1.2306156 TRUE NA 438s 3 414 414 0.2697420 0.9692395 1.6852728 TRUE FALSE 438s 4 NA NA NA NA NA NA NA 438s 5 765 765 0.4206323 0.4031263 0.9884817 FALSE TRUE 438s 6 272 272 0.1762428 0.8618360 1.2306156 TRUE FALSE 438s 7 414 414 0.2697420 0.9692395 1.6852728 TRUE FALSE 438s > plotTracks(fit) 438s > 438s > # Even if not explicitly specified, the estimated 438s > # threshold parameter is returned by the caller 438s > stopifnot(fit$params$deltaLOH == deltaLOH) 438s > 438s > proc.time() 438s user system elapsed 438s 1.885 0.081 1.969 438s Test segmentByNonPairedPSCBS,medianDH passed 438s 0 438s Begin test segmentByPairedPSCBS,DH 441s + 441s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 441s Copyright (C) 2024 The R Foundation for Statistical Computing 441s Platform: s390x-ibm-linux-gnu (64-bit) 441s 441s R is free software and comes with ABSOLUTELY NO WARRANTY. 441s You are welcome to redistribute it under certain conditions. 441s Type 'license()' or 'licence()' for distribution details. 441s 441s R is a collaborative project with many contributors. 441s Type 'contributors()' for more information and 441s 'citation()' on how to cite R or R packages in publications. 441s 441s Type 'demo()' for some demos, 'help()' for on-line help, or 441s 'help.start()' for an HTML browser interface to help. 441s Type 'q()' to quit R. 441s 441s [Previously saved workspace restored] 441s 441s > library("PSCBS") 441s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 441s 441s Attaching package: 'PSCBS' 441s 441s The following objects are masked from 'package:base': 441s 441s append, load 441s 441s > 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > # Load SNP microarray data 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > data <- PSCBS::exampleData("paired.chr01") 441s > str(data) 441s 'data.frame': 73346 obs. of 6 variables: 441s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 441s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 441s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 441s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 441s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 441s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 441s > 441s > # Drop single-locus outliers 441s > dataS <- dropSegmentationOutliers(data) 441s > 441s > # Run light-weight tests 441s > # Use only every 5th data point 441s > dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 441s > # Number of segments (for assertion) 441s > nSegs <- 3L 441s > # Number of bootstrap samples (see below) 441s > B <- 100L 441s > 441s > str(dataS) 441s 'data.frame': 14670 obs. of 6 variables: 441s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 441s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 441s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 441s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 441s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 441s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 441s > R.oo::attachLocally(dataS) 441s > 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > # Calculate DH 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > muN <- aroma.light::callNaiveGenotypes(betaN, censorAt=c(0,1)) 441s > # SNPs are identifies as those loci that have non-missing 'betaT' & 'muN' 441s > isSnp <- (!is.na(betaT) & !is.na(muN)) 441s > isHet <- isSnp & (muN == 1/2) 441s > rho <- rep(NA_real_, length=length(muN)) 441s > rho[isHet] <- 2*abs(betaT[isHet]-1/2) 441s > 441s > 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > # Paired PSCBS segmentation using TCN and DH only 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > fit <- segmentByPairedPSCBS(CT, rho=rho, 441s + chromosome=chromosome, x=x, 441s + seed=0xBEEF, verbose=-10) 441s Segmenting paired tumor-normal signals using Paired PSCBS... 441s Setup up data... 441s 'data.frame': 14670 obs. of 4 variables: 441s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 441s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 441s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 441s $ rho : num NA 0.662 NA NA NA ... 441s Setup up data...done 441s Dropping loci for which TCNs are missing... 441s Number of loci dropped: 12 441s Dropping loci for which TCNs are missing...done 441s Ordering data along genome... 441s 'data.frame': 14658 obs. of 4 variables: 441s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 441s $ x : num 554484 730720 782343 878522 916294 ... 441s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 441s $ rho : num NA NA NA NA NA ... 441s Ordering data along genome...done 441s Keeping only current chromosome for 'knownSegments'... 441s Chromosome: 1 441s Known segments for this chromosome: 441s [1] chromosome start end 441s <0 rows> (or 0-length row.names) 441s Keeping only current chromosome for 'knownSegments'...done 441s alphaTCN: 0.009 441s alphaDH: 0.001 441s Number of loci: 14658 441s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 441s Produced 2 seeds from this stream for future usage 441s Identification of change points by total copy numbers... 441s Segmenting by CBS... 441s Chromosome: 1 441s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 441s Segmenting by CBS...done 441s List of 4 441s $ data :'data.frame': 14658 obs. of 4 variables: 441s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 441s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 441s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 441s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 441s $ output :'data.frame': 3 obs. of 6 variables: 441s ..$ sampleName: chr [1:3] NA NA NA 441s ..$ chromosome: int [1:3] 1 1 1 441s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 441s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 441s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 441s ..$ mean : num [1:3] 1.39 2.07 2.63 441s $ segRows:'data.frame': 3 obs. of 2 variables: 441s ..$ startRow: int [1:3] 1 7600 10268 441s ..$ endRow : int [1:3] 7599 10267 14658 441s $ params :List of 5 441s ..$ alpha : num 0.009 441s ..$ undo : num 0 441s ..$ joinSegments : logi TRUE 441s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 441s .. ..$ chromosome: int 1 441s .. ..$ start : num -Inf 441s .. ..$ end : num Inf 441s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 441s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 441s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.577 0.001 0.584 0 0 441s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 441s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 441s - attr(*, "randomSeed")= int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 441s Identification of change points by total copy numbers...done 441s Restructure TCN segmentation results... 441s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 441s 1 1 554484 143926517 7599 1.3859 441s 2 1 143926517 185449813 2668 2.0704 441s 3 1 185449813 247137334 4391 2.6341 441s Number of TCN segments: 3 441s Restructure TCN segmentation results...done 441s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 441s Number of TCN loci in segment: 7599 441s Locus data for TCN segment: 441s 'data.frame': 7599 obs. of 5 variables: 441s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 441s $ x : num 554484 730720 782343 878522 916294 ... 441s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 441s $ rho : num NA NA NA NA NA ... 441s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 441s Number of loci: 7599 441s Number of SNPs: 2111 (27.78%) 441s Number of heterozygous SNPs: 2111 (100.00%) 441s Chromosome: 1 441s Segmenting DH signals... 441s Segmenting by CBS... 441s Chromosome: 1 441s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 441s Segmenting by CBS...done 441s List of 4 441s $ data :'data.frame': 7599 obs. of 4 variables: 441s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 441s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 441s ..$ y : num [1:7599] NA NA NA NA NA ... 441s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 441s $ output :'data.frame': 1 obs. of 6 variables: 441s ..$ sampleName: chr NA 441s ..$ chromosome: int 1 441s ..$ start : num 554484 441s ..$ end : num 1.44e+08 441s ..$ nbrOfLoci : int 2111 441s ..$ mean : num 0.524 441s $ segRows:'data.frame': 1 obs. of 2 variables: 441s ..$ startRow: int 10 441s ..$ endRow : int 7594 441s $ params :List of 5 441s ..$ alpha : num 0.001 441s ..$ undo : num 0 441s ..$ joinSegments : logi TRUE 441s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 441s .. ..$ chromosome: int 1 441s .. ..$ start : num 554484 441s .. ..$ end : num 1.44e+08 441s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 441s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 441s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.039 0 0.036 0 0 441s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 441s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 441s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 441s DH segmentation (locally-indexed) rows: 441s startRow endRow 441s 1 10 7594 441s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 441s DH segmentation rows: 441s startRow endRow 441s 1 10 7594 441s Segmenting DH signals...done 441s DH segmentation table: 441s dhStart dhEnd dhNbrOfLoci dhMean 441s 1 554484 143926517 2111 0.5237 441s startRow endRow 441s 1 10 7594 441s Rows: 441s [1] 1 441s TCN segmentation rows: 441s startRow endRow 441s 1 1 7599 441s TCN and DH segmentation rows: 441s startRow endRow 441s 1 1 7599 441s startRow endRow 441s 1 10 7594 441s NULL 441s TCN segmentation (expanded) rows: 441s startRow endRow 441s 1 1 7599 441s TCN and DH segmentation rows: 441s startRow endRow 441s 1 1 7599 441s 2 7600 10267 441s 3 10268 14658 441s startRow endRow 441s 1 10 7594 441s startRow endRow 441s 1 1 7599 441s Total CN segmentation table (expanded): 441s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 441s 1 1 554484 143926517 7599 1.3859 2111 2111 441s (TCN,DH) segmentation for one total CN segment: 441s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 1 1 1 1 554484 143926517 7599 1.3859 2111 441s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 441s 1 2111 554484 143926517 2111 0.5237 441s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 441s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 441s Number of TCN loci in segment: 2668 441s Locus data for TCN segment: 441s 'data.frame': 2668 obs. of 5 variables: 441s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 441s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 441s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 441s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 441s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 441s Number of loci: 2668 441s Number of SNPs: 774 (29.01%) 441s Number of heterozygous SNPs: 774 (100.00%) 441s Chromosome: 1 441s Segmenting DH signals... 441s Segmenting by CBS... 441s Chromosome: 1 441s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 441s Segmenting by CBS...done 441s List of 4 441s $ data :'data.frame': 2668 obs. of 4 variables: 441s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 441s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 441s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 441s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 441s $ output :'data.frame': 1 obs. of 6 variables: 441s ..$ sampleName: chr NA 441s ..$ chromosome: int 1 441s ..$ start : num 1.44e+08 441s ..$ end : num 1.85e+08 441s ..$ nbrOfLoci : int 774 441s ..$ mean : num 0.154 441s $ segRows:'data.frame': 1 obs. of 2 variables: 441s ..$ startRow: int 15 441s ..$ endRow : int 2664 441s $ params :List of 5 441s ..$ alpha : num 0.001 441s ..$ undo : num 0 441s ..$ joinSegments : logi TRUE 441s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 441s .. ..$ chromosome: int 1 441s .. ..$ start : num 1.44e+08 441s .. ..$ end : num 1.85e+08 441s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 441s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 441s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.012 0 0 441s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 441s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 441s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 441s DH segmentation (locally-indexed) rows: 441s startRow endRow 441s 1 15 2664 441s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 441s DH segmentation rows: 441s startRow endRow 441s 1 7614 10263 441s Segmenting DH signals...done 441s DH segmentation table: 441s dhStart dhEnd dhNbrOfLoci dhMean 441s 1 143926517 185449813 774 0.1542 441s startRow endRow 441s 1 7614 10263 441s Rows: 441s [1] 2 441s TCN segmentation rows: 441s startRow endRow 441s 2 7600 10267 441s TCN and DH segmentation rows: 441s startRow endRow 441s 2 7600 10267 441s startRow endRow 441s 1 7614 10263 441s startRow endRow 441s 1 1 7599 441s TCN segmentation (expanded) rows: 441s startRow endRow 441s 1 1 7599 441s 2 7600 10267 441s TCN and DH segmentation rows: 441s startRow endRow 441s 1 1 7599 441s 2 7600 10267 441s 3 10268 14658 441s startRow endRow 441s 1 10 7594 441s 2 7614 10263 441s startRow endRow 441s 1 1 7599 441s 2 7600 10267 441s Total CN segmentation table (expanded): 441s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 441s 2 1 143926517 185449813 2668 2.0704 774 774 441s (TCN,DH) segmentation for one total CN segment: 441s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 2 2 1 1 143926517 185449813 2668 2.0704 774 441s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 441s 2 774 143926517 185449813 774 0.1542 441s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 441s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 441s Number of TCN loci in segment: 4391 441s Locus data for TCN segment: 441s 'data.frame': 4391 obs. of 5 variables: 441s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 441s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 441s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 441s $ rho : num NA 0.0308 NA 0.2533 NA ... 441s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 441s Number of loci: 4391 441s Number of SNPs: 1311 (29.86%) 441s Number of heterozygous SNPs: 1311 (100.00%) 441s Chromosome: 1 441s Segmenting DH signals... 441s Segmenting by CBS... 441s Chromosome: 1 441s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 441s Segmenting by CBS...done 441s List of 4 441s $ data :'data.frame': 4391 obs. of 4 variables: 441s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 441s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 441s ..$ y : num [1:4391] NA 0.0308 NA 0.2533 NA ... 441s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 441s $ output :'data.frame': 1 obs. of 6 variables: 441s ..$ sampleName: chr NA 441s ..$ chromosome: int 1 441s ..$ start : num 1.85e+08 441s ..$ end : num 2.47e+08 441s ..$ nbrOfLoci : int 1311 441s ..$ mean : num 0.251 441s $ segRows:'data.frame': 1 obs. of 2 variables: 441s ..$ startRow: int 2 441s ..$ endRow : int 4388 441s $ params :List of 5 441s ..$ alpha : num 0.001 441s ..$ undo : num 0 441s ..$ joinSegments : logi TRUE 441s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 441s .. ..$ chromosome: int 1 441s .. ..$ start : num 1.85e+08 441s .. ..$ end : num 2.47e+08 441s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 441s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 441s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.019 0 0.028 0 0 441s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 441s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 441s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 441s DH segmentation (locally-indexed) rows: 441s startRow endRow 441s 1 2 4388 441s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 441s DH segmentation rows: 441s startRow endRow 441s 1 10269 14655 441s Segmenting DH signals...done 441s DH segmentation table: 441s dhStart dhEnd dhNbrOfLoci dhMean 441s 1 185449813 247137334 1311 0.2512 441s startRow endRow 441s 1 10269 14655 441s Rows: 441s [1] 3 441s TCN segmentation rows: 441s startRow endRow 441s 3 10268 14658 441s TCN and DH segmentation rows: 441s startRow endRow 441s 3 10268 14658 441s startRow endRow 441s 1 10269 14655 441s startRow endRow 441s 1 1 7599 441s 2 7600 10267 441s TCN segmentation (expanded) rows: 441s startRow endRow 441s 1 1 7599 441s 2 7600 10267 441s 3 10268 14658 441s TCN and DH segmentation rows: 441s startRow endRow 441s 1 1 7599 441s 2 7600 10267 441s 3 10268 14658 441s startRow endRow 441s 1 10 7594 441s 2 7614 10263 441s 3 10269 14655 441s startRow endRow 441s 1 1 7599 441s 2 7600 10267 441s 3 10268 14658 441s Total CN segmentation table (expanded): 441s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 441s 3 1 185449813 247137334 4391 2.6341 1311 1311 441s (TCN,DH) segmentation for one total CN segment: 441s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 3 3 1 1 185449813 247137334 4391 2.6341 1311 441s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 441s 3 1311 185449813 247137334 1311 0.2512 441s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 441s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 1 1 1 1 554484 143926517 7599 1.3859 2111 441s 2 1 2 1 143926517 185449813 2668 2.0704 774 441s 3 1 3 1 185449813 247137334 4391 2.6341 1311 441s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 441s 1 2111 554484 143926517 2111 0.5237 441s 2 774 143926517 185449813 774 0.1542 441s 3 1311 185449813 247137334 1311 0.2512 441s Calculating (C1,C2) per segment... 441s Calculating (C1,C2) per segment...done 441s Number of segments: 3 441s Segmenting paired tumor-normal signals using Paired PSCBS...done 441s Post-segmenting TCNs... 441s Number of segments: 3 441s Number of chromosomes: 1 441s [1] 1 441s Chromosome 1 ('chr01') of 1... 441s Rows: 441s [1] 1 2 3 441s Number of segments: 3 441s TCN segment #1 ('1') of 3... 441s Nothing todo. Only one DH segmentation. Skipping. 441s TCN segment #1 ('1') of 3...done 441s TCN segment #2 ('2') of 3... 441s Nothing todo. Only one DH segmentation. Skipping. 441s TCN segment #2 ('2') of 3...done 441s TCN segment #3 ('3') of 3... 441s Nothing todo. Only one DH segmentation. Skipping. 441s TCN segment #3 ('3') of 3...done 441s Chromosome 1 ('chr01') of 1...done 441s Update (C1,C2) per segment... 441s Update (C1,C2) per segment...done 441s Post-segmenting TCNs...done 441s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 1 1 1 1 554484 143926517 7599 1.3859 2111 441s 2 1 2 1 143926517 185449813 2668 2.0704 774 441s 3 1 3 1 185449813 247137334 4391 2.6341 1311 441s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 441s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 441s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 441s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 441s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 1 1 1 1 554484 143926517 7599 1.3859 2111 441s 2 1 2 1 143926517 185449813 2668 2.0704 774 441s 3 1 3 1 185449813 247137334 4391 2.6341 1311 441s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 441s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 441s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 441s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 441s > print(fit) 441s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 1 1 1 1 554484 143926517 7599 1.3859 2111 441s 2 1 2 1 143926517 185449813 2668 2.0704 774 441s 3 1 3 1 185449813 247137334 4391 2.6341 1311 441s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 441s 1 2111 2111 0.5237 0.3300521 1.055848 441s 2 774 774 0.1542 0.8755722 1.194828 441s 3 1311 1311 0.2512 0.9862070 1.647893 441s > 441s > # Plot results 441s > plotTracks(fit) 441s > 441s > 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > # Bootstrap segment level estimates 441s > # (used by the AB caller, which, if skipped here, 441s > # will do it automatically) 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > fit <- bootstrapTCNandDHByRegion(fit, B=B, verbose=-10) 441s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 441s Already done? 441s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 441s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 441s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 441s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 441s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 441s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 441s Number of loci: 14658 441s Number of SNPs: 4196 441s Number of non-SNPs: 10462 441s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 441s num [1:3, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : NULL 441s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 441s Segment #1 (chr 1, tcnId=1, dhId=1) of 3... 441s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 1 1 1 1 554484 143926517 7599 1.3859 2111 441s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 441s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 441s Number of TCNs: 7599 441s Number of DHs: 2111 441s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 441s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 441s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 441s Identify loci used to bootstrap DH means... 441s Heterozygous SNPs to resample for DH: 441s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 441s Identify loci used to bootstrap DH means...done 441s Identify loci used to bootstrap TCN means... 441s SNPs: 441s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 441s Non-polymorphic loci: 441s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 441s Heterozygous SNPs to resample for TCN: 441s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 441s Homozygous SNPs to resample for TCN: 441s int(0) 441s Non-polymorphic loci to resample for TCN: 441s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 441s Heterozygous SNPs with non-DH to resample for TCN: 441s int(0) 441s Loci to resample for TCN: 441s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 441s Identify loci used to bootstrap TCN means...done 441s Number of (#hets, #homs, #nonSNPs): (2111,0,5488) 441s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 441s Number of bootstrap samples: 100 441s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 441s Segment #1 (chr 1, tcnId=1, dhId=1) of 3...done 441s Segment #2 (chr 1, tcnId=2, dhId=1) of 3... 441s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 2 1 2 1 143926517 185449813 2668 2.0704 774 441s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 441s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 441s Number of TCNs: 2668 441s Number of DHs: 774 441s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 441s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 441s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 441s Identify loci used to bootstrap DH means... 441s Heterozygous SNPs to resample for DH: 441s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 441s Identify loci used to bootstrap DH means...done 441s Identify loci used to bootstrap TCN means... 441s SNPs: 441s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 441s Non-polymorphic loci: 441s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 441s Heterozygous SNPs to resample for TCN: 441s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 441s Homozygous SNPs to resample for TCN: 441s int(0) 441s Non-polymorphic loci to resample for TCN: 441s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 441s Heterozygous SNPs with non-DH to resample for TCN: 441s int(0) 441s Loci to resample for TCN: 441s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 441s Identify loci used to bootstrap TCN means...done 441s Number of (#hets, #homs, #nonSNPs): (774,0,1894) 441s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 441s Number of bootstrap samples: 100 441s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 441s Segment #2 (chr 1, tcnId=2, dhId=1) of 3...done 441s Segment #3 (chr 1, tcnId=3, dhId=1) of 3... 441s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 3 1 3 1 185449813 247137334 4391 2.6341 1311 441s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 441s 3 1311 185449813 247137334 1311 0.2512 0.986207 1.647893 441s Number of TCNs: 4391 441s Number of DHs: 1311 441s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 441s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 441s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 441s Identify loci used to bootstrap DH means... 441s Heterozygous SNPs to resample for DH: 441s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 441s Identify loci used to bootstrap DH means...done 441s Identify loci used to bootstrap TCN means... 441s SNPs: 441s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 441s Non-polymorphic loci: 441s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 441s Heterozygous SNPs to resample for TCN: 441s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 441s Homozygous SNPs to resample for TCN: 441s int(0) 441s Non-polymorphic loci to resample for TCN: 441s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 441s Heterozygous SNPs with non-DH to resample for TCN: 441s int(0) 441s Loci to resample for TCN: 441s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 441s Identify loci used to bootstrap TCN means...done 441s Number of (#hets, #homs, #nonSNPs): (1311,0,3080) 441s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 441s Number of bootstrap samples: 100 441s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 441s Segment #3 (chr 1, tcnId=3, dhId=1) of 3...done 441s Bootstrapped segment mean levels 441s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : NULL 441s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 441s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 441s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : NULL 441s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 441s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 441s Calculating polar (alpha,radius,manhattan) for change points... 441s num [1:2, 1:100, 1:2] -0.5588 -0.0962 -0.5365 -0.1285 -0.5378 ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : NULL 441s ..$ : chr [1:2] "c1" "c2" 441s Bootstrapped change points 441s num [1:2, 1:100, 1:5] -2.89 -1.78 -2.87 -1.86 -2.88 ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : NULL 441s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 441s Calculating polar (alpha,radius,manhattan) for change points...done 441s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 441s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 441s num [1:3, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 441s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 441s Field #1 ('tcn') of 4... 441s Segment #1 of 3... 441s Segment #1 of 3...done 441s Segment #2 of 3... 441s Segment #2 of 3...done 441s Segment #3 of 3... 441s Segment #3 of 3...done 441s Field #1 ('tcn') of 4...done 441s Field #2 ('dh') of 4... 441s Segment #1 of 3... 441s Segment #1 of 3...done 441s Segment #2 of 3... 441s Segment #2 of 3...done 441s Segment #3 of 3... 441s Segment #3 of 3...done 441s Field #2 ('dh') of 4...done 441s Field #3 ('c1') of 4... 441s Segment #1 of 3... 441s Segment #1 of 3...done 441s Segment #2 of 3... 441s Segment #2 of 3...done 441s Segment #3 of 3... 441s Segment #3 of 3...done 441s Field #3 ('c1') of 4...done 441s Field #4 ('c2') of 4... 441s Segment #1 of 3... 441s Segment #1 of 3...done 441s Segment #2 of 3... 441s Segment #2 of 3...done 441s Segment #3 of 3... 441s Segment #3 of 3...done 441s Field #4 ('c2') of 4...done 441s Bootstrap statistics 441s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 441s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 441s Statistical sanity checks (iff B >= 100)... 441s Available summaries: 2.5%, 5%, 95%, 97.5% 441s Available quantiles: 0.025, 0.05, 0.95, 0.975 441s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 441s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 441s Field #1 ('tcn') of 4... 441s Seg 1. mean=1.3859, range=[1.38092,1.3949], n=7599 441s Seg 2. mean=2.0704, range=[2.05747,2.08326], n=2668 441s Seg 3. mean=2.6341, range=[2.62068,2.64694], n=4391 441s Field #1 ('tcn') of 4...done 441s Field #2 ('dh') of 4... 441s Seg 1. mean=0.5237, range=[0.51753,0.532002], n=2111 441s Seg 2. mean=0.1542, range=[0.144468,0.16453], n=774 441s Seg 3. mean=0.2512, range=[0.242575,0.258832], n=1311 441s Field #2 ('dh') of 4...done 441s Field #3 ('c1') of 4... 441s Seg 1. mean=0.330052, range=[0.323996,0.336038], n=2111 441s Seg 2. mean=0.875572, range=[0.86318,0.887699], n=774 441s Seg 3. mean=0.986207, range=[0.975123,0.998982], n=1311 441s Field #3 ('c1') of 4...done 441s Field #4 ('c2') of 4... 441s Seg 1. mean=1.05585, range=[1.05006,1.06231], n=2111 441s Seg 2. mean=1.19483, range=[1.18417,1.2081], n=774 441s Seg 3. mean=1.64789, range=[1.63403,1.66098], n=1311 441s Field #4 ('c2') of 4...done 441s Statistical sanity checks (iff B >= 100)...done 441s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 441s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 441s num [1:2, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 441s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 441s Field #1 ('alpha') of 5... 441s Changepoint #1 of 2... 441s Changepoint #1 of 2...done 441s Changepoint #2 of 2... 441s Changepoint #2 of 2...done 441s Field #1 ('alpha') of 5...done 441s Field #2 ('radius') of 5... 441s Changepoint #1 of 2... 441s Changepoint #1 of 2...done 441s Changepoint #2 of 2... 441s Changepoint #2 of 2...done 441s Field #2 ('radius') of 5...done 441s Field #3 ('manhattan') of 5... 441s Changepoint #1 of 2... 441s Changepoint #1 of 2...done 441s Changepoint #2 of 2... 441s Changepoint #2 of 2...done 441s Field #3 ('manhattan') of 5...done 441s Field #4 ('d1') of 5... 441s Changepoint #1 of 2... 441s Changepoint #1 of 2...done 441s Changepoint #2 of 2... 441s Changepoint #2 of 2...done 441s Field #4 ('d1') of 5...done 441s Field #5 ('d2') of 5... 441s Changepoint #1 of 2... 441s Changepoint #1 of 2...done 441s Changepoint #2 of 2... 441s Changepoint #2 of 2...done 441s Field #5 ('d2') of 5...done 441s Bootstrap statistics 441s num [1:2, 1:4, 1:5] -2.92 -1.86 -2.91 -1.85 -2.87 ... 441s - attr(*, "dimnames")=List of 3 441s ..$ : NULL 441s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 441s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 441s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 441s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 441s > print(fit) 441s chromosome tcnId dhId start end tcnNbrOfLoci tcncat segmentByPairedPSCBS,DH.Rout 441s + [ 0 != 0 ] 441s + echo Test segmentByPairedPSCBS,DH passed 441s + echo 0 441s + echo Begin test segmentByPairedPSCBS,calls 441s + exitcode=0 441s + R CMD BATCH segmentByPairedPSCBS,calls.R 441s Mean tcnNbrOfSNPs 441s 1 1 1 1 554484 143926517 7599 1.3859 2111 441s 2 1 2 1 143926517 185449813 2668 2.0704 774 441s 3 1 3 1 185449813 247137334 4391 2.6341 1311 441s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 441s 1 2111 2111 0.5237 0.3300521 1.055848 441s 2 774 774 0.1542 0.8755722 1.194828 441s 3 1311 1311 0.2512 0.9862070 1.647893 441s > plotTracks(fit) 441s > 441s > 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > # Calling segments in allelic balance (AB) and 441s > # in loss-of-heterozygosity (LOH) 441s > # NOTE: Ideally, this should be done on whole-genome data 441s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 441s > fit <- callAB(fit, verbose=-10) 441s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 441s delta (offset adjusting for bias in DH): 0.3466649145302 441s alpha (CI quantile; significance level): 0.05 441s Calling segments... 441s Number of segments called allelic balance (AB): 2 (66.67%) of 3 441s Calling segments...done 441s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 441s > fit <- callLOH(fit, verbose=-10) 441s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 441s delta (offset adjusting for bias in C1): 0.771236438183453 441s alpha (CI quantile; significance level): 0.05 441s Calling segments... 441s Number of segments called low C1 (LowC1, "LOH_C1"): 1 (33.33%) of 3 441s Calling segments...done 441s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 441s > print(fit) 441s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 441s 1 1 1 1 554484 143926517 7599 1.3859 2111 441s 2 1 2 1 143926517 185449813 2668 2.0704 774 441s 3 1 3 1 185449813 247137334 4391 2.6341 1311 441s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall lohCall 441s 1 2111 2111 0.5237 0.3300521 1.055848 FALSE TRUE 441s 2 774 774 0.1542 0.8755722 1.194828 TRUE FALSE 441s 3 1311 1311 0.2512 0.9862070 1.647893 TRUE FALSE 441s > plotTracks(fit) 441s > 441s > proc.time() 441s user system elapsed 441s 2.421 0.087 2.518 441s Test segmentByPairedPSCBS,DH passed 441s 0 441s Begin test segmentByPairedPSCBS,calls 445s + cat segmentByPairedPSCBS,calls.Rout 445s 445s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 445s Copyright (C) 2024 The R Foundation for Statistical Computing 445s Platform: s390x-ibm-linux-gnu (64-bit) 445s 445s R is free software and comes with ABSOLUTELY NO WARRANTY. 445s You are welcome to redistribute it under certain conditions. 445s Type 'license()' or 'licence()' for distribution details. 445s 445s R is a collaborative project with many contributors. 445s Type 'contributors()' for more information and 445s 'citation()' on how to cite R or R packages in publications. 445s 445s Type 'demo()' for some demos, 'help()' for on-line help, or 445s 'help.start()' for an HTML browser interface to help. 445s Type 'q()' to quit R. 445s 445s [Previously saved workspace restored] 445s 445s > library("PSCBS") 445s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 445s 445s Attaching package: 'PSCBS' 445s 445s The following objects are masked from 'package:base': 445s 445s append, load 445s 445s > 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Load SNP microarray data 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > data <- PSCBS::exampleData("paired.chr01") 445s > str(data) 445s 'data.frame': 73346 obs. of 6 variables: 445s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 445s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 445s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 445s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 445s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 445s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 445s > 445s > 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Paired PSCBS segmentation 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Drop single-locus outliers 445s > dataS <- dropSegmentationOutliers(data) 445s > 445s > # Find centromere 445s > gaps <- findLargeGaps(dataS, minLength=2e6) 445s > knownSegments <- gapsToSegments(gaps) 445s > 445s > 445s > # Run light-weight tests by default 445s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 445s + # Use only every 5th data point 445s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 445s + # Number of segments (for assertion) 445s + nSegs <- 4L 445s + # Number of bootstrap samples (see below) 445s + B <- 100L 445s + } else { 445s + # Full tests 445s + nSegs <- 11L 445s + B <- 1000L 445s + } 445s > 445s > str(dataS) 445s 'data.frame': 14670 obs. of 6 variables: 445s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 445s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 445s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 445s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 445s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 445s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 445s > 445s > # Paired PSCBS segmentation 445s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 445s + seed=0xBEEF, verbose=-10) 445s Segmenting paired tumor-normal signals using Paired PSCBS... 445s Calling genotypes from normal allele B fractions... 445s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 445s Called genotypes: 445s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 445s - attr(*, "modelFit")=List of 1 445s ..$ :List of 7 445s .. ..$ flavor : chr "density" 445s .. ..$ cn : int 2 445s .. ..$ nbrOfGenotypeGroups: int 3 445s .. ..$ tau : num [1:2] 0.315 0.677 445s .. ..$ n : int 14640 445s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 445s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 445s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 445s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 445s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 445s .. .. ..$ type : chr [1:2] "valley" "valley" 445s .. .. ..$ x : num [1:2] 0.315 0.677 445s .. .. ..$ density: num [1:2] 0.522 0.552 445s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 445s muN 445s 0 0.5 1 445s 5221 4198 5251 445s Calling genotypes from normal allele B fractions...done 445s Normalizing betaT using betaN (TumorBoost)... 445s Normalized BAFs: 445s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 445s - attr(*, "modelFit")=List of 5 445s ..$ method : chr "normalizeTumorBoost" 445s ..$ flavor : chr "v4" 445s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 445s .. ..- attr(*, "modelFit")=List of 1 445s .. .. ..$ :List of 7 445s .. .. .. ..$ flavor : chr "density" 445s .. .. .. ..$ cn : int 2 445s .. .. .. ..$ nbrOfGenotypeGroups: int 3 445s .. .. .. ..$ tau : num [1:2] 0.315 0.677 445s .. .. .. ..$ n : int 14640 445s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 445s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 445s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 445s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 445s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 445s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 445s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 445s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 445s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 445s ..$ preserveScale: logi FALSE 445s ..$ scaleFactor : num NA 445s Normalizing betaT using betaN (TumorBoost)...done 445s Setup up data... 445s 'data.frame': 14670 obs. of 7 variables: 445s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 445s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 445s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 445s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 445s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 445s ..- attr(*, "modelFit")=List of 5 445s .. ..$ method : chr "normalizeTumorBoost" 445s .. ..$ flavor : chr "v4" 445s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 445s .. .. ..- attr(*, "modelFit")=List of 1 445s .. .. .. ..$ :List of 7 445s .. .. .. .. ..$ flavor : chr "density" 445s .. .. .. .. ..$ cn : int 2 445s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 445s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 445s .. .. .. .. ..$ n : int 14640 445s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 445s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 445s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 445s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 445s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 445s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 445s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 445s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 445s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 445s .. ..$ preserveScale: logi FALSE 445s .. ..$ scaleFactor : num NA 445s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 445s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 445s ..- attr(*, "modelFit")=List of 1 445s .. ..$ :List of 7 445s .. .. ..$ flavor : chr "density" 445s .. .. ..$ cn : int 2 445s .. .. ..$ nbrOfGenotypeGroups: int 3 445s .. .. ..$ tau : num [1:2] 0.315 0.677 445s .. .. ..$ n : int 14640 445s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 445s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 445s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 445s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 445s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 445s .. .. .. ..$ type : chr [1:2] "valley" "valley" 445s .. .. .. ..$ x : num [1:2] 0.315 0.677 445s .. .. .. ..$ density: num [1:2] 0.522 0.552 445s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 445s Setup up data...done 445s Dropping loci for which TCNs are missing... 445s Number of loci dropped: 12 445s Dropping loci for which TCNs are missing...done 445s Ordering data along genome... 445s 'data.frame': 14658 obs. of 7 variables: 445s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 445s $ x : num 554484 730720 782343 878522 916294 ... 445s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 445s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 445s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 445s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 445s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 445s Ordering data along genome...done 445s Keeping only current chromosome for 'knownSegments'... 445s Chromosome: 1 445s Known segments for this chromosome: 445s chromosome start end length 445s 1 1 -Inf 120992603 Inf 445s 2 1 120992604 141510002 20517398 445s 3 1 141510003 Inf Inf 445s Keeping only current chromosome for 'knownSegments'...done 445s alphaTCN: 0.009 445s alphaDH: 0.001 445s Number of loci: 14658 445s Calculating DHs... 445s Number of SNPs: 14658 445s Number of heterozygous SNPs: 4196 (28.63%) 445s Normalized DHs: 445s num [1:14658] NA NA NA NA NA ... 445s Calculating DHs...done 445s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 445s Produced 2 seeds from this stream for future usage 445s Identification of change points by total copy numbers... 445s Segmenting by CBS... 445s Chromosome: 1 445s Segmenting multiple segments on current chromosome... 445s Number of segments: 3 445s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 445s Produced 3 seeds from this stream for future usage 445s Segmenting by CBS... 445s Chromosome: 1 445s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 445s Segmenting by CBS...done 445s Segmenting by CBS... 445s Chromosome: 1 445s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 445s Segmenting by CBS...done 445s Segmenting multiple segments on current chromosome...done 445s Segmenting by CBS...done 445s List of 4 445s $ data :'data.frame': 14658 obs. of 4 variables: 445s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 445s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 445s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 445s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 445s $ output :'data.frame': 4 obs. of 6 variables: 445s ..$ sampleName: chr [1:4] NA NA NA NA 445s ..$ chromosome: int [1:4] 1 1 1 1 445s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.42e+08 1.85e+08 445s ..$ end : num [1:4] 1.21e+08 1.42e+08 1.85e+08 2.47e+08 445s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 445s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 445s $ segRows:'data.frame': 4 obs. of 2 variables: 445s ..$ startRow: int [1:4] 1 NA 7587 10268 445s ..$ endRow : int [1:4] 7586 NA 10267 14658 445s $ params :List of 5 445s ..$ alpha : num 0.009 445s ..$ undo : num 0 445s ..$ joinSegments : logi TRUE 445s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 445s .. ..$ chromosome: int [1:4] 1 1 2 1 445s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.42e+08 445s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 445s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 445s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 445s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.189 0.001 0.19 0 0 445s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 445s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 445s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 445s Identification of change points by total copy numbers...done 445s Restructure TCN segmentation results... 445s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 445s 1 1 554484 120992603 7586 1.3853 445s 2 1 120992604 141510002 0 NA 445s 3 1 141510003 185449813 2681 2.0689 445s 4 1 185449813 247137334 4391 2.6341 445s Number of TCN segments: 4 445s Restructure TCN segmentation results...done 445s Total CN segment #1 ([ 554484,1.20993e+08]) of 4... 445s Number of TCN loci in segment: 7586 445s Locus data for TCN segment: 445s 'data.frame': 7586 obs. of 9 variables: 445s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 445s $ x : num 554484 730720 782343 878522 916294 ... 445s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 445s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 445s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 445s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 445s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 445s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 445s $ rho : num NA NA NA NA NA ... 445s Number of loci: 7586 445s Number of SNPs: 2108 (27.79%) 445s Number of heterozygous SNPs: 2108 (100.00%) 445s Chromosome: 1 445s Segmenting DH signals... 445s Segmenting by CBS... 445s Chromosome: 1 445s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 445s Segmenting by CBS...done 445s List of 4 445s $ data :'data.frame': 7586 obs. of 4 variables: 445s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 445s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 445s ..$ y : num [1:7586] NA NA NA NA NA ... 445s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 445s $ output :'data.frame': 1 obs. of 6 variables: 445s ..$ sampleName: chr NA 445s ..$ chromosome: int 1 445s ..$ start : num 554484 445s ..$ end : num 1.21e+08 445s ..$ nbrOfLoci : int 2108 445s ..$ mean : num 0.512 445s $ segRows:'data.frame': 1 obs. of 2 variables: 445s ..$ startRow: int 10 445s ..$ endRow : int 7574 445s $ params :List of 5 445s ..$ alpha : num 0.001 445s ..$ undo : num 0 445s ..$ joinSegments : logi TRUE 445s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 445s .. ..$ chromosome: int 1 445s .. ..$ start : num 554484 445s .. ..$ end : num 1.21e+08 445s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 445s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 445s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.05 0.001 0.053 0 0 445s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 445s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 445s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 445s DH segmentation (locally-indexed) rows: 445s startRow endRow 445s 1 10 7574 445s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 445s DH segmentation rows: 445s startRow endRow 445s 1 10 7574 445s Segmenting DH signals...done 445s DH segmentation table: 445s dhStart dhEnd dhNbrOfLoci dhMean 445s 1 554484 120992603 2108 0.5116 445s startRow endRow 445s 1 10 7574 445s Rows: 445s [1] 1 445s TCN segmentation rows: 445s startRow endRow 445s 1 1 7586 445s TCN and DH segmentation rows: 445s startRow endRow 445s 1 1 7586 445s startRow endRow 445s 1 10 7574 445s NULL 445s TCN segmentation (expanded) rows: 445s startRow endRow 445s 1 1 7586 445s TCN and DH segmentation rows: 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s 3 7587 10267 445s 4 10268 14658 445s startRow endRow 445s 1 10 7574 445s startRow endRow 445s 1 1 7586 445s Total CN segmentation table (expanded): 445s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 445s 1 1 554484 120992603 7586 1.3853 2108 2108 445s (TCN,DH) segmentation for one total CN segment: 445s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 445s 1 2108 554484 120992603 2108 0.5116 445s Total CN segment #1 ([ 554484,1.20993e+08]) of 4...done 445s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4... 445s Number of TCN loci in segment: 0 445s Locus data for TCN segment: 445s 'data.frame': 0 obs. of 9 variables: 445s $ chromosome: int 445s $ x : num 445s $ CT : num 445s $ betaT : num 445s $ betaTN : num 445s $ betaN : num 445s $ muN : num 445s $ index : int 445s $ rho : num 445s Number of loci: 0 445s Number of SNPs: 0 (NaN%) 445s Number of heterozygous SNPs: 0 (NaN%) 445s Chromosome: 1 445s Segmenting DH signals... 445s Segmenting by CBS... 445s Chromosome: NA 445s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 445s Segmenting by CBS...done 445s List of 4 445s $ data :'data.frame': 0 obs. of 4 variables: 445s ..$ chromosome: int(0) 445s ..$ x : num(0) 445s ..$ y : num(0) 445s ..$ index : int(0) 445s $ output :'data.frame': 0 obs. of 6 variables: 445s ..$ sampleName: chr(0) 445s ..$ chromosome: num(0) 445s ..$ start : num(0) 445s ..$ end : num(0) 445s ..$ nbrOfLoci : int(0) 445s ..$ mean : num(0) 445s $ segRows:'data.frame': 0 obs. of 2 variables: 445s ..$ startRow: int(0) 445s ..$ endRow : int(0) 445s $ params :List of 5 445s ..$ alpha : num 0.001 445s ..$ undo : num 0 445s ..$ joinSegments : logi TRUE 445s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 445s .. ..$ chromosome: int(0) 445s .. ..$ start : num(0) 445s .. ..$ end : num(0) 445s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 445s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 445s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0.001 0.002 0 0 445s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 445s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 445s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 445s DH segmentation (locally-indexed) rows: 445s [1] startRow endRow 445s <0 rows> (or 0-length row.names) 445s int(0) 445s DH segmentation rows: 445s [1] startRow endRow 445s <0 rows> (or 0-length row.names) 445s Segmenting DH signals...done 445s DH segmentation table: 445s dhStart dhEnd dhNbrOfLoci dhMean 445s NA NA NA NA NA 445s startRow endRow 445s NA NA NA 445s Rows: 445s [1] 2 445s TCN segmentation rows: 445s startRow endRow 445s 2 NA NA 445s TCN and DH segmentation rows: 445s startRow endRow 445s 2 NA NA 445s startRow endRow 445s NA NA NA 445s startRow endRow 445s 1 1 7586 445s TCN segmentation (expanded) rows: 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s TCN and DH segmentation rows: 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s 3 7587 10267 445s 4 10268 14658 445s startRow endRow 445s 1 10 7574 445s 2 NA NA 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s Total CN segmentation table (expanded): 445s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 445s 2 1 120992604 141510002 0 NA 0 0 445s (TCN,DH) segmentation for one total CN segment: 445s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 2 2 1 1 120992604 141510002 0 NA 0 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 445s 2 0 NA NA NA NA 445s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4...done 445s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4... 445s Number of TCN loci in segment: 2681 445s Locus data for TCN segment: 445s 'data.frame': 2681 obs. of 9 variables: 445s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 445s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 445s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 445s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 445s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 445s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 445s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 445s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 445s $ rho : num 0.117 0.258 NA NA NA ... 445s Number of loci: 2681 445s Number of SNPs: 777 (28.98%) 445s Number of heterozygous SNPs: 777 (100.00%) 445s Chromosome: 1 445s Segmenting DH signals... 445s Segmenting by CBS... 445s Chromosome: 1 445s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 445s Segmenting by CBS...done 445s List of 4 445s $ data :'data.frame': 2681 obs. of 4 variables: 445s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 445s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 445s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 445s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 445s $ output :'data.frame': 1 obs. of 6 variables: 445s ..$ sampleName: chr NA 445s ..$ chromosome: int 1 445s ..$ start : num 1.42e+08 445s ..$ end : num 1.85e+08 445s ..$ nbrOfLoci : int 777 445s ..$ mean : num 0.0973 445s $ segRows:'data.frame': 1 obs. of 2 variables: 445s ..$ startRow: int 1 445s ..$ endRow : int 2677 445s $ params :List of 5 445s ..$ alpha : num 0.001 445s ..$ undo : num 0 445s ..$ joinSegments : logi TRUE 445s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 445s .. ..$ chromosome: int 1 445s .. ..$ start : num 1.42e+08 445s .. ..$ end : num 1.85e+08 445s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 445s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 445s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.011 0 0 445s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 445s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 445s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 445s DH segmentation (locally-indexed) rows: 445s startRow endRow 445s 1 1 2677 445s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 445s DH segmentation rows: 445s startRow endRow 445s 1 7587 10263 445s Segmenting DH signals...done 445s DH segmentation table: 445s dhStart dhEnd dhNbrOfLoci dhMean 445s 1 141510003 185449813 777 0.0973 445s startRow endRow 445s 1 7587 10263 445s Rows: 445s [1] 3 445s TCN segmentation rows: 445s startRow endRow 445s 3 7587 10267 445s TCN and DH segmentation rows: 445s startRow endRow 445s 3 7587 10267 445s startRow endRow 445s 1 7587 10263 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s TCN segmentation (expanded) rows: 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s 3 7587 10267 445s TCN and DH segmentation rows: 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s 3 7587 10267 445s 4 10268 14658 445s startRow endRow 445s 1 10 7574 445s 2 NA NA 445s 3 7587 10263 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s 3 7587 10267 445s Total CN segmentation table (expanded): 445s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 445s 3 1 141510003 185449813 2681 2.0689 777 777 445s (TCN,DH) segmentation for one total CN segment: 445s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 3 3 1 1 141510003 185449813 2681 2.0689 777 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 445s 3 777 141510003 185449813 777 0.0973 445s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4...done 445s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 445s Number of TCN loci in segment: 4391 445s Locus data for TCN segment: 445s 'data.frame': 4391 obs. of 9 variables: 445s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 445s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 445s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 445s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 445s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 445s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 445s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 445s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 445s $ rho : num NA 0.2186 NA 0.0503 NA ... 445s Number of loci: 4391 445s Number of SNPs: 1311 (29.86%) 445s Number of heterozygous SNPs: 1311 (100.00%) 445s Chromosome: 1 445s Segmenting DH signals... 445s Segmenting by CBS... 445s Chromosome: 1 445s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 445s Segmenting by CBS...done 445s List of 4 445s $ data :'data.frame': 4391 obs. of 4 variables: 445s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 445s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 445s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 445s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 445s $ output :'data.frame': 1 obs. of 6 variables: 445s ..$ sampleName: chr NA 445s ..$ chromosome: int 1 445s ..$ start : num 1.85e+08 445s ..$ end : num 2.47e+08 445s ..$ nbrOfLoci : int 1311 445s ..$ mean : num 0.23 445s $ segRows:'data.frame': 1 obs. of 2 variables: 445s ..$ startRow: int 2 445s ..$ endRow : int 4388 445s $ params :List of 5 445s ..$ alpha : num 0.001 445s ..$ undo : num 0 445s ..$ joinSegments : logi TRUE 445s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 445s .. ..$ chromosome: int 1 445s .. ..$ start : num 1.85e+08 445s .. ..$ end : num 2.47e+08 445s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 445s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 445s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.021 0 0 445s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 445s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 445s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 445s DH segmentation (locally-indexed) rows: 445s startRow endRow 445s 1 2 4388 445s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 445s DH segmentation rows: 445s startRow endRow 445s 1 10269 14655 445s Segmenting DH signals...done 445s DH segmentation table: 445s dhStart dhEnd dhNbrOfLoci dhMean 445s 1 185449813 247137334 1311 0.2295 445s startRow endRow 445s 1 10269 14655 445s Rows: 445s [1] 4 445s TCN segmentation rows: 445s startRow endRow 445s 4 10268 14658 445s TCN and DH segmentation rows: 445s startRow endRow 445s 4 10268 14658 445s startRow endRow 445s 1 10269 14655 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s 3 7587 10267 445s TCN segmentation (expanded) rows: 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s 3 7587 10267 445s 4 10268 14658 445s TCN and DH segmentation rows: 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s 3 7587 10267 445s 4 10268 14658 445s startRow endRow 445s 1 10 7574 445s 2 NA NA 445s 3 7587 10263 445s 4 10269 14655 445s startRow endRow 445s 1 1 7586 445s 2 NA NA 445s 3 7587 10267 445s 4 10268 14658 445s Total CN segmentation table (expanded): 445s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 445s 4 1 185449813 247137334 4391 2.6341 1311 1311 445s (TCN,DH) segmentation for one total CN segment: 445s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 4 4 1 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 445s 4 1311 185449813 247137334 1311 0.2295 445s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 445s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s 2 1 2 1 120992604 141510002 0 NA 0 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 445s 1 2108 554484 120992603 2108 0.5116 445s 2 0 NA NA NA NA 445s 3 777 141510003 185449813 777 0.0973 445s 4 1311 185449813 247137334 1311 0.2295 445s Calculating (C1,C2) per segment... 445s Calculating (C1,C2) per segment...done 445s Number of segments: 4 445s Segmenting paired tumor-normal signals using Paired PSCBS...done 445s Post-segmenting TCNs... 445s Number of segments: 4 445s Number of chromosomes: 1 445s [1] 1 445s Chromosome 1 ('chr01') of 1... 445s Rows: 445s [1] 1 2 3 4 445s Number of segments: 4 445s TCN segment #1 ('1') of 4... 445s Nothing todo. Only one DH segmentation. Skipping. 445s TCN segment #1 ('1') of 4...done 445s TCN segment #2 ('2') of 4... 445s Nothing todo. Only one DH segmentation. Skipping. 445s TCN segment #2 ('2') of 4...done 445s TCN segment #3 ('3') of 4... 445s Nothing todo. Only one DH segmentation. Skipping. 445s TCN segment #3 ('3') of 4...done 445s TCN segment #4 ('4') of 4... 445s Nothing todo. Only one DH segmentation. Skipping. 445s TCN segment #4 ('4') of 4...done 445s Chromosome 1 ('chr01') of 1...done 445s Update (C1,C2) per segment... 445s Update (C1,C2) per segment...done 445s Post-segmenting TCNs...done 445s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s 2 1 2 1 120992604 141510002 0 NA 0 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 445s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 445s 2 0 NA NA NA NA NA NA 445s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 445s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 445s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s 2 1 2 1 120992604 141510002 0 NA 0 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 445s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 445s 2 0 NA NA NA NA NA NA 445s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 445s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 445s > print(fit) 445s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s 2 1 2 1 120992604 141510002 0 NA 0 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 445s 1 2108 2108 0.5116 0.3382903 1.047010 445s 2 0 NA NA NA NA 445s 3 777 777 0.0973 0.9337980 1.135102 445s 4 1311 1311 0.2295 1.0147870 1.619313 445s > 445s > # Plot results 445s > plotTracks(fit) 445s > 445s > # Sanity check 445s > stopifnot(nbrOfSegments(fit) == nSegs) 445s > 445s > 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Bootstrap segment level estimates 445s > # (used by the AB caller, which, if skipped here, 445s > # will do it automatically) 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > fit <- bootstrapTCNandDHByRegion(fit, B=B, verbose=-10) 445s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 445s Already done? 445s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 445s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 445s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 445s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 445s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 445s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 445s Number of loci: 14658 445s Number of SNPs: 4196 445s Number of non-SNPs: 10462 445s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 445s num [1:4, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : NULL 445s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 445s Segment #1 (chr 1, tcnId=1, dhId=1) of 4... 445s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 445s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.04701 445s Number of TCNs: 7586 445s Number of DHs: 2108 445s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 445s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 445s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 445s Identify loci used to bootstrap DH means... 445s Heterozygous SNPs to resample for DH: 445s int [1:2108] 10 12 24 28 31 33 34 39 46 48 ... 445s Identify loci used to bootstrap DH means...done 445s Identify loci used to bootstrap TCN means... 445s SNPs: 445s int [1:2108] 10 12 24 28 31 33 34 39 46 48 ... 445s Non-polymorphic loci: 445s int [1:5478] 1 2 3 4 5 6 7 8 9 11 ... 445s Heterozygous SNPs to resample for TCN: 445s int [1:2108] 10 12 24 28 31 33 34 39 46 48 ... 445s Homozygous SNPs to resample for TCN: 445s int(0) 445s Non-polymorphic loci to resample for TCN: 445s int [1:5478] 1 2 3 4 5 6 7 8 9 11 ... 445s Heterozygous SNPs with non-DH to resample for TCN: 445s int(0) 445s Loci to resample for TCN: 445s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 445s Identify loci used to bootstrap TCN means...done 445s Number of (#hets, #homs, #nonSNPs): (2108,0,5478) 445s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 445s Number of bootstrap samples: 100 445s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 445s Segment #1 (chr 1, tcnId=1, dhId=1) of 4...done 445s Segment #2 (chr 1, tcnId=2, dhId=1) of 4... 445s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 2 1 2 1 120992604 141510002 0 NA 0 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 445s 2 0 NA NA 0 NA NA NA 445s Number of TCNs: 0 445s Number of DHs: 0 445s int 0 445s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 445s int(0) 445s Identify loci used to bootstrap DH means... 445s Heterozygous SNPs to resample for DH: 445s int 0 445s Identify loci used to bootstrap DH means...done 445s Identify loci used to bootstrap TCN means... 445s SNPs: 445s int(0) 445s Non-polymorphic loci: 445s int(0) 445s Heterozygous SNPs to resample for TCN: 445s int(0) 445s Homozygous SNPs to resample for TCN: 445s int(0) 445s Non-polymorphic loci to resample for TCN: 445s int(0) 445s Heterozygous SNPs with non-DH to resample for TCN: 445s int(0) 445s Loci to resample for TCN: 445s int(0) 445s Identify loci used to bootstrap TCN means...done 445s Number of (#hets, #homs, #nonSNPs): (0,0,0) 445s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 445s Number of bootstrap samples: 100 445s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 445s Segment #2 (chr 1, tcnId=2, dhId=1) of 4...done 445s Segment #3 (chr 1, tcnId=3, dhId=1) of 4... 445s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 445s 3 777 141510003 185449813 777 0.0973 0.933798 1.135102 445s Number of TCNs: 2681 445s Number of DHs: 777 445s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 445s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 445s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 445s Identify loci used to bootstrap DH means... 445s Heterozygous SNPs to resample for DH: 445s int [1:777] 7587 7588 7594 7614 7616 7626 7627 7628 7635 7638 ... 445s Identify loci used to bootstrap DH means...done 445s Identify loci used to bootstrap TCN means... 445s SNPs: 445s int [1:777] 7587 7588 7594 7614 7616 7626 7627 7628 7635 7638 ... 445s Non-polymorphic loci: 445s int [1:1904] 7589 7590 7591 7592 7593 7595 7596 7597 7598 7599 ... 445s Heterozygous SNPs to resample for TCN: 445s int [1:777] 7587 7588 7594 7614 7616 7626 7627 7628 7635 7638 ... 445s Homozygous SNPs to resample for TCN: 445s int(0) 445s Non-polymorphic loci to resample for TCN: 445s int [1:1904] 7589 7590 7591 7592 7593 7595 7596 7597 7598 7599 ... 445s Heterozygous SNPs with non-DH to resample for TCN: 445s int(0) 445s Loci to resample for TCN: 445s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 445s Identify loci used to bootstrap TCN means...done 445s Number of (#hets, #homs, #nonSNPs): (777,0,1904) 445s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 445s Number of bootstrap samples: 100 445s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 445s Segment #3 (chr 1, tcnId=3, dhId=1) of 4...done 445s Segment #4 (chr 1, tcnId=4, dhId=1) of 4... 445s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 445s 4 1311 185449813 247137334 1311 0.2295 1.014787 1.619313 445s Number of TCNs: 4391 445s Number of DHs: 1311 445s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 445s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 445s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 445s Identify loci used to bootstrap DH means... 445s Heterozygous SNPs to resample for DH: 445s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 445s Identify loci used to bootstrap DH means...done 445s Identify loci used to bootstrap TCN means... 445s SNPs: 445s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 445s Non-polymorphic loci: 445s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 445s Heterozygous SNPs to resample for TCN: 445s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 445s Homozygous SNPs to resample for TCN: 445s int(0) 445s Non-polymorphic loci to resample for TCN: 445s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 445s Heterozygous SNPs with non-DH to resample for TCN: 445s int(0) 445s Loci to resample for TCN: 445s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 445s Identify loci used to bootstrap TCN means...done 445s Number of (#hets, #homs, #nonSNPs): (1311,0,3080) 445s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 445s Number of bootstrap samples: 100 445s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 445s Segment #4 (chr 1, tcnId=4, dhId=1) of 4...done 445s Bootstrapped segment mean levels 445s num [1:4, 1:100, 1:4] 1.39 NA 2.08 2.63 1.38 ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : NULL 445s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 445s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 445s num [1:4, 1:100, 1:4] 1.39 NA 2.08 2.63 1.38 ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : NULL 445s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 445s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 445s Calculating polar (alpha,radius,manhattan) for change points... 445s num [1:3, 1:100, 1:2] NA NA -0.0752 NA NA ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : NULL 445s ..$ : chr [1:2] "c1" "c2" 445s Bootstrapped change points 445s num [1:3, 1:100, 1:5] NA NA -1.73 NA NA ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : NULL 445s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 445s Calculating polar (alpha,radius,manhattan) for change points...done 445s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 445s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 445s num [1:4, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : chr [1:4] + [ 0 != 0 ] 445s + echo Test segmentByPairedPSCBS,calls passed 445s + echo 0 445s + echo Begin test segmentByPairedPSCBS,futures 445s + exitcode=0 445s + R CMD BATCH segmentByPairedPSCBS,futures.R 445s "2.5%" "5%" "95%" "97.5%" 445s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 445s Field #1 ('tcn') of 4... 445s Segment #1 of 4... 445s Segment #1 of 4...done 445s Segment #2 of 4... 445s Segment #2 of 4...done 445s Segment #3 of 4... 445s Segment #3 of 4...done 445s Segment #4 of 4... 445s Segment #4 of 4...done 445s Field #1 ('tcn') of 4...done 445s Field #2 ('dh') of 4... 445s Segment #1 of 4... 445s Segment #1 of 4...done 445s Segment #2 of 4... 445s Segment #2 of 4...done 445s Segment #3 of 4... 445s Segment #3 of 4...done 445s Segment #4 of 4... 445s Segment #4 of 4...done 445s Field #2 ('dh') of 4...done 445s Field #3 ('c1') of 4... 445s Segment #1 of 4... 445s Segment #1 of 4...done 445s Segment #2 of 4... 445s Segment #2 of 4...done 445s Segment #3 of 4... 445s Segment #3 of 4...done 445s Segment #4 of 4... 445s Segment #4 of 4...done 445s Field #3 ('c1') of 4...done 445s Field #4 ('c2') of 4... 445s Segment #1 of 4... 445s Segment #1 of 4...done 445s Segment #2 of 4... 445s Segment #2 of 4...done 445s Segment #3 of 4... 445s Segment #3 of 4...done 445s Segment #4 of 4... 445s Segment #4 of 4...done 445s Field #4 ('c2') of 4...done 445s Bootstrap statistics 445s num [1:4, 1:4, 1:4] 1.38 NA 2.06 2.63 1.38 ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 445s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 445s Statistical sanity checks (iff B >= 100)... 445s Available summaries: 2.5%, 5%, 95%, 97.5% 445s Available quantiles: 0.025, 0.05, 0.95, 0.975 445s num [1:4, 1:4, 1:4] 1.38 NA 2.06 2.63 1.38 ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 445s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 445s Field #1 ('tcn') of 4... 445s Seg 1. mean=1.3853, range=[1.37909,1.39287], n=7586 445s Seg 2. mean=NA, range=[NA,NA], n=0 445s Seg 3. mean=2.0689, range=[2.05903,2.079], n=2681 445s Seg 4. mean=2.6341, range=[2.62504,2.64649], n=4391 445s Field #1 ('tcn') of 4...done 445s Field #2 ('dh') of 4... 445s Seg 1. mean=0.5116, range=[0.502148,0.519941], n=2108 445s Seg 2. mean=NA, range=[NA,NA], n=NA 445s Seg 3. mean=0.0973, range=[0.0906366,0.105818], n=777 445s Seg 4. mean=0.2295, range=[0.222919,0.237005], n=1311 445s Field #2 ('dh') of 4...done 445s Field #3 ('c1') of 4... 445s Seg 1. mean=0.33829, range=[0.332209,0.345936], n=2108 445s Seg 2. mean=NA, range=[NA,NA], n=NA 445s Seg 3. mean=0.933798, range=[0.924112,0.941776], n=777 445s Seg 4. mean=1.01479, range=[1.00381,1.02461], n=1311 445s Field #3 ('c1') of 4...done 445s Field #4 ('c2') of 4... 445s Seg 1. mean=1.04701, range=[1.03882,1.05318], n=2108 445s Seg 2. mean=NA, range=[NA,NA], n=NA 445s Seg 3. mean=1.1351, range=[1.12454,1.1465], n=777 445s Seg 4. mean=1.61931, range=[1.60862,1.63328], n=1311 445s Field #4 ('c2') of 4...done 445s Statistical sanity checks (iff B >= 100)...done 445s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 445s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 445s num [1:3, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 445s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 445s Field #1 ('alpha') of 5... 445s Changepoint #1 of 3... 445s Changepoint #1 of 3...done 445s Changepoint #2 of 3... 445s Changepoint #2 of 3...done 445s Changepoint #3 of 3... 445s Changepoint #3 of 3...done 445s Field #1 ('alpha') of 5...done 445s Field #2 ('radius') of 5... 445s Changepoint #1 of 3... 445s Changepoint #1 of 3...done 445s Changepoint #2 of 3... 445s Changepoint #2 of 3...done 445s Changepoint #3 of 3... 445s Changepoint #3 of 3...done 445s Field #2 ('radius') of 5...done 445s Field #3 ('manhattan') of 5... 445s Changepoint #1 of 3... 445s Changepoint #1 of 3...done 445s Changepoint #2 of 3... 445s Changepoint #2 of 3...done 445s Changepoint #3 of 3... 445s Changepoint #3 of 3...done 445s Field #3 ('manhattan') of 5...done 445s Field #4 ('d1') of 5... 445s Changepoint #1 of 3... 445s Changepoint #1 of 3...done 445s Changepoint #2 of 3... 445s Changepoint #2 of 3...done 445s Changepoint #3 of 3... 445s Changepoint #3 of 3...done 445s Field #4 ('d1') of 5...done 445s Field #5 ('d2') of 5... 445s Changepoint #1 of 3... 445s Changepoint #1 of 3...done 445s Changepoint #2 of 3... 445s Changepoint #2 of 3...done 445s Changepoint #3 of 3... 445s Changepoint #3 of 3...done 445s Field #5 ('d2') of 5...done 445s Bootstrap statistics 445s num [1:3, 1:4, 1:5] NA NA -1.77 NA NA ... 445s - attr(*, "dimnames")=List of 3 445s ..$ : NULL 445s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 445s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 445s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 445s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 445s > print(fit) 445s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s 2 1 2 1 120992604 141510002 0 NA 0 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 445s 1 2108 2108 0.5116 0.3382903 1.047010 445s 2 0 NA NA NA NA 445s 3 777 777 0.0973 0.9337980 1.135102 445s 4 1311 1311 0.2295 1.0147870 1.619313 445s > plotTracks(fit) 445s > 445s > 445s > 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Calling segments with run of homozygosity (ROH) 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > fit <- callROH(fit, verbose=-10) 445s Calling ROH... 445s Segment #1 of 4... 445s Calling ROH for a single segment... 445s Number of SNPs: 7586 445s Calling ROH for a single segment...done 445s Segment #1 of 4...done 445s Segment #2 of 4... 445s Calling ROH for a single segment... 445s Number of SNPs: 0 445s Calling ROH for a single segment...done 445s Segment #2 of 4...done 445s Segment #3 of 4... 445s Calling ROH for a single segment... 445s Number of SNPs: 2681 445s Calling ROH for a single segment...done 445s Segment #3 of 4...done 445s Segment #4 of 4... 445s Calling ROH for a single segment... 445s Number of SNPs: 4391 445s Calling ROH for a single segment...done 445s Segment #4 of 4...done 445s ROH calls: 445s logi [1:4] FALSE NA FALSE FALSE 445s Mode FALSE NA's 445s logical 3 1 445s Calling ROH...done 445s > print(fit) 445s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s 2 1 2 1 120992604 141510002 0 NA 0 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall 445s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE 445s 2 0 NA NA NA NA NA 445s 3 777 777 0.0973 0.9337980 1.135102 FALSE 445s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE 445s > plotTracks(fit) 445s > 445s > 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Estimate background 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > kappa <- estimateKappa(fit, verbose=-10) 445s Estimate global background (including normal contamination and more)... 445s Number of segments: 3 445s Estimating threshold Delta0.5 from the empirical density of C1:s... 445s adjust: 1 445s minDensity: 0.2 445s ploidy: 2 445s All peaks: 445s type x density 445s 1 peak 0.3362194 1.101272 445s 3 peak 0.9811492 1.065711 445s C1=0 and C1=1 peaks: 445s type x density 445s 1 peak 0.3362194 1.101272 445s 3 peak 0.9811492 1.065711 445s Estimate of Delta0.5: 0.65868427808456 445s Estimating threshold Delta0.5 from the empirical density of C1:s...done 445s Number of segments with C1 < Delta0.5: 1 445s Estimate of kappa: 0.33829026 445s Estimate global background (including normal contamination and more)...done 445s Warning message: 445s In density.default(c1, weights = weights, adjust = adjust, from = from, : 445s Selecting bandwidth *not* using 'weights' 445s > print(kappa) 445s [1] 0.3382903 445s > ## [1] 0.226011 445s > 445s > 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Calling segments in allelic balance (AB) 445s > # NOTE: Ideally, this should be done on whole-genome data 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Explicitly estimate the threshold in DH for calling AB 445s > # (which be done by default by the caller, if skipped here) 445s > deltaAB <- estimateDeltaAB(fit, flavor="qq(DH)", verbose=-10) 445s Estimating DH threshold for calling allelic imbalances... 445s flavor: qq(DH) 445s scale: 1 445s Estimating DH threshold for AB caller... 445s quantile #1: 0.05 445s Symmetric quantile #2: 0.9 445s Number of segments: 3 445s Weighted 5% quantile of DH: 0.257710 445s Number of segments with small DH: 2 445s Number of data points: 7072 445s Number of finite data points: 2088 445s Estimate of (1-0.9):th and 50% quantiles: (0.0310411,0.163658) 445s Estimate of 0.9:th "symmetric" quantile: 0.296275 445s Estimating DH threshold for AB caller...done 445s Estimated delta: 0.296 445s Estimating DH threshold for calling allelic imbalances...done 445s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 445s + # Ad hoc workaround for not utilizing all of the data 445s + # in the test, which results in a poor estimate 445s + deltaAB <- 0.165 445s + } 445s > print(deltaAB) 445s [1] 0.165 445s > ## [1] 0.1657131 445s > 445s > fit <- callAB(fit, delta=deltaAB, verbose=-10) 445s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 445s delta (offset adjusting for bias in DH): 0.165 445s alpha (CI quantile; significance level): 0.05 445s Calling segments... 445s Number of segments called allelic balance (AB): 1 (25.00%) of 4 445s Calling segments...done 445s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 445s > print(fit) 445s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s 2 1 2 1 120992604 141510002 0 NA 0 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall 445s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE FALSE 445s 2 0 NA NA NA NA NA NA 445s 3 777 777 0.0973 0.9337980 1.135102 FALSE TRUE 445s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE FALSE 445s > plotTracks(fit) 445s > 445s > # Even if not explicitly specified, the estimated 445s > # threshold parameter is returned by the caller 445s > stopifnot(fit$params$deltaAB == deltaAB) 445s > 445s > 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Calling segments in loss-of-heterozygosity (LOH) 445s > # NOTE: Ideally, this should be done on whole-genome data 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Explicitly estimate the threshold in C1 for calling LOH 445s > # (which be done by default by the caller, if skipped here) 445s > deltaLOH <- estimateDeltaLOH(fit, flavor="minC1|nonAB", verbose=-10) 445s Estimating DH threshold for calling LOH... 445s flavor: minC1|nonAB 445s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1... 445s Argument 'midpoint': 0.5 445s Number of segments: 4 445s Number of segments in allelic balance: 1 (25.0%) of 4 445s Number of segments not in allelic balance: 2 (50.0%) of 4 445s Number of segments in allelic balance and TCN <= 3.00: 1 (25.0%) of 4 445s C: 2.07 445s Corrected C1 (=C/2): 1.03 445s Number of DHs: 777 445s Weights: 1 445s Weighted median of (corrected) C1 in allelic balance: 1.034 445s Smallest C1 among segments not in allelic balance: 0.338 445s There are 1 segments with in total 2108 heterozygous SNPs with this level. 445s Midpoint between the two: 0.686 445s Estimating DH threshold for calling LOH as the midpoint between guessed C1=0 and C1=1...done 445s delta: 0.686 445s Estimating DH threshold for calling LOH...done 445s > print(deltaLOH) 445s [1] 0.6863701 445s > ## [1] 0.625175 445s > 445s > fit <- callLOH(fit, delta=deltaLOH, verbose=-10) 445s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 445s delta (offset adjusting for bias in C1): 0.68637013 445s alpha (CI quantile; significance level): 0.05 445s Calling segments... 445s Number of segments called low C1 (LowC1, "LOH_C1"): 1 (25.00%) of 4 445s Calling segments...done 445s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 445s > print(fit) 445s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s 2 1 2 1 120992604 141510002 0 NA 0 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall lohCall 445s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE FALSE TRUE 445s 2 0 NA NA NA NA NA NA NA 445s 3 777 777 0.0973 0.9337980 1.135102 FALSE TRUE FALSE 445s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE FALSE FALSE 445s > plotTracks(fit) 445s > 445s > # Even if not explicitly specified, the estimated 445s > # threshold parameter is returned by the caller 445s > stopifnot(fit$params$deltaLOH == deltaLOH) 445s > 445s > 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > # Calling segments that are gained, copy neutral, and lost 445s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 445s > fit <- callGNL(fit, verbose=-10) 445s Calling gain, neutral, and loss based TCNs of AB segments... 445s Calling neutral TCNs... 445s callCopyNeutralByTCNofAB... 445s Alpha: 0.05 445s Delta CN: 0.33085487 445s Calling copy-neutral segments... 445s Retrieve TCN confidence intervals for all segments... 445s Interval: [0.025,0.975] 445s Retrieve TCN confidence intervals for all segments...done 445s Estimating TCN confidence interval of copy-neutral AB segments... 445s calcStatsForCopyNeutralABs... 445s Identifying copy neutral AB segments... 445s Number of AB segments: 1 445s Identifying segments that are copy neutral states... 445s Number of segments in allelic balance: 1 445s Identifying segments that are copy neutral states...done 445s Number of copy-neutral AB segments: 1 445s Extracting all copy neutral AB segments across all chromosomes into one big segment... 445s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall lohCall 445s 3 777 777 0.0973 0.933798 1.135102 FALSE TRUE FALSE 445s Extracting all copy neutral AB segments across all chromosomes into one big segment...done 445s Identifying copy neutral AB segments...done 445s Bootstrap the identified copy-neutral states... 445s Bootstrap the identified copy-neutral states...done 445s tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets dhNbrOfLoci dhMean c1Mean 445s 3 2681 2.0689 777 777 777 0.0973 0.933798 445s c2Mean tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% 445s 3 1.135102 2.055164 2.057694 2.078831 2.081454 0.08974138 0.09080508 0.1035891 445s dh_97.5% c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% 445s 3 0.1050478 0.923788 0.925412 0.9417056 0.9433752 1.124908 1.126631 1.143571 445s c2_97.5% 445s 3 1.145214 445s calcStatsForCopyNeutralABs...done 445s Bootstrap statistics for copy-neutral AB segments: 445s tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets dhNbrOfLoci dhMean c1Mean 445s 3 2681 2.0689 777 777 777 0.0973 0.933798 445s c2Mean tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% 445s 3 1.135102 2.055164 2.057694 2.078831 2.081454 0.08974138 0.09080508 0.1035891 445s dh_97.5% c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% 445s 3 0.1050478 0.923788 0.925412 0.9417056 0.9433752 1.124908 1.126631 1.143571 445s c2_97.5% 445s 3 1.145214 445s [1] "TCN statistics:" 445s tcnMean tcn_2.5% tcn_5% tcn_95% tcn_97.5% 445s 2.068900 2.055164 2.057694 2.078831 2.081454 445s 95%-confidence interval of TCN mean for the copy-neutral state: [2.05516,2.08145] (mean=2.0689) 445s Estimating TCN confidence interval of copy-neutral AB segments...done 445s Identify all copy-neutral segments... 445s DeltaCN: +/-0.330855 445s Call ("acceptance") region: [1.72431,2.41231] 445s Total number of segments: 4 445s Number of segments called allelic balance: 1 445s Number of segments called copy neutral: 1 445s Number of AB segments called copy neutral: 1 445s Number of non-AB segments called copy neutral: 0 445s Identify all copy-neutral segments...done 445s Calling copy-neutral segments...done 445s callCopyNeutralByTCNofAB...done 445s Calling neutral TCNs...done 445s Number of NTCN calls: 1 (25.00%) of 4 445s Mean TCN of AB segments: 2.06831 445s Calling loss... 445s Number of loss calls: 1 (25.00%) of 4 445s Calling loss...done 445s Calling gain... 445s Number of loss calls: 1 (25.00%) of 4 445s Calling gain...done 445s Calling gain, neutral, and loss based TCNs of AB segments...done 445s Warning message: 445s In density.default(c1, weights = weights, adjust = adjust, from = from, : 445s Selecting bandwidth *not* using 'weights' 445s > print(fit) 445s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 445s 1 1 1 1 554484 120992603 7586 1.3853 2108 445s 2 1 2 1 120992604 141510002 0 NA 0 445s 3 1 3 1 141510003 185449813 2681 2.0689 777 445s 4 1 4 1 185449813 247137334 4391 2.6341 1311 445s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall abCall lohCall 445s 1 2108 2108 0.5116 0.3382903 1.047010 FALSE FALSE TRUE 445s 2 0 NA NA NA NA NA NA NA 445s 3 777 777 0.0973 0.9337980 1.135102 FALSE TRUE FALSE 445s 4 1311 1311 0.2295 1.0147870 1.619313 FALSE FALSE FALSE 445s ntcnCall lossCall gainCall 445s 1 FALSE TRUE FALSE 445s 2 NA NA NA 445s 3 TRUE FALSE FALSE 445s 4 FALSE FALSE TRUE 445s > plotTracks(fit) 445s > 445s > proc.time() 445s user system elapsed 445s 3.835 0.101 3.957 445s Test segmentByPairedPSCBS,calls passed 445s 0 445s Begin test segmentByPairedPSCBS,futures 455s + cat segmentByPairedPSCBS,futures.Rout 455s 455s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 455s Copyright (C) 2024 The R Foundation for Statistical Computing 455s Platform: s390x-ibm-linux-gnu (64-bit) 455s 455s R is free software and comes with ABSOLUTELY NO WARRANTY. 455s You are welcome to redistribute it under certain conditions. 455s Type 'license()' or 'licence()' for distribution details. 455s 455s R is a collaborative project with many contributors. 455s Type 'contributors()' for more information and 455s 'citation()' on how to cite R or R packages in publications. 455s 455s Type 'demo()' for some demos, 'help()' for on-line help, or 455s 'help.start()' for an HTML browser interface to help. 455s Type 'q()' to quit R. 455s 455s [Previously saved workspace restored] 455s 455s > library(PSCBS) 455s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 455s 455s Attaching package: 'PSCBS' 455s 455s The following objects are masked from 'package:base': 455s 455s append, load 455s 455s > library(utils) 455s > 455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 455s > # Load SNP microarray data 455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 455s > data <- PSCBS::exampleData("paired.chr01") 455s > 455s > 455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 455s > # Paired PSCBS segmentation 455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 455s > # Drop single-locus outliers 455s > dataS <- dropSegmentationOutliers(data) 455s > 455s > # Run light-weight tests by default 455s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 455s + # Use only every 5th data point 455s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 455s + # Number of segments (for assertion) 455s + nSegs <- 4L 455s + } else { 455s + # Full tests 455s + nSegs <- 11L 455s + } 455s > 455s > str(dataS) 455s 'data.frame': 14670 obs. of 6 variables: 455s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 455s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 455s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 455s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 455s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 455s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 455s > 455s > 455s > ## Create multiple chromosomes 455s > data <- list() 455s > for (cc in 1:3) { 455s + dataS$chromosome <- cc 455s + data[[cc]] <- dataS 455s + } 455s > data <- Reduce(rbind, data) 455s > str(data) 455s 'data.frame': 44010 obs. of 6 variables: 455s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 455s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 455s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 455s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 455s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 455s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 455s > 455s > 455s > message("*** segmentByPairedPSCBS() via futures ...") 455s *** segmentByPairedPSCBS() via futures ... 455s > 455s > library("future") 455s > oplan <- plan() 455s > 455s > strategies <- c("sequential", "multisession") 455s > 455s > ## Test 'future.batchtools' futures? 455s > pkg <- "future.batchtools" 455s > if (require(pkg, character.only=TRUE)) { 455s + strategies <- c(strategies, "batchtools_local") 455s + } 455s Loading required package: future.batchtools 455s Warning message: 455s In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : 455s there is no package called 'future.batchtools' 455s > 455s > message("Future strategies to test: ", paste(sQuote(strategies), collapse=", ")) 455s Future strategies to test: 'sequential', 'multisession' 455s > 455s > fits <- list() 455s > for (strategy in strategies) { 455s + message(sprintf("- segmentByPairedPSCBS() using '%s' futures ...", strategy)) 455s + plan(strategy) 455s + fit <- segmentByPairedPSCBS(data, seed=0xBEEF, verbose=TRUE) 455s + fits[[strategy]] <- fit 455s + equal <- all.equal(fit, fits[[1]]) 455s + if (!equal) { 455s + str(fit) 455s + str(fits[[1]]) 455s + print(equal) 455s + stop(sprintf("segmentByPairedPSCBS() using '%s' futures does not produce the same results as when using '%s' futures", strategy, names(fits)[1])) 455s + } 455s + } 455s - segmentByPairedPSCBS() using 'sequential' futures ... 455s Segmenting paired tumor-normal signals using Paired PSCBS... 455s Calling genotypes from normal allele B fractions... 455s num [1:44010] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 455s Called genotypes: 455s num [1:44010] 1 0.5 0 0 0 0 1 0 1 0.5 ... 455s - attr(*, "modelFit")=List of 1 455s ..$ :List of 7 455s .. ..$ flavor : chr "density" 455s .. ..$ cn : int 2 455s .. ..$ nbrOfGenotypeGroups: int 3 455s .. ..$ tau : num [1:2] 0.312 0.678 455s .. ..$ n : int 43920 455s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 455s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 455s .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 455s .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 455s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 455s .. .. ..$ type : chr [1:2] "valley" "valley" 455s .. .. ..$ x : num [1:2] 0.312 0.678 455s .. .. ..$ density: num [1:2] 0.465 0.497 455s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 455s muN 455s 0 0.5 1 455s 15627 12633 15750 455s Calling genotypes from normal allele B fractions...done 455s Normalizing betaT using betaN (TumorBoost)... 455s Normalized BAFs: 455s num [1:44010] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 455s - attr(*, "modelFit")=List of 5 455s ..$ method : chr "normalizeTumorBoost" 455s ..$ flavor : chr "v4" 455s ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 455s .. ..- attr(*, "modelFit")=List of 1 455s .. .. ..$ :List of 7 455s .. .. .. ..$ flavor : chr "density" 455s .. .. .. ..$ cn : int 2 455s .. .. .. ..$ nbrOfGenotypeGroups: int 3 455s .. .. .. ..$ tau : num [1:2] 0.312 0.678 455s .. .. .. ..$ n : int 43920 455s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 455s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 455s .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 455s .. .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 455s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 455s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 455s .. .. .. .. ..$ x : num [1:2] 0.312 0.678 455s .. .. .. .. ..$ density: num [1:2] 0.465 0.497 455s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 455s ..$ preserveScale: logi FALSE 455s ..$ scaleFactor : num NA 455s Normalizing betaT using betaN (TumorBoost)...done 455s Setup up data... 455s 'data.frame': 44010 obs. of 7 variables: 455s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 455s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 455s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 455s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 455s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 455s ..- attr(*, "modelFit")=List of 5 455s .. ..$ method : chr "normalizeTumorBoost" 455s .. ..$ flavor : chr "v4" 455s .. ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 455s .. .. ..- attr(*, "modelFit")=List of 1 455s .. .. .. ..$ :List of 7 455s .. .. .. .. ..$ flavor : chr "density" 455s .. .. .. .. ..$ cn : int 2 455s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 455s .. .. .. .. ..$ tau : num [1:2] 0.312 0.678 455s .. .. .. .. ..$ n : int 43920 455s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 455s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 455s .. .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 455s .. .. .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 455s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 455s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 455s .. .. .. .. .. ..$ x : num [1:2] 0.312 0.678 455s .. .. .. .. .. ..$ density: num [1:2] 0.465 0.497 455s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 455s .. ..$ preserveScale: logi FALSE 455s .. ..$ scaleFactor : num NA 456s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 456s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 456s ..- attr(*, "modelFit")=List of 1 456s .. ..$ :List of 7 456s .. .. ..$ flavor : chr "density" 456s .. .. ..$ cn : int 2 456s .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. ..$ tau : num [1:2] 0.312 0.678 456s .. .. ..$ n : int 43920 456s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 456s .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 456s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. ..$ x : num [1:2] 0.312 0.678 456s .. .. .. ..$ density: num [1:2] 0.465 0.497 456s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s Setup up data...done 456s Dropping loci for which TCNs are missing... 456s Number of loci dropped: 36 456s Dropping loci for which TCNs are missing...done 456s Ordering data along genome... 456s 'data.frame': 43974 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Segmenting multiple chromosomes... 456s Number of chromosomes: 3 456s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 456s Produced 3 seeds from this stream for future usage 456s Chromosome #1 ('Chr01') of 3... 456s 'data.frame': 14658 obs. of 8 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s Known segments: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Segmenting paired tumor-normal signals using Paired PSCBS... 456s Setup up data... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Setup up data...done 456s Ordering data along genome... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Keeping only current chromosome for 'knownSegments'... 456s Chromosome: 1 456s Known segments for this chromosome: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Keeping only current chromosome for 'knownSegments'...done 456s alphaTCN: 0.009 456s alphaDH: 0.001 456s Number of loci: 14658 456s Calculating DHs... 456s Number of SNPs: 14658 456s Number of heterozygous SNPs: 4209 (28.71%) 456s Normalized DHs: 456s num [1:14658] NA NA NA NA NA ... 456s Calculating DHs...done 456s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 456s Produced 2 seeds from this stream for future usage 456s Identification of change points by total copy numbers... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 14658 obs. of 4 variables: 456s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 3 obs. of 6 variables: 456s ..$ sampleName: chr [1:3] NA NA NA 456s ..$ chromosome: int [1:3] 1 1 1 456s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 456s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 456s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 456s ..$ mean : num [1:3] 1.39 2.07 2.63 456s $ segRows:'data.frame': 3 obs. of 2 variables: 456s ..$ startRow: int [1:3] 1 7600 10268 456s ..$ endRow : int [1:3] 7599 10267 14658 456s $ params :List of 5 456s ..$ alpha : num 0.009 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num -Inf 456s .. ..$ end : num Inf 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.575 0.001 0.579 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s Identification of change points by total copy numbers...done 456s Restructure TCN segmentation results... 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 456s 1 1 554484 143926517 7599 1.3859 456s 2 1 143926517 185449813 2668 2.0704 456s 3 1 185449813 247137334 4391 2.6341 456s Number of TCN segments: 3 456s Restructure TCN segmentation results...done 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 456s Number of TCN loci in segment: 7599 456s Locus data for TCN segment: 456s 'data.frame': 7599 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s $ rho : num NA NA NA NA NA ... 456s Number of loci: 7599 456s Number of SNPs: 2120 (27.90%) 456s Number of heterozygous SNPs: 2120 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 7599 obs. of 4 variables: 456s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:7599] NA NA NA NA NA ... 456s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 554484 456s ..$ end : num 1.44e+08 456s ..$ nbrOfLoci : int 2120 456s ..$ mean : num 0.51 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 10 456s ..$ endRow : int 7594 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 554484 456s .. ..$ end : num 1.44e+08 456s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.037 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 10 7594 456s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10 7594 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 554484 143926517 2120 0.5101 456s startRow endRow 456s 1 10 7594 456s Rows: 456s [1] 1 456s TCN segmentation rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s startRow endRow 456s 1 10 7594 456s NULL 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s startRow endRow 456s 1 1 7599 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 1 1 554484 143926517 7599 1.3859 2120 2120 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 456s Number of TCN loci in segment: 2668 456s Locus data for TCN segment: 456s 'data.frame': 2668 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 456s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 456s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 456s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 456s Number of loci: 2668 456s Number of SNPs: 775 (29.05%) 456s Number of heterozygous SNPs: 775 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 2668 obs. of 4 variables: 456s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 456s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 1.44e+08 456s ..$ end : num 1.85e+08 456s ..$ nbrOfLoci : int 775 456s ..$ mean : num 0.097 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 15 456s ..$ endRow : int 2664 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 1.44e+08 456s .. ..$ end : num 1.85e+08 456s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.008 0.001 0.011 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 15 2664 456s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 7614 10263 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 143926517 185449813 775 0.097 456s startRow endRow 456s 1 7614 10263 456s Rows: 456s [1] 2 456s TCN segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s startRow endRow 456s 1 7614 10263 456s startRow endRow 456s 1 1 7599 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 2 1 143926517 185449813 2668 2.0704 775 775 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 2 2 1 1 143926517 185449813 2668 2.0704 775 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 2 775 143926517 185449813 775 0.097 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 456s Number of TCN loci in segment: 4391 456s Locus data for TCN segment: 456s 'data.frame': 4391 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 456s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 456s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 456s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s $ rho : num NA 0.2186 NA 0.0503 NA ... 456s Number of loci: 4391 456s Number of SNPs: 1314 (29.92%) 456s Number of heterozygous SNPs: 1314 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 4391 obs. of 4 variables: 456s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 456s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 1.85e+08 456s ..$ end : num 2.47e+08 456s ..$ nbrOfLoci : int 1314 456s ..$ mean : num 0.23 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 2 456s ..$ endRow : int 4388 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 1.85e+08 456s .. ..$ end : num 2.47e+08 456s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.02 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 2 4388 456s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10269 14655 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 185449813 247137334 1314 0.2295 456s startRow endRow 456s 1 10269 14655 456s Rows: 456s [1] 3 456s TCN segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s startRow endRow 456s 1 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s 3 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 3 1 185449813 247137334 4391 2.6341 1314 1314 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 3 3 1 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 3 1314 185449813 247137334 1314 0.2295 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s 2 775 143926517 185449813 775 0.0970 456s 3 1314 185449813 247137334 1314 0.2295 456s Calculating (C1,C2) per segment... 456s Calculating (C1,C2) per segment...done 456s Number of segments: 3 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s Post-segmenting TCNs... 456s Number of segments: 3 456s Number of chromosomes: 1 456s [1] 1 456s Chromosome 1 ('chr01') of 1... 456s Rows: 456s [1] 1 2 3 456s Number of segments: 3 456s TCN segment #1 ('1') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #1 ('1') of 3...done 456s TCN segment #2 ('2') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #2 ('2') of 3...done 456s TCN segment #3 ('3') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #3 ('3') of 3...done 456s Chromosome 1 ('chr01') of 1...done 456s Update (C1,C2) per segment... 456s Update (C1,C2) per segment...done 456s Post-segmenting TCNs...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s Chromosome #1 ('Chr01') of 3...done 456s Chromosome #2 ('Chr02') of 3... 456s 'data.frame': 14658 obs. of 8 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 14659 14660 14661 14662 14663 14664 14665 14666 14667 14668 ... 456s Known segments: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Segmenting paired tumor-normal signals using Paired PSCBS... 456s Setup up data... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Setup up data...done 456s Ordering data along genome... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Keeping only current chromosome for 'knownSegments'... 456s Chromosome: 2 456s Known segments for this chromosome: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Keeping only current chromosome for 'knownSegments'...done 456s alphaTCN: 0.009 456s alphaDH: 0.001 456s Number of loci: 14658 456s Calculating DHs... 456s Number of SNPs: 14658 456s Number of heterozygous SNPs: 4209 (28.71%) 456s Normalized DHs: 456s num [1:14658] NA NA NA NA NA ... 456s Calculating DHs...done 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Produced 2 seeds from this stream for future usage 456s Identification of change points by total copy numbers... 456s Segmenting by CBS... 456s Chromosome: 2 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 14658 obs. of 4 variables: 456s ..$ chromosome: int [1:14658] 2 2 2 2 2 2 2 2 2 2 ... 456s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 3 obs. of 6 variables: 456s ..$ sampleName: chr [1:3] NA NA NA 456s ..$ chromosome: int [1:3] 2 2 2 456s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 456s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 456s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 456s ..$ mean : num [1:3] 1.39 2.07 2.63 456s $ segRows:'data.frame': 3 obs. of 2 variables: 456s ..$ startRow: int [1:3] 1 7600 10268 456s ..$ endRow : int [1:3] 7599 10267 14658 456s $ params :List of 5 456s ..$ alpha : num 0.009 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 2 456s .. ..$ start : num -Inf 456s .. ..$ end : num Inf 456s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.607 0.001 0.608 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s Identification of change points by total copy numbers...done 456s Restructure TCN segmentation results... 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 456s 1 2 554484 143926517 7599 1.3859 456s 2 2 143926517 185449813 2668 2.0704 456s 3 2 185449813 247137334 4391 2.6341 456s Number of TCN segments: 3 456s Restructure TCN segmentation results...done 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 456s Number of TCN loci in segment: 7599 456s Locus data for TCN segment: 456s 'data.frame': 7599 obs. of 9 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s $ rho : num NA NA NA NA NA ... 456s Number of loci: 7599 456s Number of SNPs: 2120 (27.90%) 456s Number of heterozygous SNPs: 2120 (100.00%) 456s Chromosome: 2 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 2 456s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 7599 obs. of 4 variables: 456s ..$ chromosome: int [1:7599] 2 2 2 2 2 2 2 2 2 2 ... 456s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:7599] NA NA NA NA NA ... 456s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 2 456s ..$ start : num 554484 456s ..$ end : num 1.44e+08 456s ..$ nbrOfLoci : int 2120 456s ..$ mean : num 0.51 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 10 456s ..$ endRow : int 7594 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 2 456s .. ..$ start : num 554484 456s .. ..$ end : num 1.44e+08 456s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.04 0 0.037 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 10 7594 456s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10 7594 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 554484 143926517 2120 0.5101 456s startRow endRow 456s 1 10 7594 456s Rows: 456s [1] 1 456s TCN segmentation rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s startRow endRow 456s 1 10 7594 456s NULL 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s startRow endRow 456s 1 1 7599 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 1 2 554484 143926517 7599 1.3859 2120 2120 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 2 554484 143926517 7599 1.3859 2120 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 456s Number of TCN loci in segment: 2668 456s Locus data for TCN segment: 456s 'data.frame': 2668 obs. of 9 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 456s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 456s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 456s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 456s Number of loci: 2668 456s Number of SNPs: 775 (29.05%) 456s Number of heterozygous SNPs: 775 (100.00%) 456s Chromosome: 2 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 2 456s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 2668 obs. of 4 variables: 456s ..$ chromosome: int [1:2668] 2 2 2 2 2 2 2 2 2 2 ... 456s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 456s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 2 456s ..$ start : num 1.44e+08 456s ..$ end : num 1.85e+08 456s ..$ nbrOfLoci : int 775 456s ..$ mean : num 0.097 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 15 456s ..$ endRow : int 2664 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 2 456s .. ..$ start : num 1.44e+08 456s .. ..$ end : num 1.85e+08 456s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0.001 0.01 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 15 2664 456s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 7614 10263 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 143926517 185449813 775 0.097 456s startRow endRow 456s 1 7614 10263 456s Rows: 456s [1] 2 456s TCN segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s startRow endRow 456s 1 7614 10263 456s startRow endRow 456s 1 1 7599 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 2 2 143926517 185449813 2668 2.0704 775 775 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 2 2 1 2 143926517 185449813 2668 2.0704 775 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 2 775 143926517 185449813 775 0.097 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 456s Number of TCN loci in segment: 4391 456s Locus data for TCN segment: 456s 'data.frame': 4391 obs. of 9 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 456s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 456s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 456s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s $ rho : num NA 0.2186 NA 0.0503 NA ... 456s Number of loci: 4391 456s Number of SNPs: 1314 (29.92%) 456s Number of heterozygous SNPs: 1314 (100.00%) 456s Chromosome: 2 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 2 456s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 4391 obs. of 4 variables: 456s ..$ chromosome: int [1:4391] 2 2 2 2 2 2 2 2 2 2 ... 456s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 456s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 2 456s ..$ start : num 1.85e+08 456s ..$ end : num 2.47e+08 456s ..$ nbrOfLoci : int 1314 456s ..$ mean : num 0.23 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 2 456s ..$ endRow : int 4388 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 2 456s .. ..$ start : num 1.85e+08 456s .. ..$ end : num 2.47e+08 456s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.019 0 0.025 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 2 4388 456s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10269 14655 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 185449813 247137334 1314 0.2295 456s startRow endRow 456s 1 10269 14655 456s Rows: 456s [1] 3 456s TCN segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s startRow endRow 456s 1 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s 3 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 3 2 185449813 247137334 4391 2.6341 1314 1314 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 3 3 1 2 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 3 1314 185449813 247137334 1314 0.2295 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s 2 775 143926517 185449813 775 0.0970 456s 3 1314 185449813 247137334 1314 0.2295 456s Calculating (C1,C2) per segment... 456s Calculating (C1,C2) per segment...done 456s Number of segments: 3 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s Post-segmenting TCNs... 456s Number of segments: 3 456s Number of chromosomes: 1 456s [1] 2 456s Chromosome 1 ('chr02') of 1... 456s Rows: 456s [1] 1 2 3 456s Number of segments: 3 456s TCN segment #1 ('1') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #1 ('1') of 3...done 456s TCN segment #2 ('2') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #2 ('2') of 3...done 456s TCN segment #3 ('3') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #3 ('3') of 3...done 456s Chromosome 1 ('chr02') of 1...done 456s Update (C1,C2) per segment... 456s Update (C1,C2) per segment...done 456s Post-segmenting TCNs...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s Chromosome #2 ('Chr02') of 3...done 456s Chromosome #3 ('Chr03') of 3... 456s 'data.frame': 14658 obs. of 8 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 29317 29318 29319 29320 29321 29322 29323 29324 29325 29326 ... 456s Known segments: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Segmenting paired tumor-normal signals using Paired PSCBS... 456s Setup up data... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Setup up data...done 456s Ordering data along genome... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Keeping only current chromosome for 'knownSegments'... 456s Chromosome: 3 456s Known segments for this chromosome: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Keeping only current chromosome for 'knownSegments'...done 456s alphaTCN: 0.009 456s alphaDH: 0.001 456s Number of loci: 14658 456s Calculating DHs... 456s Number of SNPs: 14658 456s Number of heterozygous SNPs: 4209 (28.71%) 456s Normalized DHs: 456s num [1:14658] NA NA NA NA NA ... 456s Calculating DHs...done 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Produced 2 seeds from this stream for future usage 456s Identification of change points by total copy numbers... 456s Segmenting by CBS... 456s Chromosome: 3 456s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 14658 obs. of 4 variables: 456s ..$ chromosome: int [1:14658] 3 3 3 3 3 3 3 3 3 3 ... 456s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 3 obs. of 6 variables: 456s ..$ sampleName: chr [1:3] NA NA NA 456s ..$ chromosome: int [1:3] 3 3 3 456s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 456s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 456s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 456s ..$ mean : num [1:3] 1.39 2.07 2.63 456s $ segRows:'data.frame': 3 obs. of 2 variables: 456s ..$ startRow: int [1:3] 1 7600 10268 456s ..$ endRow : int [1:3] 7599 10267 14658 456s $ params :List of 5 456s ..$ alpha : num 0.009 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 3 456s .. ..$ start : num -Inf 456s .. ..$ end : num Inf 456s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.585 0.002 0.601 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s Identification of change points by total copy numbers...done 456s Restructure TCN segmentation results... 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 456s 1 3 554484 143926517 7599 1.3859 456s 2 3 143926517 185449813 2668 2.0704 456s 3 3 185449813 247137334 4391 2.6341 456s Number of TCN segments: 3 456s Restructure TCN segmentation results...done 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 456s Number of TCN loci in segment: 7599 456s Locus data for TCN segment: 456s 'data.frame': 7599 obs. of 9 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s $ rho : num NA NA NA NA NA ... 456s Number of loci: 7599 456s Number of SNPs: 2120 (27.90%) 456s Number of heterozygous SNPs: 2120 (100.00%) 456s Chromosome: 3 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 3 456s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 7599 obs. of 4 variables: 456s ..$ chromosome: int [1:7599] 3 3 3 3 3 3 3 3 3 3 ... 456s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:7599] NA NA NA NA NA ... 456s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 3 456s ..$ start : num 554484 456s ..$ end : num 1.44e+08 456s ..$ nbrOfLoci : int 2120 456s ..$ mean : num 0.51 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 10 456s ..$ endRow : int 7594 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 3 456s .. ..$ start : num 554484 456s .. ..$ end : num 1.44e+08 456s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.039 0.001 0.036 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 10 7594 456s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10 7594 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 554484 143926517 2120 0.5101 456s startRow endRow 456s 1 10 7594 456s Rows: 456s [1] 1 456s TCN segmentation rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s startRow endRow 456s 1 10 7594 456s NULL 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s startRow endRow 456s 1 1 7599 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 1 3 554484 143926517 7599 1.3859 2120 2120 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 3 554484 143926517 7599 1.3859 2120 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 456s Number of TCN loci in segment: 2668 456s Locus data for TCN segment: 456s 'data.frame': 2668 obs. of 9 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 456s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 456s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 456s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 456s Number of loci: 2668 456s Number of SNPs: 775 (29.05%) 456s Number of heterozygous SNPs: 775 (100.00%) 456s Chromosome: 3 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 3 456s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 2668 obs. of 4 variables: 456s ..$ chromosome: int [1:2668] 3 3 3 3 3 3 3 3 3 3 ... 456s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 456s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 3 456s ..$ start : num 1.44e+08 456s ..$ end : num 1.85e+08 456s ..$ nbrOfLoci : int 775 456s ..$ mean : num 0.097 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 15 456s ..$ endRow : int 2664 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 3 456s .. ..$ start : num 1.44e+08 456s .. ..$ end : num 1.85e+08 456s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.011 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 15 2664 456s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 7614 10263 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 143926517 185449813 775 0.097 456s startRow endRow 456s 1 7614 10263 456s Rows: 456s [1] 2 456s TCN segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s startRow endRow 456s 1 7614 10263 456s startRow endRow 456s 1 1 7599 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 2 3 143926517 185449813 2668 2.0704 775 775 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 2 2 1 3 143926517 185449813 2668 2.0704 775 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 2 775 143926517 185449813 775 0.097 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 456s Number of TCN loci in segment: 4391 456s Locus data for TCN segment: 456s 'data.frame': 4391 obs. of 9 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 456s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 456s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 456s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s $ rho : num NA 0.2186 NA 0.0503 NA ... 456s Number of loci: 4391 456s Number of SNPs: 1314 (29.92%) 456s Number of heterozygous SNPs: 1314 (100.00%) 456s Chromosome: 3 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 3 456s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 4391 obs. of 4 variables: 456s ..$ chromosome: int [1:4391] 3 3 3 3 3 3 3 3 3 3 ... 456s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 456s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 3 456s ..$ start : num 1.85e+08 456s ..$ end : num 2.47e+08 456s ..$ nbrOfLoci : int 1314 456s ..$ mean : num 0.23 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 2 456s ..$ endRow : int 4388 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 3 456s .. ..$ start : num 1.85e+08 456s .. ..$ end : num 2.47e+08 456s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0.001 0.022 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 2 4388 456s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10269 14655 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 185449813 247137334 1314 0.2295 456s startRow endRow 456s 1 10269 14655 456s Rows: 456s [1] 3 456s TCN segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s startRow endRow 456s 1 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s 3 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 3 3 185449813 247137334 4391 2.6341 1314 1314 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 3 3 1 3 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 3 1314 185449813 247137334 1314 0.2295 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s 2 775 143926517 185449813 775 0.0970 456s 3 1314 185449813 247137334 1314 0.2295 456s Calculating (C1,C2) per segment... 456s Calculating (C1,C2) per segment...done 456s Number of segments: 3 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s Post-segmenting TCNs... 456s Number of segments: 3 456s Number of chromosomes: 1 456s [1] 3 456s Chromosome 1 ('chr03') of 1... 456s Rows: 456s [1] 1 2 3 456s Number of segments: 3 456s TCN segment #1 ('1') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #1 ('1') of 3...done 456s TCN segment #2 ('2') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #2 ('2') of 3...done 456s TCN segment #3 ('3') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #3 ('3') of 3...done 456s Chromosome 1 ('chr03') of 1...done 456s Update (C1,C2) per segment... 456s Update (C1,C2) per segment...done 456s Post-segmenting TCNs...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s Chromosome #3 ('Chr03') of 3...done 456s Merging (independently) segmented chromosome... 456s List of 5 456s $ data :Classes 'PairedPSCNData' and 'data.frame': 43974 obs. of 8 variables: 456s ..$ chromosome: int [1:43974] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:43974] 554484 730720 782343 878522 916294 ... 456s ..$ CT : num [1:43974] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ betaT : num [1:43974] 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s ..$ betaTN : num [1:43974] -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s ..$ betaN : num [1:43974] 0.116 0.284 0.909 0.082 0.86 ... 456s ..$ muN : num [1:43974] 0 0 1 0 1 1 1 0 1 0.5 ... 456s ..$ rho : num [1:43974] NA NA NA NA NA ... 456s $ output :Classes 'PairedPSCNSegments' and 'data.frame': 11 obs. of 15 variables: 456s ..$ chromosome : int [1:11] 1 1 1 NA 2 2 2 NA 3 3 ... 456s ..$ tcnId : int [1:11] 1 2 3 NA 1 2 3 NA 1 2 ... 456s ..$ dhId : int [1:11] 1 1 1 NA 1 1 1 NA 1 1 ... 456s ..$ tcnStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 456s ..$ tcnEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 456s ..$ tcnNbrOfLoci: int [1:11] 7599 2668 4391 NA 7599 2668 4391 NA 7599 2668 ... 456s ..$ tcnMean : num [1:11] 1.39 2.07 2.63 NA 1.39 ... 456s ..$ tcnNbrOfSNPs: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 456s ..$ tcnNbrOfHets: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 456s ..$ dhStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 456s ..$ dhEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 456s ..$ dhNbrOfLoci : int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 456s ..$ dhMean : num [1:11] 0.51 0.097 0.23 NA 0.51 ... 456s ..$ c1Mean : num [1:11] 0.339 0.935 1.015 NA 0.339 ... 456s ..$ c2Mean : num [1:11] 1.05 1.14 1.62 NA 1.05 ... 456s $ tcnSegRows:'data.frame': 11 obs. of 2 variables: 456s ..$ startRow: int [1:11] 1 7600 10268 NA 14659 22258 24926 NA 29317 36916 ... 456s ..$ endRow : int [1:11] 7599 10267 14658 NA 22257 24925 29316 NA 36915 39583 ... 456s $ dhSegRows :'data.frame': 11 obs. of 2 variables: 456s ..$ startRow: int [1:11] 10 7614 10269 NA 14668 22272 24927 NA 29326 36930 ... 456s ..$ endRow : int [1:11] 7594 10263 14655 NA 22252 24921 29313 NA 36910 39579 ... 456s $ params :List of 7 456s ..$ alphaTCN : num 0.009 456s ..$ alphaDH : num 0.001 456s ..$ flavor : chr "tcn&dh" 456s ..$ tbn : logi FALSE 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 456s .. ..$ chromosome: int(0) 456s .. ..$ start : int(0) 456s .. ..$ end : int(0) 456s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 456s - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" 456s Merging (independently) segmented chromosome...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s 4 NA NA NA NA NA NA NA NA 456s 5 2 1 1 554484 143926517 7599 1.3859 2120 456s 6 2 2 1 143926517 185449813 2668 2.0704 775 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s 4 NA NA NA NA NA NA NA 456s 5 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 6 2 2 1 143926517 185449813 2668 2.0704 775 456s 7 2 3 1 185449813 247137334 4391 2.6341 1314 456s 8 NA NA NA NA NA NA NA NA 456s 9 3 1 1 554484 143926517 7599 1.3859 2120 456s 10 3 2 1 143926517 185449813 2668 2.0704 775 456s 11 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 7 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s 8 NA NA NA NA NA NA NA 456s 9 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 10 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 11 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s Segmenting multiple chromosomes...done 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s - segmentByPairedPSCBS() using 'multisession' futures ... 456s Segmenting paired tumor-normal signals using Paired PSCBS... 456s Calling genotypes from normal allele B fractions... 456s num [1:44010] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 456s Called genotypes: 456s num [1:44010] 1 0.5 0 0 0 0 1 0 1 0.5 ... 456s - attr(*, "modelFit")=List of 1 456s ..$ :List of 7 456s .. ..$ flavor : chr "density" 456s .. ..$ cn : int 2 456s .. ..$ nbrOfGenotypeGroups: int 3 456s .. ..$ tau : num [1:2] 0.312 0.678 456s .. ..$ n : int 43920 456s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 456s .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 456s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. ..$ x : num [1:2] 0.312 0.678 456s .. .. ..$ density: num [1:2] 0.465 0.497 456s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s muN 456s 0 0.5 1 456s 15627 12633 15750 456s Calling genotypes from normal allele B fractions...done 456s Normalizing betaT using betaN (TumorBoost)... 456s Normalized BAFs: 456s num [1:44010] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 456s - attr(*, "modelFit")=List of 5 456s ..$ method : chr "normalizeTumorBoost" 456s ..$ flavor : chr "v4" 456s ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 456s .. ..- attr(*, "modelFit")=List of 1 456s .. .. ..$ :List of 7 456s .. .. .. ..$ flavor : chr "density" 456s .. .. .. ..$ cn : int 2 456s .. .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. .. ..$ tau : num [1:2] 0.312 0.678 456s .. .. .. ..$ n : int 43920 456s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 456s .. .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 456s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. .. ..$ x : num [1:2] 0.312 0.678 456s .. .. .. .. ..$ density: num [1:2] 0.465 0.497 456s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s ..$ preserveScale: logi FALSE 456s ..$ scaleFactor : num NA 456s Normalizing betaT using betaN (TumorBoost)...done 456s Setup up data... 456s 'data.frame': 44010 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 456s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 456s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 456s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 456s ..- attr(*, "modelFit")=List of 5 456s .. ..$ method : chr "normalizeTumorBoost" 456s .. ..$ flavor : chr "v4" 456s .. ..$ delta : num [1:44010] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 456s .. .. ..- attr(*, "modelFit")=List of 1 456s .. .. .. ..$ :List of 7 456s .. .. .. .. ..$ flavor : chr "density" 456s .. .. .. .. ..$ cn : int 2 456s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. .. .. ..$ tau : num [1:2] 0.312 0.678 456s .. .. .. .. ..$ n : int 43920 456s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 456s .. .. .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 456s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. .. .. ..$ x : num [1:2] 0.312 0.678 456s .. .. .. .. .. ..$ density: num [1:2] 0.465 0.497 456s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s .. ..$ preserveScale: logi FALSE 456s .. ..$ scaleFactor : num NA 456s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 456s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 456s ..- attr(*, "modelFit")=List of 1 456s .. ..$ :List of 7 456s .. .. ..$ flavor : chr "density" 456s .. .. ..$ cn : int 2 456s .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. ..$ tau : num [1:2] 0.312 0.678 456s .. .. ..$ n : int 43920 456s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. ..$ x : num [1:5] 0.0999 0.312 0.4986 0.6775 0.8922 456s .. .. .. ..$ density: num [1:5] 1.623 0.465 1.126 0.497 1.588 456s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. ..$ x : num [1:2] 0.312 0.678 456s .. .. .. ..$ density: num [1:2] 0.465 0.497 456s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s Setup up data...done 456s Dropping loci for which TCNs are missing... 456s Number of loci dropped: 36 456s Dropping loci for which TCNs are missing...done 456s Ordering data along genome... 456s 'data.frame': 43974 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Segmenting multiple chromosomes... 456s Number of chromosomes: 3 456s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 456s Produced 3 seeds from this stream for future usage 456s Chromosome #1 ('Chr01') of 3... 456s 'data.frame': 14658 obs. of 8 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s Known segments: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Segmenting paired tumor-normal signals using Paired PSCBS... 456s Setup up data... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Setup up data...done 456s Ordering data along genome... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Keeping only current chromosome for 'knownSegments'... 456s Chromosome: 1 456s Known segments for this chromosome: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Keeping only current chromosome for 'knownSegments'...done 456s alphaTCN: 0.009 456s alphaDH: 0.001 456s Number of loci: 14658 456s Calculating DHs... 456s Number of SNPs: 14658 456s Number of heterozygous SNPs: 4209 (28.71%) 456s Normalized DHs: 456s num [1:14658] NA NA NA NA NA ... 456s Calculating DHs...done 456s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 456s Produced 2 seeds from this stream for future usage 456s Identification of change points by total copy numbers... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 14658 obs. of 4 variables: 456s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 3 obs. of 6 variables: 456s ..$ sampleName: chr [1:3] NA NA NA 456s ..$ chromosome: int [1:3] 1 1 1 456s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 456s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 456s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 456s ..$ mean : num [1:3] 1.39 2.07 2.63 456s $ segRows:'data.frame': 3 obs. of 2 variables: 456s ..$ startRow: int [1:3] 1 7600 10268 456s ..$ endRow : int [1:3] 7599 10267 14658 456s $ params :List of 5 456s ..$ alpha : num 0.009 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num -Inf 456s .. ..$ end : num Inf 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.576 0.001 0.577 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s Identification of change points by total copy numbers...done 456s Restructure TCN segmentation results... 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 456s 1 1 554484 143926517 7599 1.3859 456s 2 1 143926517 185449813 2668 2.0704 456s 3 1 185449813 247137334 4391 2.6341 456s Number of TCN segments: 3 456s Restructure TCN segmentation results...done 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 456s Number of TCN loci in segment: 7599 456s Locus data for TCN segment: 456s 'data.frame': 7599 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s $ rho : num NA NA NA NA NA ... 456s Number of loci: 7599 456s Number of SNPs: 2120 (27.90%) 456s Number of heterozygous SNPs: 2120 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 7599 obs. of 4 variables: 456s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:7599] NA NA NA NA NA ... 456s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 554484 456s ..$ end : num 1.44e+08 456s ..$ nbrOfLoci : int 2120 456s ..$ mean : num 0.51 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 10 456s ..$ endRow : int 7594 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 554484 456s .. ..$ end : num 1.44e+08 456s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.04 0 0.036 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 10 7594 456s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10 7594 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 554484 143926517 2120 0.5101 456s startRow endRow 456s 1 10 7594 456s Rows: 456s [1] 1 456s TCN segmentation rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s startRow endRow 456s 1 10 7594 456s NULL 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s startRow endRow 456s 1 1 7599 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 1 1 554484 143926517 7599 1.3859 2120 2120 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 456s Number of TCN loci in segment: 2668 456s Locus data for TCN segment: 456s 'data.frame': 2668 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 456s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 456s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 456s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 456s Number of loci: 2668 456s Number of SNPs: 775 (29.05%) 456s Number of heterozygous SNPs: 775 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 2668 obs. of 4 variables: 456s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 456s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 1.44e+08 456s ..$ end : num 1.85e+08 456s ..$ nbrOfLoci : int 775 456s ..$ mean : num 0.097 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 15 456s ..$ endRow : int 2664 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 1.44e+08 456s .. ..$ end : num 1.85e+08 456s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.009 0 0.011 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 15 2664 456s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 7614 10263 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 143926517 185449813 775 0.097 456s startRow endRow 456s 1 7614 10263 456s Rows: 456s [1] 2 456s TCN segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s startRow endRow 456s 1 7614 10263 456s startRow endRow 456s 1 1 7599 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 2 1 143926517 185449813 2668 2.0704 775 775 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 2 2 1 1 143926517 185449813 2668 2.0704 775 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 2 775 143926517 185449813 775 0.097 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 456s Number of TCN loci in segment: 4391 456s Locus data for TCN segment: 456s 'data.frame': 4391 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 456s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 456s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 456s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s $ rho : num NA 0.2186 NA 0.0503 NA ... 456s Number of loci: 4391 456s Number of SNPs: 1314 (29.92%) 456s Number of heterozygous SNPs: 1314 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 4391 obs. of 4 variables: 456s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 456s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 1.85e+08 456s ..$ end : num 2.47e+08 456s ..$ nbrOfLoci : int 1314 456s ..$ mean : num 0.23 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 2 456s ..$ endRow : int 4388 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 1.85e+08 456s .. ..$ end : num 2.47e+08 456s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.019 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 2 4388 456s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10269 14655 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 185449813 247137334 1314 0.2295 456s startRow endRow 456s 1 10269 14655 456s Rows: 456s [1] 3 456s TCN segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s startRow endRow 456s 1 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s 3 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 3 1 185449813 247137334 4391 2.6341 1314 1314 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 3 3 1 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 3 1314 185449813 247137334 1314 0.2295 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s 2 775 143926517 185449813 775 0.0970 456s 3 1314 185449813 247137334 1314 0.2295 456s Calculating (C1,C2) per segment... 456s Calculating (C1,C2) per segment...done 456s Number of segments: 3 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s Post-segmenting TCNs... 456s Number of segments: 3 456s Number of chromosomes: 1 456s [1] 1 456s Chromosome 1 ('chr01') of 1... 456s Rows: 456s [1] 1 2 3 456s Number of segments: 3 456s TCN segment #1 ('1') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #1 ('1') of 3...done 456s TCN segment #2 ('2') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #2 ('2') of 3...done 456s TCN segment #3 ('3') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #3 ('3') of 3...done 456s Chromosome 1 ('chr01') of 1...done 456s Update (C1,C2) per segment... 456s Update (C1,C2) per segment...done 456s Post-segmenting TCNs...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s Chromosome #1 ('Chr01') of 3...done 456s Chromosome #2 ('Chr02') of 3... 456s 'data.frame': 14658 obs. of 8 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 14659 14660 14661 14662 14663 14664 14665 14666 14667 14668 ... 456s Known segments: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Segmenting paired tumor-normal signals using Paired PSCBS... 456s Setup up data... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Setup up data...done 456s Ordering data along genome... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Keeping only current chromosome for 'knownSegments'... 456s Chromosome: 2 456s Known segments for this chromosome: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Keeping only current chromosome for 'knownSegments'...done 456s alphaTCN: 0.009 456s alphaDH: 0.001 456s Number of loci: 14658 456s Calculating DHs... 456s Number of SNPs: 14658 456s Number of heterozygous SNPs: 4209 (28.71%) 456s Normalized DHs: 456s num [1:14658] NA NA NA NA NA ... 456s Calculating DHs...done 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Produced 2 seeds from this stream for future usage 456s Identification of change points by total copy numbers... 456s Segmenting by CBS... 456s Chromosome: 2 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 14658 obs. of 4 variables: 456s ..$ chromosome: int [1:14658] 2 2 2 2 2 2 2 2 2 2 ... 456s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 3 obs. of 6 variables: 456s ..$ sampleName: chr [1:3] NA NA NA 456s ..$ chromosome: int [1:3] 2 2 2 456s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 456s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 456s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 456s ..$ mean : num [1:3] 1.39 2.07 2.63 456s $ segRows:'data.frame': 3 obs. of 2 variables: 456s ..$ startRow: int [1:3] 1 7600 10268 456s ..$ endRow : int [1:3] 7599 10267 14658 456s $ params :List of 5 456s ..$ alpha : num 0.009 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 2 456s .. ..$ start : num -Inf 456s .. ..$ end : num Inf 456s ..$ seed : int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.605 0 0.61 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -821273412 -52578226 1415511586 721384351 -665928286 1316562960 456s Identification of change points by total copy numbers...done 456s Restructure TCN segmentation results... 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 456s 1 2 554484 143926517 7599 1.3859 456s 2 2 143926517 185449813 2668 2.0704 456s 3 2 185449813 247137334 4391 2.6341 456s Number of TCN segments: 3 456s Restructure TCN segmentation results...done 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 456s Number of TCN loci in segment: 7599 456s Locus data for TCN segment: 456s 'data.frame': 7599 obs. of 9 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s $ rho : num NA NA NA NA NA ... 456s Number of loci: 7599 456s Number of SNPs: 2120 (27.90%) 456s Number of heterozygous SNPs: 2120 (100.00%) 456s Chromosome: 2 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 2 456s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 7599 obs. of 4 variables: 456s ..$ chromosome: int [1:7599] 2 2 2 2 2 2 2 2 2 2 ... 456s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:7599] NA NA NA NA NA ... 456s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 2 456s ..$ start : num 554484 456s ..$ end : num 1.44e+08 456s ..$ nbrOfLoci : int 2120 456s ..$ mean : num 0.51 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 10 456s ..$ endRow : int 7594 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 2 456s .. ..$ start : num 554484 456s .. ..$ end : num 1.44e+08 456s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.036 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 10 7594 456s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10 7594 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 554484 143926517 2120 0.5101 456s startRow endRow 456s 1 10 7594 456s Rows: 456s [1] 1 456s TCN segmentation rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s startRow endRow 456s 1 10 7594 456s NULL 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s startRow endRow 456s 1 1 7599 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 1 2 554484 143926517 7599 1.3859 2120 2120 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 2 554484 143926517 7599 1.3859 2120 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 456s Number of TCN loci in segment: 2668 456s Locus data for TCN segment: 456s 'data.frame': 2668 obs. of 9 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 456s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 456s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 456s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 456s Number of loci: 2668 456s Number of SNPs: 775 (29.05%) 456s Number of heterozygous SNPs: 775 (100.00%) 456s Chromosome: 2 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 2 456s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 2668 obs. of 4 variables: 456s ..$ chromosome: int [1:2668] 2 2 2 2 2 2 2 2 2 2 ... 456s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 456s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 2 456s ..$ start : num 1.44e+08 456s ..$ end : num 1.85e+08 456s ..$ nbrOfLoci : int 775 456s ..$ mean : num 0.097 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 15 456s ..$ endRow : int 2664 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 2 456s .. ..$ start : num 1.44e+08 456s .. ..$ end : num 1.85e+08 456s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.009 0 0.011 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 15 2664 456s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 7614 10263 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 143926517 185449813 775 0.097 456s startRow endRow 456s 1 7614 10263 456s Rows: 456s [1] 2 456s TCN segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s startRow endRow 456s 1 7614 10263 456s startRow endRow 456s 1 1 7599 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 2 2 143926517 185449813 2668 2.0704 775 775 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 2 2 1 2 143926517 185449813 2668 2.0704 775 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 2 775 143926517 185449813 775 0.097 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 456s Number of TCN loci in segment: 4391 456s Locus data for TCN segment: 456s 'data.frame': 4391 obs. of 9 variables: 456s $ chromosome: int 2 2 2 2 2 2 2 2 2 2 ... 456s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 456s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 456s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 456s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s $ rho : num NA 0.2186 NA 0.0503 NA ... 456s Number of loci: 4391 456s Number of SNPs: 1314 (29.92%) 456s Number of heterozygous SNPs: 1314 (100.00%) 456s Chromosome: 2 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 2 456s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 4391 obs. of 4 variables: 456s ..$ chromosome: int [1:4391] 2 2 2 2 2 2 2 2 2 2 ... 456s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 456s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 2 456s ..$ start : num 1.85e+08 456s ..$ end : num 2.47e+08 456s ..$ nbrOfLoci : int 1314 456s ..$ mean : num 0.23 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 2 456s ..$ endRow : int 4388 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 2 456s .. ..$ start : num 1.85e+08 456s .. ..$ end : num 2.47e+08 456s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0.001 0.021 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 2 4388 456s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10269 14655 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 185449813 247137334 1314 0.2295 456s startRow endRow 456s 1 10269 14655 456s Rows: 456s [1] 3 456s TCN segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s startRow endRow 456s 1 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s 3 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 3 2 185449813 247137334 4391 2.6341 1314 1314 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 3 3 1 2 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 3 1314 185449813 247137334 1314 0.2295 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s 2 775 143926517 185449813 775 0.0970 456s 3 1314 185449813 247137334 1314 0.2295 456s Calculating (C1,C2) per segment... 456s Calculating (C1,C2) per segment...done 456s Number of segments: 3 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s Post-segmenting TCNs... 456s Number of segments: 3 456s Number of chromosomes: 1 456s [1] 2 456s Chromosome 1 ('chr02') of 1... 456s Rows: 456s [1] 1 2 3 456s Number of segments: 3 456s TCN segment #1 ('1') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #1 ('1') of 3...done 456s TCN segment #2 ('2') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #2 ('2') of 3...done 456s TCN segment #3 ('3') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #3 ('3') of 3...done 456s Chromosome 1 ('chr02') of 1...done 456s Update (C1,C2) per segment... 456s Update (C1,C2) per segment...done 456s Post-segmenting TCNs...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 2 1 1 554484 143926517 7599 1.3859 2120 456s 2 2 2 1 143926517 185449813 2668 2.0704 775 456s 3 2 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s Chromosome #2 ('Chr02') of 3...done 456s Chromosome #3 ('Chr03') of 3... 456s 'data.frame': 14658 obs. of 8 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 29317 29318 29319 29320 29321 29322 29323 29324 29325 29326 ... 456s Known segments: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Segmenting paired tumor-normal signals using Paired PSCBS... 456s Setup up data... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Setup up data...done 456s Ordering data along genome... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Keeping only current chromosome for 'knownSegments'... 456s Chromosome: 3 456s Known segments for this chromosome: 456s [1] chromosome start end 456s <0 rows> (or 0-length row.names) 456s Keeping only current chromosome for 'knownSegments'...done 456s alphaTCN: 0.009 456s alphaDH: 0.001 456s Number of loci: 14658 456s Calculating DHs... 456s Number of SNPs: 14658 456s Number of heterozygous SNPs: 4209 (28.71%) 456s Normalized DHs: 456s num [1:14658] NA NA NA NA NA ... 456s Calculating DHs...done 456s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 456s Produced 2 seeds from this stream for future usage 456s Identification of change points by total copy numbers... 456s Segmenting by CBS... 456s Chromosome: 3 456s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 14658 obs. of 4 variables: 456s ..$ chromosome: int [1:14658] 3 3 3 3 3 3 3 3 3 3 ... 456s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 3 obs. of 6 variables: 456s ..$ sampleName: chr [1:3] NA NA NA 456s ..$ chromosome: int [1:3] 3 3 3 456s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 456s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 456s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 456s ..$ mean : num [1:3] 1.39 2.07 2.63 456s $ segRows:'data.frame': 3 obs. of 2 variables: 456s ..$ startRow: int [1:3] 1 7600 10268 456s ..$ endRow : int [1:3] 7599 10267 14658 456s $ params :List of 5 456s ..$ alpha : num 0.009 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 3 456s .. ..$ start : num -Inf 456s .. ..$ end : num Inf 456s ..$ seed : int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.573 0.001 0.581 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1924040949 -1632234809 -437763632 -1464377300 676654412 2080370711 456s Identification of change points by total copy numbers...done 456s Restructure TCN segmentation results... 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 456s 1 3 554484 143926517 7599 1.3859 456s 2 3 143926517 185449813 2668 2.0704 456s 3 3 185449813 247137334 4391 2.6341 456s Number of TCN segments: 3 456s Restructure TCN segmentation results...done 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 456s Number of TCN loci in segment: 7599 456s Locus data for TCN segment: 456s 'data.frame': 7599 obs. of 9 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s $ rho : num NA NA NA NA NA ... 456s Number of loci: 7599 456s Number of SNPs: 2120 (27.90%) 456s Number of heterozygous SNPs: 2120 (100.00%) 456s Chromosome: 3 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 3 456s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 7599 obs. of 4 variables: 456s ..$ chromosome: int [1:7599] 3 3 3 3 3 3 3 3 3 3 ... 456s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:7599] NA NA NA NA NA ... 456s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 3 456s ..$ start : num 554484 456s ..$ end : num 1.44e+08 456s ..$ nbrOfLoci : int 2120 456s ..$ mean : num 0.51 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 10 456s ..$ endRow : int 7594 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 3 456s .. ..$ start : num 554484 456s .. ..$ end : num 1.44e+08 456s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.04 0.001 0.038 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 10 7594 456s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10 7594 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 554484 143926517 2120 0.5101 456s startRow endRow 456s 1 10 7594 456s Rows: 456s [1] 1 456s TCN segmentation rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s startRow endRow 456s 1 10 7594 456s NULL 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s startRow endRow 456s 1 1 7599 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 1 3 554484 143926517 7599 1.3859 2120 2120 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 3 554484 143926517 7599 1.3859 2120 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 456s Number of TCN loci in segment: 2668 456s Locus data for TCN segment: 456s 'data.frame': 2668 obs. of 9 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 456s $ betaT : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaTN : num 0.027542 1.030222 1.094093 0.046763 -0.000948 ... 456s $ betaN : num 0.1624 0.8788 0.8225 0.1201 0.0317 ... 456s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 456s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 456s Number of loci: 2668 456s Number of SNPs: 775 (29.05%) 456s Number of heterozygous SNPs: 775 (100.00%) 456s Chromosome: 3 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 3 456s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 2668 obs. of 4 variables: 456s ..$ chromosome: int [1:2668] 3 3 3 3 3 3 3 3 3 3 ... 456s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 456s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 456s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 3 456s ..$ start : num 1.44e+08 456s ..$ end : num 1.85e+08 456s ..$ nbrOfLoci : int 775 456s ..$ mean : num 0.097 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 15 456s ..$ endRow : int 2664 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 3 456s .. ..$ start : num 1.44e+08 456s .. ..$ end : num 1.85e+08 456s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.009 0 0.012 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 15 2664 456s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 7614 10263 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 143926517 185449813 775 0.097 456s startRow endRow 456s 1 7614 10263 456s Rows: 456s [1] 2 456s TCN segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 2 7600 10267 456s startRow endRow 456s 1 7614 10263 456s startRow endRow 456s 1 1 7599 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 2 3 143926517 185449813 2668 2.0704 775 775 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 2 2 1 3 143926517 185449813 2668 2.0704 775 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 2 775 143926517 185449813 775 0.097 456s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 456s Number of TCN loci in segment: 4391 456s Locus data for TCN segment: 456s 'data.frame': 4391 obs. of 9 variables: 456s $ chromosome: int 3 3 3 3 3 3 3 3 3 3 ... 456s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 456s $ betaT : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 456s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 456s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s $ rho : num NA 0.2186 NA 0.0503 NA ... 456s Number of loci: 4391 456s Number of SNPs: 1314 (29.92%) 456s Number of heterozygous SNPs: 1314 (100.00%) 456s Chromosome: 3 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 3 456s Random seed temporarily set (seed=c(10407, -1371615447, -889757879, 1692656974, -1723952224, 1378814990, 1816467252), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 4391 obs. of 4 variables: 456s ..$ chromosome: int [1:4391] 3 3 3 3 3 3 3 3 3 3 ... 456s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 456s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 3 456s ..$ start : num 1.85e+08 456s ..$ end : num 2.47e+08 456s ..$ nbrOfLoci : int 1314 456s ..$ mean : num 0.23 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 2 456s ..$ endRow : int 4388 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 3 456s .. ..$ start : num 1.85e+08 456s .. ..$ end : num 2.47e+08 456s ..$ seed : int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.022 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 -1371615447 -889757879 1692656974 -1723952224 1378814990 1816467252 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 2 4388 456s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10269 14655 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 185449813 247137334 1314 0.2295 456s startRow endRow 456s 1 10269 14655 456s Rows: 456s [1] 3 456s TCN segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 3 10268 14658 456s startRow endRow 456s 1 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s startRow endRow 456s 1 10 7594 456s 2 7614 10263 456s 3 10269 14655 456s startRow endRow 456s 1 1 7599 456s 2 7600 10267 456s 3 10268 14658 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 3 3 185449813 247137334 4391 2.6341 1314 1314 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 3 3 1 3 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 3 1314 185449813 247137334 1314 0.2295 456s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2120 554484 143926517 2120 0.5101 456s 2 775 143926517 185449813 775 0.0970 456s 3 1314 185449813 247137334 1314 0.2295 456s Calculating (C1,C2) per segment... 456s Calculating (C1,C2) per segment...done 456s Number of segments: 3 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s Post-segmenting TCNs... 456s Number of segments: 3 456s Number of chromosomes: 1 456s [1] 3 456s Chromosome 1 ('chr03') of 1... 456s Rows: 456s [1] 1 2 3 456s Number of segments: 3 456s TCN segment #1 ('1') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #1 ('1') of 3...done 456s TCN segment #2 ('2') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #2 ('2') of 3...done 456s TCN segment #3 ('3') of 3... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #3 ('3') of 3...done 456s Chromosome 1 ('chr03') of 1...done 456s Update (C1,C2) per segment... 456s Update (C1,C2) per segment...done 456s Post-segmenting TCNs...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 3 1 1 554484 143926517 7599 1.3859 2120 456s 2 3 2 1 143926517 185449813 2668 2.0704 775 456s 3 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s Chromosome #3 ('Chr03') of 3...done 456s Merging (independently) segmented chromosome... 456s List of 5 456s $ data :Classes 'PairedPSCNData' and 'data.frame': 43974 obs. of 8 variables: 456s ..$ chromosome: int [1:43974] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:43974] 554484 730720 782343 878522 916294 ... 456s ..$ CT : num [1:43974] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ betaT : num [1:43974] 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s ..$ betaTN : num [1:43974] -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s ..$ betaN : num [1:43974] 0.116 0.284 0.909 0.082 0.86 ... 456s ..$ muN : num [1:43974] 0 0 1 0 1 1 1 0 1 0.5 ... 456s ..$ rho : num [1:43974] NA NA NA NA NA ... 456s $ output :Classes 'PairedPSCNSegments' and 'data.frame': 11 obs. of 15 variables: 456s ..$ chromosome : int [1:11] 1 1 1 NA 2 2 2 NA 3 3 ... 456s ..$ tcnId : int [1:11] 1 2 3 NA 1 2 3 NA 1 2 ... 456s ..$ dhId : int [1:11] 1 1 1 NA 1 1 1 NA 1 1 ... 456s ..$ tcnStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 456s ..$ tcnEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 456s ..$ tcnNbrOfLoci: int [1:11] 7599 2668 4391 NA 7599 2668 4391 NA 7599 2668 ... 456s ..$ tcnMean : num [1:11] 1.39 2.07 2.63 NA 1.39 ... 456s ..$ tcnNbrOfSNPs: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 456s ..$ tcnNbrOfHets: int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 456s ..$ dhStart : num [1:11] 5.54e+05 1.44e+08 1.85e+08 NA 5.54e+05 ... 456s ..$ dhEnd : num [1:11] 1.44e+08 1.85e+08 2.47e+08 NA 1.44e+08 ... 456s ..$ dhNbrOfLoci : int [1:11] 2120 775 1314 NA 2120 775 1314 NA 2120 775 ... 456s ..$ dhMean : num [1:11] 0.51 0.097 0.23 NA 0.51 ... 456s ..$ c1Mean : num [1:11] 0.339 0.935 1.015 NA 0.339 ... 456s ..$ c2Mean : num [1:11] 1.05 1.14 1.62 NA 1.05 ... 456s $ tcnSegRows:'data.frame': 11 obs. of 2 variables: 456s ..$ startRow: int [1:11] 1 7600 10268 NA 14659 22258 24926 NA 29317 36916 ... 456s ..$ endRow : int [1:11] 7599 10267 14658 NA 22257 24925 29316 NA 36915 39583 ... 456s $ dhSegRows :'data.frame': 11 obs. of 2 variables: 456s ..$ startRow: int [1:11] 10 7614 10269 NA 14668 22272 24927 NA 29326 36930 ... 456s ..$ endRow : int [1:11] 7594 10263 14655 NA 22252 24921 29313 NA 36910 39579 ... 456s $ params :List of 7 456s ..$ alphaTCN : num 0.009 456s ..$ alphaDH : num 0.001 456s ..$ flavor : chr "tcn&dh" 456s ..$ tbn : logi FALSE 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 456s .. ..$ chromosome: int(0) 456s .. ..$ start : int(0) 456s .. ..$ end : int(0) 456s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 456s - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" 456s Merging (independently) segmented chromosome...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 143926517 7599 1.3859 2120 456s 2 1 2 1 143926517 185449813 2668 2.0704 775 456s 3 1 3 1 185449813 247137334 4391 2.6341 1314 456s 4 NA NA NA NA NA NA NA NA 456s 5 2 1 1 554484 143926517 7599 1.3859 2120 456s 6 2 2 1 143926517 185449813 2668 2.0704 775 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 2 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 3 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s 4 NA NA NA NA NA NA NA 456s 5 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 6 2 2 1 143926517 185449813 2668 2.0704 775 456s 7 2 3 1 185449813 247137334 4391 2.6341 1314 456s 8 NA NA NA NA NA NA NA NA 456s 9 3 1 1 554484 143926517 7599 1.3859 2120 456s 10 3 2 1 143926517 185449813 2668 2.0704 775 456s 11 3 3 1 185449813 247137334 4391 2.6341 1314 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 6 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 7 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s 8 NA NA NA NA NA NA NA 456s 9 2120 554484 143926517 2120 0.5101 0.3394762 1.046424 456s 10 775 143926517 185449813 775 0.0970 0.9347856 1.135614 456s 11 1314 185449813 247137334 1314 0.2295 1.0147870 1.619313 456s Segmenting multiple chromosomes...done 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s > 456s > message("*** segmentByPairedPSCBS() via futures ... DONE") 456s *** segmentByPairedPSCBS() via futures ... DONE 456s > 456s > 456s > message("*** segmentByPairedPSCBS() via futures with known segments ...") 456s *** segmentByPairedPSCBS() via futures with known segments ... 456s > fits <- list() 456s > dataT <- subset(data, chromosome == 1) 456s > gaps <- findLargeGaps(dataT, minLength=2e6) 456s > knownSegments <- gapsToSegments(gaps) 456s > 456s > for (strategy in strategies) { 456s + message(sprintf("- segmentByPairedPSCBS() w/ known segments using '%s' futures ...", strategy)) 456s + plan(strategy) 456s + fit <- segmentByPairedPSCBS(dataT, knownSegments=knownSegments, seed=0xBEEF, verbose=TRUE) 456s + fits[[strategy]] <- fit 456s + equal <- all.equal(fit, fits[[1]]) 456s + if (!equal) { 456s + str(fit) 456s + str(fits[[1]]) 456s + print(equal) 456s + stop(sprintf("segmentByPairedPSCBS() w/ known segments using '%s' futures does not produce the same results as when using '%s' futures", strategy, names(fits)[1])) 456s + } 456s + } 456s - segmentByPairedPSCBS() w/ known segments using 'sequential' futures ... 456s Segmenting paired tumor-normal signals using Paired PSCBS... 456s Calling genotypes from normal allele B fractions... 456s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 456s Called genotypes: 456s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 456s - attr(*, "modelFit")=List of 1 456s ..$ :List of 7 456s .. ..$ flavor : chr "density" 456s .. ..$ cn : int 2 456s .. ..$ nbrOfGenotypeGroups: int 3 456s .. ..$ tau : num [1:2] 0.315 0.677 456s .. ..$ n : int 14640 456s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 456s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 456s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. ..$ x : num [1:2] 0.315 0.677 456s .. .. ..$ density: num [1:2] 0.522 0.552 456s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s muN 456s 0 0.5 1 456s 5221 4198 5251 456s Calling genotypes from normal allele B fractions...done 456s Normalizing betaT using betaN (TumorBoost)... 456s Normalized BAFs: 456s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 456s - attr(*, "modelFit")=List of 5 456s ..$ method : chr "normalizeTumorBoost" 456s ..$ flavor : chr "v4" 456s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 456s .. ..- attr(*, "modelFit")=List of 1 456s .. .. ..$ :List of 7 456s .. .. .. ..$ flavor : chr "density" 456s .. .. .. ..$ cn : int 2 456s .. .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. .. ..$ tau : num [1:2] 0.315 0.677 456s .. .. .. ..$ n : int 14640 456s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 456s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 456s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 456s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 456s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s ..$ preserveScale: logi FALSE 456s ..$ scaleFactor : num NA 456s Normalizing betaT using betaN (TumorBoost)...done 456s Setup up data... 456s 'data.frame': 14670 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 456s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 456s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 456s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 456s ..- attr(*, "modelFit")=List of 5 456s .. ..$ method : chr "normalizeTumorBoost" 456s .. ..$ flavor : chr "v4" 456s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 456s .. .. ..- attr(*, "modelFit")=List of 1 456s .. .. .. ..$ :List of 7 456s .. .. .. .. ..$ flavor : chr "density" 456s .. .. .. .. ..$ cn : int 2 456s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 456s .. .. .. .. ..$ n : int 14640 456s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 456s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 456s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 456s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 456s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s .. ..$ preserveScale: logi FALSE 456s .. ..$ scaleFactor : num NA 456s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 456s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 456s ..- attr(*, "modelFit")=List of 1 456s .. ..$ :List of 7 456s .. .. ..$ flavor : chr "density" 456s .. .. ..$ cn : int 2 456s .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. ..$ tau : num [1:2] 0.315 0.677 456s .. .. ..$ n : int 14640 456s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 456s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 456s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. ..$ x : num [1:2] 0.315 0.677 456s .. .. .. ..$ density: num [1:2] 0.522 0.552 456s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s Setup up data...done 456s Dropping loci for which TCNs are missing... 456s Number of loci dropped: 12 456s Dropping loci for which TCNs are missing...done 456s Ordering data along genome... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Keeping only current chromosome for 'knownSegments'... 456s Chromosome: 1 456s Known segments for this chromosome: 456s chromosome start end length 456s 1 1 -Inf 120908858 Inf 456s 2 1 120908859 142693887 21785028 456s 3 1 142693888 Inf Inf 456s Keeping only current chromosome for 'knownSegments'...done 456s alphaTCN: 0.009 456s alphaDH: 0.001 456s Number of loci: 14658 456s Calculating DHs... 456s Number of SNPs: 14658 456s Number of heterozygous SNPs: 4196 (28.63%) 456s Normalized DHs: 456s num [1:14658] NA NA NA NA NA ... 456s Calculating DHs...done 456s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 456s Produced 2 seeds from this stream for future usage 456s Identification of change points by total copy numbers... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 456s Produced 3 seeds from this stream for future usage 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 14658 obs. of 4 variables: 456s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 4 obs. of 6 variables: 456s ..$ sampleName: chr [1:4] NA NA NA NA 456s ..$ chromosome: int [1:4] 1 1 1 1 456s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.43e+08 1.85e+08 456s ..$ end : num [1:4] 1.21e+08 1.43e+08 1.85e+08 2.47e+08 456s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 456s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 456s $ segRows:'data.frame': 4 obs. of 2 variables: 456s ..$ startRow: int [1:4] 1 NA 7587 10268 456s ..$ endRow : int [1:4] 7586 NA 10267 14658 456s $ params :List of 5 456s ..$ alpha : num 0.009 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 456s .. ..$ chromosome: int [1:4] 1 1 2 1 456s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.43e+08 456s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 456s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.189 0 0.192 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s Identification of change points by total copy numbers...done 456s Restructure TCN segmentation results... 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 456s 1 1 554484 120908858 7586 1.3853 456s 2 1 120908859 142693887 0 NA 456s 3 1 142693888 185449813 2681 2.0689 456s 4 1 185449813 247137334 4391 2.6341 456s Number of TCN segments: 4 456s Restructure TCN segmentation results...done 456s Total CN segment #1 ([ 554484,1.20909e+08]) of 4... 456s Number of TCN loci in segment: 7586 456s Locus data for TCN segment: 456s 'data.frame': 7586 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s $ rho : num NA NA NA NA NA ... 456s Number of loci: 7586 456s Number of SNPs: 2108 (27.79%) 456s Number of heterozygous SNPs: 2108 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 7586 obs. of 4 variables: 456s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:7586] NA NA NA NA NA ... 456s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 554484 456s ..$ end : num 1.21e+08 456s ..$ nbrOfLoci : int 2108 456s ..$ mean : num 0.512 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 10 456s ..$ endRow : int 7574 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 554484 456s .. ..$ end : num 1.21e+08 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.05 0 0.053 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 10 7574 456s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10 7574 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 554484 120908858 2108 0.5116 456s startRow endRow 456s 1 10 7574 456s Rows: 456s [1] 1 456s TCN segmentation rows: 456s startRow endRow 456s 1 1 7586 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s startRow endRow 456s 1 10 7574 456s NULL 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7586 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s startRow endRow 456s 1 10 7574 456s startRow endRow 456s 1 1 7586 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 1 1 554484 120908858 7586 1.3853 2108 2108 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 120908858 7586 1.3853 2108 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2108 554484 120908858 2108 0.5116 456s Total CN segment #1 ([ 554484,1.20909e+08]) of 4...done 456s Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4... 456s Number of TCN loci in segment: 0 456s Locus data for TCN segment: 456s 'data.frame': 0 obs. of 9 variables: 456s $ chromosome: int 456s $ x : num 456s $ CT : num 456s $ betaT : num 456s $ betaTN : num 456s $ betaN : num 456s $ muN : num 456s $ index : int 456s $ rho : num 456s Number of loci: 0 456s Number of SNPs: 0 (NaN%) 456s Number of heterozygous SNPs: 0 (NaN%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: NA 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 0 obs. of 4 variables: 456s ..$ chromosome: int(0) 456s ..$ x : num(0) 456s ..$ y : num(0) 456s ..$ index : int(0) 456s $ output :'data.frame': 0 obs. of 6 variables: 456s ..$ sampleName: chr(0) 456s ..$ chromosome: num(0) 456s ..$ start : num(0) 456s ..$ end : num(0) 456s ..$ nbrOfLoci : int(0) 456s ..$ mean : num(0) 456s $ segRows:'data.frame': 0 obs. of 2 variables: 456s ..$ startRow: int(0) 456s ..$ endRow : int(0) 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s + [ 0 != 0 ] 456s + echo Test segmentByPairedPSCBS,futures passed 456s + echo 0 456s + echo Begin test segmentByPairedPSCBS,noNormalBAFs 456s + exitcode=0 456s + R CMD BATCH segmentByPairedPSCBS,noNormalBAFs.R 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 456s .. ..$ chromosome: int(0) 456s .. ..$ start : num(0) 456s .. ..$ end : num(0) 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.002 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s DH segmentation (locally-indexed) rows: 456s [1] startRow endRow 456s <0 rows> (or 0-length row.names) 456s int(0) 456s DH segmentation rows: 456s [1] startRow endRow 456s <0 rows> (or 0-length row.names) 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s NA NA NA NA NA 456s startRow endRow 456s NA NA NA 456s Rows: 456s [1] 2 456s TCN segmentation rows: 456s startRow endRow 456s 2 NA NA 456s TCN and DH segmentation rows: 456s startRow endRow 456s 2 NA NA 456s startRow endRow 456s NA NA NA 456s startRow endRow 456s 1 1 7586 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s startRow endRow 456s 1 10 7574 456s 2 NA NA 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 2 1 120908859 142693887 0 NA 0 0 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 2 2 1 1 120908859 142693887 0 NA 0 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 2 0 NA NA NA NA 456s Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4...done 456s Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4... 456s Number of TCN loci in segment: 2681 456s Locus data for TCN segment: 456s 'data.frame': 2681 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 456s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 456s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 456s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 456s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 456s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 456s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 456s $ rho : num 0.117 0.258 NA NA NA ... 456s Number of loci: 2681 456s Number of SNPs: 777 (28.98%) 456s Number of heterozygous SNPs: 777 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 2681 obs. of 4 variables: 456s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 456s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 456s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 1.43e+08 456s ..$ end : num 1.85e+08 456s ..$ nbrOfLoci : int 777 456s ..$ mean : num 0.0973 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 1 456s ..$ endRow : int 2677 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 1.43e+08 456s .. ..$ end : num 1.85e+08 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.011 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 1 2677 456s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 7587 10263 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 142693888 185449813 777 0.0973 456s startRow endRow 456s 1 7587 10263 456s Rows: 456s [1] 3 456s TCN segmentation rows: 456s startRow endRow 456s 3 7587 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 3 7587 10267 456s startRow endRow 456s 1 7587 10263 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s startRow endRow 456s 1 10 7574 456s 2 NA NA 456s 3 7587 10263 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 3 1 142693888 185449813 2681 2.0689 777 777 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 3 3 1 1 142693888 185449813 2681 2.0689 777 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 3 777 142693888 185449813 777 0.0973 456s Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4...done 456s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 456s Number of TCN loci in segment: 4391 456s Locus data for TCN segment: 456s 'data.frame': 4391 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 456s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 456s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 456s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 456s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s $ rho : num NA 0.2186 NA 0.0503 NA ... 456s Number of loci: 4391 456s Number of SNPs: 1311 (29.86%) 456s Number of heterozygous SNPs: 1311 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 4391 obs. of 4 variables: 456s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 456s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 1.85e+08 456s ..$ end : num 2.47e+08 456s ..$ nbrOfLoci : int 1311 456s ..$ mean : num 0.23 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 2 456s ..$ endRow : int 4388 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 1.85e+08 456s .. ..$ end : num 2.47e+08 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.021 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 2 4388 456s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10269 14655 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 185449813 247137334 1311 0.2295 456s startRow endRow 456s 1 10269 14655 456s Rows: 456s [1] 4 456s TCN segmentation rows: 456s startRow endRow 456s 4 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 4 10268 14658 456s startRow endRow 456s 1 10269 14655 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s startRow endRow 456s 1 10 7574 456s 2 NA NA 456s 3 7587 10263 456s 4 10269 14655 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 4 1 185449813 247137334 4391 2.6341 1311 1311 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 4 4 1 1 185449813 247137334 4391 2.6341 1311 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 4 1311 185449813 247137334 1311 0.2295 456s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 120908858 7586 1.3853 2108 456s 2 1 2 1 120908859 142693887 0 NA 0 456s 3 1 3 1 142693888 185449813 2681 2.0689 777 456s 4 1 4 1 185449813 247137334 4391 2.6341 1311 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2108 554484 120908858 2108 0.5116 456s 2 0 NA NA NA NA 456s 3 777 142693888 185449813 777 0.0973 456s 4 1311 185449813 247137334 1311 0.2295 456s Calculating (C1,C2) per segment... 456s Calculating (C1,C2) per segment...done 456s Number of segments: 4 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s Post-segmenting TCNs... 456s Number of segments: 4 456s Number of chromosomes: 1 456s [1] 1 456s Chromosome 1 ('chr01') of 1... 456s Rows: 456s [1] 1 2 3 4 456s Number of segments: 4 456s TCN segment #1 ('1') of 4... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #1 ('1') of 4...done 456s TCN segment #2 ('2') of 4... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #2 ('2') of 4...done 456s TCN segment #3 ('3') of 4... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #3 ('3') of 4...done 456s TCN segment #4 ('4') of 4... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #4 ('4') of 4...done 456s Chromosome 1 ('chr01') of 1...done 456s Update (C1,C2) per segment... 456s Update (C1,C2) per segment...done 456s Post-segmenting TCNs...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 120908858 7586 1.3853 2108 456s 2 1 2 1 120908859 142693887 0 NA 0 456s 3 1 3 1 142693888 185449813 2681 2.0689 777 456s 4 1 4 1 185449813 247137334 4391 2.6341 1311 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 456s 2 0 NA NA NA NA NA NA 456s 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 456s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 120908858 7586 1.3853 2108 456s 2 1 2 1 120908859 142693887 0 NA 0 456s 3 1 3 1 142693888 185449813 2681 2.0689 777 456s 4 1 4 1 185449813 247137334 4391 2.6341 1311 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 456s 2 0 NA NA NA NA NA NA 456s 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 456s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 456s - segmentByPairedPSCBS() w/ known segments using 'multisession' futures ... 456s Segmenting paired tumor-normal signals using Paired PSCBS... 456s Calling genotypes from normal allele B fractions... 456s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 456s Called genotypes: 456s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 456s - attr(*, "modelFit")=List of 1 456s ..$ :List of 7 456s .. ..$ flavor : chr "density" 456s .. ..$ cn : int 2 456s .. ..$ nbrOfGenotypeGroups: int 3 456s .. ..$ tau : num [1:2] 0.315 0.677 456s .. ..$ n : int 14640 456s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 456s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 456s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. ..$ x : num [1:2] 0.315 0.677 456s .. .. ..$ density: num [1:2] 0.522 0.552 456s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s muN 456s 0 0.5 1 456s 5221 4198 5251 456s Calling genotypes from normal allele B fractions...done 456s Normalizing betaT using betaN (TumorBoost)... 456s Normalized BAFs: 456s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 456s - attr(*, "modelFit")=List of 5 456s ..$ method : chr "normalizeTumorBoost" 456s ..$ flavor : chr "v4" 456s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 456s .. ..- attr(*, "modelFit")=List of 1 456s .. .. ..$ :List of 7 456s .. .. .. ..$ flavor : chr "density" 456s .. .. .. ..$ cn : int 2 456s .. .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. .. ..$ tau : num [1:2] 0.315 0.677 456s .. .. .. ..$ n : int 14640 456s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 456s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 456s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 456s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 456s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s ..$ preserveScale: logi FALSE 456s ..$ scaleFactor : num NA 456s Normalizing betaT using betaN (TumorBoost)...done 456s Setup up data... 456s 'data.frame': 14670 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 456s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 456s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 456s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 456s ..- attr(*, "modelFit")=List of 5 456s .. ..$ method : chr "normalizeTumorBoost" 456s .. ..$ flavor : chr "v4" 456s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 456s .. .. ..- attr(*, "modelFit")=List of 1 456s .. .. .. ..$ :List of 7 456s .. .. .. .. ..$ flavor : chr "density" 456s .. .. .. .. ..$ cn : int 2 456s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 456s .. .. .. .. ..$ n : int 14640 456s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 456s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 456s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 456s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 456s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s .. ..$ preserveScale: logi FALSE 456s .. ..$ scaleFactor : num NA 456s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 456s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 456s ..- attr(*, "modelFit")=List of 1 456s .. ..$ :List of 7 456s .. .. ..$ flavor : chr "density" 456s .. .. ..$ cn : int 2 456s .. .. ..$ nbrOfGenotypeGroups: int 3 456s .. .. ..$ tau : num [1:2] 0.315 0.677 456s .. .. ..$ n : int 14640 456s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 456s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 456s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 456s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 456s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 456s .. .. .. ..$ type : chr [1:2] "valley" "valley" 456s .. .. .. ..$ x : num [1:2] 0.315 0.677 456s .. .. .. ..$ density: num [1:2] 0.522 0.552 456s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 456s Setup up data...done 456s Dropping loci for which TCNs are missing... 456s Number of loci dropped: 12 456s Dropping loci for which TCNs are missing...done 456s Ordering data along genome... 456s 'data.frame': 14658 obs. of 7 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s Ordering data along genome...done 456s Keeping only current chromosome for 'knownSegments'... 456s Chromosome: 1 456s Known segments for this chromosome: 456s chromosome start end length 456s 1 1 -Inf 120908858 Inf 456s 2 1 120908859 142693887 21785028 456s 3 1 142693888 Inf Inf 456s Keeping only current chromosome for 'knownSegments'...done 456s alphaTCN: 0.009 456s alphaDH: 0.001 456s Number of loci: 14658 456s Calculating DHs... 456s Number of SNPs: 14658 456s Number of heterozygous SNPs: 4196 (28.63%) 456s Normalized DHs: 456s num [1:14658] NA NA NA NA NA ... 456s Calculating DHs...done 456s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 456s Produced 2 seeds from this stream for future usage 456s Identification of change points by total copy numbers... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 456s Produced 3 seeds from this stream for future usage 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 14658 obs. of 4 variables: 456s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 456s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 4 obs. of 6 variables: 456s ..$ sampleName: chr [1:4] NA NA NA NA 456s ..$ chromosome: int [1:4] 1 1 1 1 456s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.43e+08 1.85e+08 456s ..$ end : num [1:4] 1.21e+08 1.43e+08 1.85e+08 2.47e+08 456s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 456s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 456s $ segRows:'data.frame': 4 obs. of 2 variables: 456s ..$ startRow: int [1:4] 1 NA 7587 10268 456s ..$ endRow : int [1:4] 7586 NA 10267 14658 456s $ params :List of 5 456s ..$ alpha : num 0.009 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 456s .. ..$ chromosome: int [1:4] 1 1 2 1 456s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.43e+08 456s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 456s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.199 0.001 0.192 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s Identification of change points by total copy numbers...done 456s Restructure TCN segmentation results... 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 456s 1 1 554484 120908858 7586 1.3853 456s 2 1 120908859 142693887 0 NA 456s 3 1 142693888 185449813 2681 2.0689 456s 4 1 185449813 247137334 4391 2.6341 456s Number of TCN segments: 4 456s Restructure TCN segmentation results...done 456s Total CN segment #1 ([ 554484,1.20909e+08]) of 4... 456s Number of TCN loci in segment: 7586 456s Locus data for TCN segment: 456s 'data.frame': 7586 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 554484 730720 782343 878522 916294 ... 456s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 456s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 456s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 456s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 456s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 456s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 456s $ rho : num NA NA NA NA NA ... 456s Number of loci: 7586 456s Number of SNPs: 2108 (27.79%) 456s Number of heterozygous SNPs: 2108 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 7586 obs. of 4 variables: 456s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 456s ..$ y : num [1:7586] NA NA NA NA NA ... 456s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 554484 456s ..$ end : num 1.21e+08 456s ..$ nbrOfLoci : int 2108 456s ..$ mean : num 0.512 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 10 456s ..$ endRow : int 7574 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 554484 456s .. ..$ end : num 1.21e+08 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.05 0 0.054 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 10 7574 456s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10 7574 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 554484 120908858 2108 0.5116 456s startRow endRow 456s 1 10 7574 456s Rows: 456s [1] 1 456s TCN segmentation rows: 456s startRow endRow 456s 1 1 7586 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s startRow endRow 456s 1 10 7574 456s NULL 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7586 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s startRow endRow 456s 1 10 7574 456s startRow endRow 456s 1 1 7586 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 1 1 554484 120908858 7586 1.3853 2108 2108 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 120908858 7586 1.3853 2108 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2108 554484 120908858 2108 0.5116 456s Total CN segment #1 ([ 554484,1.20909e+08]) of 4...done 456s Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4... 456s Number of TCN loci in segment: 0 456s Locus data for TCN segment: 456s 'data.frame': 0 obs. of 9 variables: 456s $ chromosome: int 456s $ x : num 456s $ CT : num 456s $ betaT : num 456s $ betaTN : num 456s $ betaN : num 456s $ muN : num 456s $ index : int 456s $ rho : num 456s Number of loci: 0 456s Number of SNPs: 0 (NaN%) 456s Number of heterozygous SNPs: 0 (NaN%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: NA 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 0 obs. of 4 variables: 456s ..$ chromosome: int(0) 456s ..$ x : num(0) 456s ..$ y : num(0) 456s ..$ index : int(0) 456s $ output :'data.frame': 0 obs. of 6 variables: 456s ..$ sampleName: chr(0) 456s ..$ chromosome: num(0) 456s ..$ start : num(0) 456s ..$ end : num(0) 456s ..$ nbrOfLoci : int(0) 456s ..$ mean : num(0) 456s $ segRows:'data.frame': 0 obs. of 2 variables: 456s ..$ startRow: int(0) 456s ..$ endRow : int(0) 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 456s .. ..$ chromosome: int(0) 456s .. ..$ start : num(0) 456s .. ..$ end : num(0) 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0 0 0.001 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s DH segmentation (locally-indexed) rows: 456s [1] startRow endRow 456s <0 rows> (or 0-length row.names) 456s int(0) 456s DH segmentation rows: 456s [1] startRow endRow 456s <0 rows> (or 0-length row.names) 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s NA NA NA NA NA 456s startRow endRow 456s NA NA NA 456s Rows: 456s [1] 2 456s TCN segmentation rows: 456s startRow endRow 456s 2 NA NA 456s TCN and DH segmentation rows: 456s startRow endRow 456s 2 NA NA 456s startRow endRow 456s NA NA NA 456s startRow endRow 456s 1 1 7586 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s startRow endRow 456s 1 10 7574 456s 2 NA NA 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 2 1 120908859 142693887 0 NA 0 0 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 2 2 1 1 120908859 142693887 0 NA 0 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 2 0 NA NA NA NA 456s Total CN segment #2 ([1.20909e+08,1.42694e+08]) of 4...done 456s Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4... 456s Number of TCN loci in segment: 2681 456s Locus data for TCN segment: 456s 'data.frame': 2681 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 456s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 456s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 456s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 456s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 456s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 456s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 456s $ rho : num 0.117 0.258 NA NA NA ... 456s Number of loci: 2681 456s Number of SNPs: 777 (28.98%) 456s Number of heterozygous SNPs: 777 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 2681 obs. of 4 variables: 456s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 456s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 456s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 1.43e+08 456s ..$ end : num 1.85e+08 456s ..$ nbrOfLoci : int 777 456s ..$ mean : num 0.0973 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 1 456s ..$ endRow : int 2677 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 1.43e+08 456s .. ..$ end : num 1.85e+08 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.009 0 0.01 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 1 2677 456s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 7587 10263 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 142693888 185449813 777 0.0973 456s startRow endRow 456s 1 7587 10263 456s Rows: 456s [1] 3 456s TCN segmentation rows: 456s startRow endRow 456s 3 7587 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 3 7587 10267 456s startRow endRow 456s 1 7587 10263 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s startRow endRow 456s 1 10 7574 456s 2 NA NA 456s 3 7587 10263 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 3 1 142693888 185449813 2681 2.0689 777 777 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 3 3 1 1 142693888 185449813 2681 2.0689 777 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 3 777 142693888 185449813 777 0.0973 456s Total CN segment #3 ([1.42694e+08,1.8545e+08]) of 4...done 456s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 456s Number of TCN loci in segment: 4391 456s Locus data for TCN segment: 456s 'data.frame': 4391 obs. of 9 variables: 456s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 456s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 456s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 456s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 456s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 456s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 456s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s $ rho : num NA 0.2186 NA 0.0503 NA ... 456s Number of loci: 4391 456s Number of SNPs: 1311 (29.86%) 456s Number of heterozygous SNPs: 1311 (100.00%) 456s Chromosome: 1 456s Segmenting DH signals... 456s Segmenting by CBS... 456s Chromosome: 1 456s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 456s Segmenting by CBS...done 456s List of 4 456s $ data :'data.frame': 4391 obs. of 4 variables: 456s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 456s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 456s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 456s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 456s $ output :'data.frame': 1 obs. of 6 variables: 456s ..$ sampleName: chr NA 456s ..$ chromosome: int 1 456s ..$ start : num 1.85e+08 456s ..$ end : num 2.47e+08 456s ..$ nbrOfLoci : int 1311 456s ..$ mean : num 0.23 456s $ segRows:'data.frame': 1 obs. of 2 variables: 456s ..$ startRow: int 2 456s ..$ endRow : int 4388 456s $ params :List of 5 456s ..$ alpha : num 0.001 456s ..$ undo : num 0 456s ..$ joinSegments : logi TRUE 456s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 456s .. ..$ chromosome: int 1 456s .. ..$ start : num 1.85e+08 456s .. ..$ end : num 2.47e+08 456s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 456s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.02 0 0 456s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 456s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 456s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 456s DH segmentation (locally-indexed) rows: 456s startRow endRow 456s 1 2 4388 456s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 456s DH segmentation rows: 456s startRow endRow 456s 1 10269 14655 456s Segmenting DH signals...done 456s DH segmentation table: 456s dhStart dhEnd dhNbrOfLoci dhMean 456s 1 185449813 247137334 1311 0.2295 456s startRow endRow 456s 1 10269 14655 456s Rows: 456s [1] 4 456s TCN segmentation rows: 456s startRow endRow 456s 4 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 4 10268 14658 456s startRow endRow 456s 1 10269 14655 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s TCN segmentation (expanded) rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s TCN and DH segmentation rows: 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s startRow endRow 456s 1 10 7574 456s 2 NA NA 456s 3 7587 10263 456s 4 10269 14655 456s startRow endRow 456s 1 1 7586 456s 2 NA NA 456s 3 7587 10267 456s 4 10268 14658 456s Total CN segmentation table (expanded): 456s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 456s 4 1 185449813 247137334 4391 2.6341 1311 1311 456s (TCN,DH) segmentation for one total CN segment: 456s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 4 4 1 1 185449813 247137334 4391 2.6341 1311 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 4 1311 185449813 247137334 1311 0.2295 456s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 120908858 7586 1.3853 2108 456s 2 1 2 1 120908859 142693887 0 NA 0 456s 3 1 3 1 142693888 185449813 2681 2.0689 777 456s 4 1 4 1 185449813 247137334 4391 2.6341 1311 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 456s 1 2108 554484 120908858 2108 0.5116 456s 2 0 NA NA NA NA 456s 3 777 142693888 185449813 777 0.0973 456s 4 1311 185449813 247137334 1311 0.2295 456s Calculating (C1,C2) per segment... 456s Calculating (C1,C2) per segment...done 456s Number of segments: 4 456s Segmenting paired tumor-normal signals using Paired PSCBS...done 456s Post-segmenting TCNs... 456s Number of segments: 4 456s Number of chromosomes: 1 456s [1] 1 456s Chromosome 1 ('chr01') of 1... 456s Rows: 456s [1] 1 2 3 4 456s Number of segments: 4 456s TCN segment #1 ('1') of 4... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #1 ('1') of 4...done 456s TCN segment #2 ('2') of 4... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #2 ('2') of 4...done 456s TCN segment #3 ('3') of 4... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #3 ('3') of 4...done 456s TCN segment #4 ('4') of 4... 456s Nothing todo. Only one DH segmentation. Skipping. 456s TCN segment #4 ('4') of 4...done 456s Chromosome 1 ('chr01') of 1...done 456s Update (C1,C2) per segment... 456s Update (C1,C2) per segment...done 456s Post-segmenting TCNs...done 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 120908858 7586 1.3853 2108 456s 2 1 2 1 120908859 142693887 0 NA 0 456s 3 1 3 1 142693888 185449813 2681 2.0689 777 456s 4 1 4 1 185449813 247137334 4391 2.6341 1311 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 456s 2 0 NA NA NA NA NA NA 456s 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 456s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 456s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 456s 1 1 1 1 554484 120908858 7586 1.3853 2108 456s 2 1 2 1 120908859 142693887 0 NA 0 456s 3 1 3 1 142693888 185449813 2681 2.0689 777 456s 4 1 4 1 185449813 247137334 4391 2.6341 1311 456s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 456s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 456s 2 0 NA NA NA NA NA NA 456s 3 777 142693888 185449813 777 0.0973 0.9337980 1.135102 456s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 456s > 456s > message("*** segmentByPairedPSCBS() via futures ... DONE") 456s *** segmentByPairedPSCBS() via futures ... DONE 456s > 456s > 456s > ## Cleanup 456s > plan(oplan) 456s > rm(list=c("fits", "data", "fit")) 456s > 456s > proc.time() 456s user system elapsed 456s 9.959 0.140 10.172 456s Test segmentByPairedPSCBS,futures passed 456s 0 456s Begin test segmentByPairedPSCBS,noNormalBAFs 458s + cat segmentByPairedPSCBS,noNormalBAFs.Rout 458s 458s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 458s Copyright (C) 2024 The R Foundation for Statistical Computing 458s Platform: s390x-ibm-linux-gnu (64-bit) 458s 458s R is free software and comes with ABSOLUTELY NO WARRANTY. 458s You are welcome to redistribute it under certain conditions. 458s Type 'license()' or 'licence()' for distribution details. 458s 458s R is a collaborative project with many contributors. 458s Type 'contributors()' for more information and 458s 'citation()' on how to cite R or R packages in publications. 458s 458s Type 'demo()' for some demos, 'help()' for on-line help, or 458s 'help.start()' for an HTML browser interface to help. 458s Type 'q()' to quit R. 458s 458s [Previously saved workspace restored] 458s 458s > library("PSCBS") 458s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 458s 458s Attaching package: 'PSCBS' 458s 458s The following objects are masked from 'package:base': 458s 458s append, load 458s 458s > 458s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 458s > # Load SNP microarray data 458s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 458s > data <- PSCBS::exampleData("paired.chr01") 458s > str(data) 458s 'data.frame': 73346 obs. of 6 variables: 458s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 458s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 458s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 458s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 458s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 458s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 458s > 458s > # Drop single-locus outliers 458s > dataS <- dropSegmentationOutliers(data) 458s > 458s > # Run light-weight tests by default 458s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 458s + # Use only every 5th data point 458s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 458s + # Number of segments (for assertion) 458s + nSegs <- 3L 458s + # Number of bootstrap samples (see below) 458s + B <- 100L 458s + } else { 458s + # Full tests 458s + nSegs <- 8L 458s + B <- 1000L 458s + } 458s > 458s > str(dataS) 458s 'data.frame': 14670 obs. of 6 variables: 458s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 458s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 458s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 458s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 458s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 458s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 458s > 458s > R.oo::attachLocally(dataS) 458s > 458s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 458s > # Simulate that genotypes are known by other means 458s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 458s > library("aroma.light") 458s aroma.light v3.32.0 (2023-10-24) successfully loaded. See ?aroma.light for help. 458s > muN <- aroma.light::callNaiveGenotypes(betaN, censorAt=c(0,1)) 458s > 458s > 458s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 458s > # Paired PSCBS segmentation 458s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 458s > fit <- segmentByPairedPSCBS(CT, betaT=betaT, muN=muN, tbn=FALSE, 458s + chromosome=chromosome, x=x, 458s + seed=0xBEEF, verbose=-10) 458s Segmenting paired tumor-normal signals using Paired PSCBS... 458s Setup up data... 458s 'data.frame': 14670 obs. of 6 variables: 458s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 458s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 458s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 458s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 458s $ betaTN : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 458s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 458s ..- attr(*, "modelFit")=List of 1 458s .. ..$ :List of 7 458s .. .. ..$ flavor : chr "density" 458s .. .. ..$ cn : int 2 458s .. .. ..$ nbrOfGenotypeGroups: int 3 458s .. .. ..$ tau : num [1:2] 0.315 0.677 458s .. .. ..$ n : int 14640 458s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 458s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 458s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 458s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 458s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 458s .. .. .. ..$ type : chr [1:2] "valley" "valley" 458s .. .. .. ..$ x : num [1:2] 0.315 0.677 458s .. .. .. ..$ density: num [1:2] 0.522 0.552 458s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 458s Setup up data...done 458s Dropping loci for which TCNs are missing... 458s Number of loci dropped: 12 458s Dropping loci for which TCNs are missing...done 458s Ordering data along genome... 458s 'data.frame': 14658 obs. of 6 variables: 458s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 458s $ x : num 554484 730720 782343 878522 916294 ... 458s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 458s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 458s $ betaTN : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 458s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 458s Ordering data along genome...done 458s Keeping only current chromosome for 'knownSegments'... 458s Chromosome: 1 458s Known segments for this chromosome: 458s [1] chromosome start end 458s <0 rows> (or 0-length row.names) 458s Keeping only current chromosome for 'knownSegments'...done 458s alphaTCN: 0.009 458s alphaDH: 0.001 458s Number of loci: 14658 458s Calculating DHs... 458s Number of SNPs: 14658 458s Number of heterozygous SNPs: 4196 (28.63%) 458s Normalized DHs: 458s num [1:14658] NA NA NA NA NA ... 458s Calculating DHs...done 458s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 458s Produced 2 seeds from this stream for future usage 458s Identification of change points by total copy numbers... 458s Segmenting by CBS... 458s Chromosome: 1 458s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 458s Segmenting by CBS...done 458s List of 4 458s $ data :'data.frame': 14658 obs. of 4 variables: 458s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 458s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 458s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 458s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 458s $ output :'data.frame': 3 obs. of 6 variables: 458s ..$ sampleName: chr [1:3] NA NA NA 458s ..$ chromosome: int [1:3] 1 1 1 458s ..$ start : num [1:3] 5.54e+05 1.44e+08 1.85e+08 458s ..$ end : num [1:3] 1.44e+08 1.85e+08 2.47e+08 458s ..$ nbrOfLoci : int [1:3] 7599 2668 4391 458s ..$ mean : num [1:3] 1.39 2.07 2.63 458s $ segRows:'data.frame': 3 obs. of 2 variables: 458s ..$ startRow: int [1:3] 1 7600 10268 458s ..$ endRow : int [1:3] 7599 10267 14658 458s $ params :List of 5 458s ..$ alpha : num 0.009 458s ..$ undo : num 0 458s ..$ joinSegments : logi TRUE 458s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 458s .. ..$ chromosome: int 1 458s .. ..$ start : num -Inf 458s .. ..$ end : num Inf 458s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 458s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 458s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.556 0 0.557 0 0 458s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 458s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 458s - attr(*, "randomSeed")= int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 458s Identification of change points by total copy numbers...done 458s Restructure TCN segmentation results... 458s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 458s 1 1 554484 143926517 7599 1.3859 458s 2 1 143926517 185449813 2668 2.0704 458s 3 1 185449813 247137334 4391 2.6341 458s Number of TCN segments: 3 458s Restructure TCN segmentation results...done 458s Total CN segment #1 ([ 554484,1.43927e+08]) of 3... 458s Number of TCN loci in segment: 7599 458s Locus data for TCN segment: 458s 'data.frame': 7599 obs. of 8 variables: 458s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 458s $ x : num 554484 730720 782343 878522 916294 ... 458s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 458s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 458s $ betaTN : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 458s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 458s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 458s $ rho : num NA NA NA NA NA ... 458s Number of loci: 7599 458s Number of SNPs: 2111 (27.78%) 458s Number of heterozygous SNPs: 2111 (100.00%) 458s Chromosome: 1 458s Segmenting DH signals... 458s Segmenting by CBS... 458s Chromosome: 1 458s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 458s Segmenting by CBS...done 458s List of 4 458s $ data :'data.frame': 7599 obs. of 4 variables: 458s ..$ chromosome: int [1:7599] 1 1 1 1 1 1 1 1 1 1 ... 458s ..$ x : num [1:7599] 554484 730720 782343 878522 916294 ... 458s ..$ y : num [1:7599] NA NA NA NA NA ... 458s ..$ index : int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 458s $ output :'data.frame': 1 obs. of 6 variables: 458s ..$ sampleName: chr NA 458s ..$ chromosome: int 1 458s ..$ start : num 554484 458s ..$ end : num 1.44e+08 458s ..$ nbrOfLoci : int 2111 458s ..$ mean : num 0.524 458s $ segRows:'data.frame': 1 obs. of 2 variables: 458s ..$ startRow: int 10 458s ..$ endRow : int 7594 458s $ params :List of 5 458s ..$ alpha : num 0.001 458s ..$ undo : num 0 458s ..$ joinSegments : logi TRUE 458s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 458s .. ..$ chromosome: int 1 458s .. ..$ start : num 554484 458s .. ..$ end : num 1.44e+08 458s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 458s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 458s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.03 0 0.036 0 0 458s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 458s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 458s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 458s DH segmentation (locally-indexed) rows: 458s startRow endRow 458s 1 10 7594 458s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 458s DH segmentation rows: 458s startRow endRow 458s 1 10 7594 458s Segmenting DH signals...done 458s DH segmentation table: 458s dhStart dhEnd dhNbrOfLoci dhMean 458s 1 554484 143926517 2111 0.5237 458s startRow endRow 458s 1 10 7594 458s Rows: 458s [1] 1 458s TCN segmentation rows: 458s startRow endRow 458s 1 1 7599 458s TCN and DH segmentation rows: 458s startRow endRow 458s 1 1 7599 458s startRow endRow 458s 1 10 7594 458s NULL 458s TCN segmentation (expanded) rows: 458s startRow endRow 458s 1 1 7599 458s TCN and DH segmentation rows: 458s startRow endRow 458s 1 1 7599 458s 2 7600 10267 458s 3 10268 14658 458s startRow endRow 458s 1 10 7594 458s startRow endRow 458s 1 1 7599 458s Total CN segmentation table (expanded): 458s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 458s 1 1 554484 143926517 7599 1.3859 2111 2111 458s (TCN,DH) segmentation for one total CN segment: 458s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 1 1 1 1 554484 143926517 7599 1.3859 2111 458s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 458s 1 2111 554484 143926517 2111 0.5237 458s Total CN segment #1 ([ 554484,1.43927e+08]) of 3...done 458s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3... 458s Number of TCN loci in segment: 2668 458s Locus data for TCN segment: 458s 'data.frame': 2668 obs. of 8 variables: 458s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 458s $ x : num 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 458s $ CT : num 2.1 2.1 2.09 1.8 2.34 ... 458s $ betaT : num 0.1899 0.909 0.9166 0.1668 0.0308 ... 458s $ betaTN : num 0.1899 0.909 0.9166 0.1668 0.0308 ... 458s $ muN : num 0 1 1 0 0 1 0 0 0 0 ... 458s $ index : int 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 458s $ rho : num NA NA NA NA NA NA NA NA NA NA ... 458s Number of loci: 2668 458s Number of SNPs: 774 (29.01%) 458s Number of heterozygous SNPs: 774 (100.00%) 458s Chromosome: 1 458s Segmenting DH signals... 458s Segmenting by CBS... 458s Chromosome: 1 458s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 458s Segmenting by CBS...done 458s List of 4 458s $ data :'data.frame': 2668 obs. of 4 variables: 458s ..$ chromosome: int [1:2668] 1 1 1 1 1 1 1 1 1 1 ... 458s ..$ x : num [1:2668] 1.44e+08 1.44e+08 1.44e+08 1.44e+08 1.44e+08 ... 458s ..$ y : num [1:2668] NA NA NA NA NA NA NA NA NA NA ... 458s ..$ index : int [1:2668] 1 2 3 4 5 6 7 8 9 10 ... 458s $ output :'data.frame': 1 obs. of 6 variables: 458s ..$ sampleName: chr NA 458s ..$ chromosome: int 1 458s ..$ start : num 1.44e+08 458s ..$ end : num 1.85e+08 458s ..$ nbrOfLoci : int 774 458s ..$ mean : num 0.154 458s $ segRows:'data.frame': 1 obs. of 2 variables: 458s ..$ startRow: int 15 458s ..$ endRow : int 2664 458s $ params :List of 5 458s ..$ alpha : num 0.001 458s ..$ undo : num 0 458s ..$ joinSegments : logi TRUE 458s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 458s .. ..$ chromosome: int 1 458s .. ..$ start : num 1.44e+08 458s .. ..$ end : num 1.85e+08 458s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 458s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 458s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.012 0 0 458s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 458s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 458s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 458s DH segmentation (locally-indexed) rows: 458s startRow endRow 458s 1 15 2664 458s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 458s DH segmentation rows: 458s startRow endRow 458s 1 7614 10263 458s Segmenting DH signals...done 458s DH segmentation table: 458s dhStart dhEnd dhNbrOfLoci dhMean 458s 1 143926517 185449813 774 0.1542 458s startRow endRow 458s 1 7614 10263 458s Rows: 458s [1] 2 458s TCN segmentation rows: 458s startRow endRow 458s 2 7600 10267 458s TCN and DH segmentation rows: 458s startRow endRow 458s 2 7600 10267 458s startRow endRow 458s 1 7614 10263 458s startRow endRow 458s 1 1 7599 458s TCN segmentation (expanded) rows: 458s startRow endRow 458s 1 1 7599 458s 2 7600 10267 458s TCN and DH segmentation rows: 458s startRow endRow 458s 1 1 7599 458s 2 7600 10267 458s 3 10268 14658 458s startRow endRow 458s 1 10 7594 458s 2 7614 10263 458s startRow endRow 458s 1 1 7599 458s 2 7600 10267 458s Total CN segmentation table (expanded): 458s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 458s 2 1 143926517 185449813 2668 2.0704 774 774 458s (TCN,DH) segmentation for one total CN segment: 458s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 2 2 1 1 143926517 185449813 2668 2.0704 774 458s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 458s 2 774 143926517 185449813 774 0.1542 458s Total CN segment #2 ([1.43927e+08,1.8545e+08]) of 3...done 458s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 458s Number of TCN loci in segment: 4391 458s Locus data for TCN segment: 458s 'data.frame': 4391 obs. of 8 variables: 458s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 458s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 458s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 458s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 458s $ betaTN : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 458s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 458s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 458s $ rho : num NA 0.0308 NA 0.2533 NA ... 458s Number of loci: 4391 458s Number of SNPs: 1311 (29.86%) 458s Number of heterozygous SNPs: 1311 (100.00%) 458s Chromosome: 1 458s Segmenting DH signals... 458s Segmenting by CBS... 458s Chromosome: 1 458s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 458s Segmenting by CBS...done 458s List of 4 458s $ data :'data.frame': 4391 obs. of 4 variables: 458s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 458s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 458s ..$ y : num [1:4391] NA 0.0308 NA 0.2533 NA ... 458s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 458s $ output :'data.frame': 1 obs. of 6 variables: 458s ..$ sampleName: chr NA 458s ..$ chromosome: int 1 458s ..$ start : num 1.85e+08 458s ..$ end : num 2.47e+08 458s ..$ nbrOfLoci : int 1311 458s ..$ mean : num 0.251 458s $ segRows:'data.frame': 1 obs. of 2 variables: 458s ..$ startRow: int 2 458s ..$ endRow : int 4388 458s $ params :List of 5 458s ..$ alpha : num 0.001 458s ..$ undo : num 0 458s ..$ joinSegments : logi TRUE 458s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 458s .. ..$ chromosome: int 1 458s .. ..$ start : num 1.85e+08 458s .. ..$ end : num 2.47e+08 458s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 458s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 458s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.028 0 0 458s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 458s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 458s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 458s DH segmentation (locally-indexed) rows: 458s startRow endRow 458s 1 2 4388 458s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 458s DH segmentation rows: 458s startRow endRow 458s 1 10269 14655 458s Segmenting DH signals...done 458s DH segmentation table: 458s dhStart dhEnd dhNbrOfLoci dhMean 458s 1 185449813 247137334 1311 0.2512 458s startRow endRow 458s 1 10269 14655 458s Rows: 458s [1] 3 458s TCN segmentation rows: 458s startRow endRow 458s 3 10268 14658 458s TCN and DH segmentation rows: 458s startRow endRow 458s 3 10268 14658 458s startRow endRow 458s 1 10269 14655 458s startRow endRow 458s 1 1 7599 458s 2 7600 10267 458s TCN segmentation (expanded) rows: 458s startRow endRow 458s 1 1 7599 458s 2 7600 10267 458s 3 10268 14658 458s TCN and DH segmentation rows: 458s startRow endRow 458s 1 1 7599 458s 2 7600 10267 458s 3 10268 14658 458s startRow endRow 458s 1 10 7594 458s 2 7614 10263 458s 3 10269 14655 458s startRow endRow 458s 1 1 7599 458s 2 7600 10267 458s 3 10268 14658 458s Total CN segmentation table (expanded): 458s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 458s 3 1 185449813 247137334 4391 2.6341 1311 1311 458s (TCN,DH) segmentation for one total CN segment: 458s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 3 3 1 1 185449813 247137334 4391 2.6341 1311 458s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 458s 3 1311 185449813 247137334 1311 0.2512 458s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 458s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 1 1 1 1 554484 143926517 7599 1.3859 2111 458s 2 1 2 1 143926517 185449813 2668 2.0704 774 458s 3 1 3 1 185449813 247137334 4391 2.6341 1311 458s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 458s 1 2111 554484 143926517 2111 0.5237 458s 2 774 143926517 185449813 774 0.1542 458s 3 1311 185449813 247137334 1311 0.2512 458s Calculating (C1,C2) per segment... 458s Calculating (C1,C2) per segment...done 458s Number of segments: 3 458s Segmenting paired tumor-normal signals using Paired PSCBS...done 458s Post-segmenting TCNs... 458s Number of segments: 3 458s Number of chromosomes: 1 458s [1] 1 458s Chromosome 1 ('chr01') of 1... 458s Rows: 458s [1] 1 2 3 458s Number of segments: 3 458s TCN segment #1 ('1') of 3... 458s Nothing todo. Only one DH segmentation. Skipping. 458s TCN segment #1 ('1') of 3...done 458s TCN segment #2 ('2') of 3... 458s Nothing todo. Only one DH segmentation. Skipping. 458s TCN segment #2 ('2') of 3...done 458s TCN segment #3 ('3') of 3... 458s Nothing todo. Only one DH segmentation. Skipping. 458s TCN segment #3 ('3') of 3...done 458s Chromosome 1 ('chr01') of 1...done 458s Update (C1,C2) per segment... 458s Update (C1,C2) per segment...done 458s Post-segmenting TCNs...done 458s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 1 1 1 1 554484 143926517 7599 1.3859 2111 458s 2 1 2 1 143926517 185449813 2668 2.0704 774 458s 3 1 3 1 185449813 247137334 4391 2.6341 1311 458s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 458s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 458s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 458s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 458s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 1 1 1 1 554484 143926517 7599 1.3859 2111 458s 2 1 2 1 143926517 185449813 2668 2.0704 774 458s 3 1 3 1 185449813 247137334 4391 2.6341 1311 458s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 458s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 458s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 458s 3 1311 185449813 247137334 1311 0.2512 0.9862070 1.647893 458s > print(fit) 458s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 1 1 1 1 554484 143926517 7599 1.3859 2111 458s 2 1 2 1 143926517 185449813 2668 2.0704 774 458s 3 1 3 1 185449813 247137334 4391 2.6341 1311 458s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 458s 1 2111 2111 0.5237 0.3300521 1.055848 458s 2 774 774 0.1542 0.8755722 1.194828 458s 3 1311 1311 0.2512 0.9862070 1.647893 458s > 458s > # Plot results 458s > plotTracks(fit) 458s > 458s > # Sanity check 458s > stopifnot(nbrOfSegments(fit) == nSegs) 458s > 458s > 458s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 458s > # Bootstrap segment level estimates 458s > # (used by the AB caller, which, if skipped here, 458s > # will do it automatically) 458s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 458s > fit <- bootstrapTCNandDHByRegion(fit, B=B, verbose=-10) 458s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint... 458s Already done? 458s tcn_2.5% tcn_5% tcn_95% tcn_97.5% dh_2.5% dh_5% dh_95% dh_97.5% 458s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 458s c1_2.5% c1_5% c1_95% c1_97.5% c2_2.5% c2_5% c2_95% c2_97.5% 458s FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 458s Bootstrapping (TCN,DH,C1,C2) segment mean levels... 458s Identifying heterozygous & homozygous SNPs and non-polymorphic loci... 458s Number of loci: 14658 458s Number of SNPs: 4196 458s Number of non-SNPs: 10462 458s Identifying heterozygous & homozygous SNPs and non-polymorphic loci...done 458s num [1:3, 1:100, 1:4] NA NA NA NA NA NA NA NA NA NA ... 458s - attr(*, "dimnames")=List of 3 458s ..$ : NULL 458s ..$ : NULL 458s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 458s Segment #1 (chr 1, tcnId=1, dhId=1) of 3... 458s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 1 1 1 1 554484 143926517 7599 1.3859 2111 458s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 458s 1 2111 554484 143926517 2111 0.5237 0.3300521 1.055848 458s Number of TCNs: 7599 458s Number of DHs: 2111 458s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 458s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 458s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 458s Identify loci used to bootstrap DH means... 458s Heterozygous SNPs to resample for DH: 458s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 458s Identify loci used to bootstrap DH means...done 458s Identify loci used to bootstrap TCN means... 458s SNPs: 458s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 458s Non-polymorphic loci: 458s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 458s Heterozygous SNPs to resample for TCN: 458s int [1:2111] 10 12 24 28 31 33 34 39 46 48 ... 458s Homozygous SNPs to resample for TCN: 458s int(0) 458s Non-polymorphic loci to resample for TCN: 458s int [1:5488] 1 2 3 4 5 6 7 8 9 11 ... 458s Heterozygous SNPs with non-DH to resample for TCN: 458s int(0) 458s Loci to resample for TCN: 458s int [1:7599] 1 2 3 4 5 6 7 8 9 10 ... 458s Identify loci used to bootstrap TCN means...done 458s Number of (#hets, #homs, #nonSNPs): (2111,0,5488) 458s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 458s Number of bootstrap samples: 100 458s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 458s Segment #1 (chr 1, tcnId=1, dhId=1) of 3...done 458s Segment #2 (chr 1, tcnId=2, dhId=1) of 3... 458s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 2 1 2 1 143926517 185449813 2668 2.0704 774 458s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 458s 2 774 143926517 185449813 774 0.1542 0.8755722 1.194828 458s Number of TCNs: 2668 458s Number of DHs: 774 458s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 458s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 458s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 458s Identify loci used to bootstrap DH means... 458s Heterozygous SNPs to resample for DH: 458s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 458s Identify loci used to bootstrap DH means...done 458s Identify loci used to bootstrap TCN means... 458s SNPs: 458s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 458s Non-polymorphic loci: 458s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 458s Heterozygous SNPs to resample for TCN: 458s int [1:774] 7614 7616 7626 7627 7628 7635 7638 7639 7640 7642 ... 458s Homozygous SNPs to resample for TCN: 458s int(0) 458s Non-polymorphic loci to resample for TCN: 458s int [1:1894] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 458s Heterozygous SNPs with non-DH to resample for TCN: 458s int(0) 458s Loci to resample for TCN: 458s int [1:2668] 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 ... 458s Identify loci used to bootstrap TCN means...done 458s Number of (#hets, #homs, #nonSNPs): (774,0,1894) 458s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 458s Number of bootstrap samples: 100 458s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 458s Segment #2 (chr 1, tcnId=2, dhId=1) of 3...done 458s Segment #3 (chr 1, tcnId=3, dhId=1) of 3... 458s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 458s 3 1 3 1 185449813 247137334 4391 2.6341 1311 458s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 458s 3 1311 185449813 247137334 1311 0.2512 0.986207 1.647893 458s Number of TCNs: 4391 458s Number of DHs: 1311 458s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 458s int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 458s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 458s Identify loci used to bootstrap DH means... 458s Heterozygous SNPs to resample for DH: 458s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 458s Identify loci used to bootstrap DH means...done 458s Identify loci used to bootstrap TCN means... 458s SNPs: 458s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 458s Non-polymorphic loci: 458s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 458s Heterozygous SNPs to resample for TCN: 458s int [1:1311] 10269 10271 10281 10282 10283 10293 10295 10297 10300 10302 ... 458s Homozygous SNPs to resample for TCN: 458s int(0) 458s Non-polymorphic loci to resample for TCN: 458s int [1:3080] 10268 10270 10272 10273 10274 10275 10276 10277 10278 10279 ... 458s Heterozygous SNPs with non-DH to resample for TCN: 458s int(0) 458s Loci to resample for TCN: 458s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 458s Identify loci used to bootstrap TCN means...done 458s Number of (#hets, #homs, #nonSNPs): (1311,0,3080) 458s Bootstrapping while preserving (#hets, #homs, #nonSNPs)... 458s Number of bootstrap samples: 100 458s Bootstrapping while preserving (#hets, #homs, #nonSNPs)...done 458s Segment #3 (chr 1, tcnId=3, dhId=1) of 3...done 458s Bootstrapped segment mean levels 458s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 458s - attr(*, "dimnames")=List of 3 458s ..$ : NULL 458s ..$ : NULL 458s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 458s Calculating (C1,C2) mean levels from (TCN,DH) mean levels... 458s num [1:3, 1:100, 1:4] 1.38 2.08 2.63 1.38 2.07 ... 458s - attr(*, "dimnames")=List of 3 458s ..$ : NULL 458s ..$ : NULL 458s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 458s Calculating (C1,C2) mean levels from (TCN,DH) mean levels...done 458s Calculating polar (alpha,radius,manhattan) for change points... 458s num [1:2, 1:100, 1:2] -0.5588 -0.0962 -0.5365 -0.1285 -0.5378 ... 458s - attr(*, "dimnames")=List of 3 458s ..$ : NULL 458s ..$ : NULL 458s ..$ : chr [1:2] "c1" "c2" 458s Bootstrapped change points 458s num [1:2, 1:100, 1:5] -2.89 -1.78 -2.87 -1.86 -2.88 ... 458s - attr(*, "dimnames")=List of 3 458s ..$ : NULL 458s ..$ : NULL 458s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 458s Calculating polar (alpha,radius,manhattan) for change points...done 458s Bootstrapping (TCN,DH,C1,C2) segment mean levels...done 458s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data... 458s num [1:3, 1:4, 1:4] NA NA NA NA NA NA NA NA NA NA ... 458s - attr(*, "dimnames")=List of 3 458s ..$ : NULL 458s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 458s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 458s Field #1 ('tcn') of 4... 458s Segment #1 of 3... 458s Segment #1 of 3...done 458s Segment #2 of 3... 458s Segment #2 of 3...done 458s Segment #3 of 3... 458s Segment #3 of 3...done 458s Field #1 ('tcn') of 4...done 458s Field #2 ('dh') of 4... 458s Segment #1 of 3... 458s Segment #1 of 3...done 458s Segment #2 of 3... 458s Segment #2 of 3...done 458s Segment #3 of 3... 458s Segment #3 of 3...done 458s Field #2 ('dh') of 4...done 458s Field #3 ('c1') of 4... 458s Segment #1 of 3... 458s Segment #1 of 3...done 458s Segment #2 of 3... 458s Segment #2 of 3...done 458s Segment #3 of 3... 458s Segment #3 of 3...done 458s Field #3 ('c1') of 4...done 458s Field #4 ('c2') of 4... 458s Segment #1 of 3... 458s Segment #1 of 3...done 458s Segment #2 of 3... 458s Segment #2 of 3...done 458s Segment #3 of 3... 458s Segment #3 of 3...done 458s Field #4 ('c2') of 4...done 458s Bootstrap statistics 458s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 458s - attr(*, "dimnames")=List of 3 458s ..$ : NULL 458s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 458s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 458s Statistical sanity checks (iff B >= 100)... 458s Available summaries: 2.5%, 5%, 95%, 97.5% 458s Available quantiles: 0.025, 0.05, 0.95, 0.975 458s num [1:3, 1:4, 1:4] 1.38 2.06 2.62 1.38 2.06 ... 458s - attr(*, "dimnames")=List of 3 458s ..$ : NULL 458s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 458s ..$ : chr [1:4] "tcn" "dh" "c1" "c2" 458s Field #1 ('tcn') of 4... 458s Seg 1. mean=1.3859, range=[1.38092,1.3949], n=7599 458s Seg 2. mean=2.0704, range=[2.05747,2.08326], n=2668 458s Seg 3. mean=2.6341, range=[2.62068,2.64694], n=4391 458s Field #1 ('tcn') of 4...done 458s Field #2 ('dh') of 4... 458s Seg 1. mean=0.5237, range=[0.51753,0.532002], n=2111 458s Seg 2. mean=0.1542, range=[0.144468,0.16453], n=774 458s Seg 3. mean=0.2512, range=[0.242575,0.258832], n=1311 458s Field #2 ('dh') of 4...done 458s Field #3 ('c1') of 4... 458s Seg 1. mean=0.330052, range=[0.323996,0.336038], n=2111 458s Seg 2. mean=0.875572, range=[0.86318,0.887699], n=774 458s Seg 3. mean=0.986207, range=[0.975123,0.998982], n=1311 458s Field #3 ('c1') of 4...done 458s Field #4 ('c2') of 4... 459s Seg 1. mean=1.05585, range=[1.05006,1.06231], n=2111 459s Seg 2. mean=1.19483, range=[1.18417,1.2081], n=774 459s Seg 3. mean=1.64789, range=[1.63403,1.66098], n=1311 459s Field #4 ('c2') of 4...done 459s Statistical sanity checks (iff B >= 100)...done 459s Summarizing bootstrapped segment ('tcn', 'dh', 'c1', 'c2') data...done 459s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data... 459s num [1:2, 1:4, 1:5] NA NA NA NA NA NA NA NA NA NA ... 459s - attr(*, "dimnames")=List of 3 459s ..$ : NULL 459s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 459s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 459s Field #1 ('alpha') of 5... 459s Changepoint #1 of 2... 459s Changepoint #1 of 2...done 459s Changepoint #2 of 2... 459s Changepoint #2 of 2...done 459s Field #1 ('alpha') of 5...done 459s Field #2 ('radius') of 5... 459s Changepoint #1 of 2... 459s Changepoint #1 of 2...done 459s Changepoint #2 of 2... 459s Changepoint #2 of 2...done 459s Field #2 ('radius') of 5...done 459s Field #3 ('manhattan') of 5... 459s Changepoint #1 of 2... 459s Changepoint #1 of 2...done 459s Changepoint #2 of 2... 459s Changepoint #2 of 2...done 459s Field #3 ('manhattan') of 5...done 459s Field #4 ('d1') of 5... 459s Changepoint #1 of 2... 459s Changepoint #1 of 2...done 459s Changepoint #2 of 2... 459s Changepoint #2 of 2...done 459s Field #4 ('d1') of 5...done 459s Field #5 ('d2') of 5... 459s Changepoint #1 of 2... 459s Changepoint #1 of 2...done 459s Changepoint #2 of 2... 459s Changepoint #2 of 2...done 459s Field #5 ('d2') of 5...done 459s Bootstrap statistics 459s num [1:2, 1:4, 1:5] -2.92 -1.86 -2.91 -1.85 -2.87 ... 459s - attr(*, "dimnames")=List of 3 459s ..$ : NULL 459s ..$ : chr [1:4] "2.5%" "5%" "95%" "97.5%" 459s ..$ : chr [1:5] "alpha" "radius" "manhattan" "d1" ... 459s Summarizing bootstrapped changepoint ('alpha', 'radius', 'manhattan', 'd1', 'd2') data...done 459s Resample (TCN,DH) signals and re-estimate summaries for segment & changepoint...done 459s > print(fit) 459s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 459s 1 1 1 1 554484 143926517 7599 1.3859 2111 459s 2 1 2 1 143926517 185449813 2668 2.0704 774 459s 3 1 3 1 185449813 247137334 4391 2.6341 1311 459s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 459s 1 2111 2111 0.5237 0.3300521 1.055848 459s 2 774 774 0.1542 0.8755722 1.194828 459s 3 1311 1311 0.2512 0.9862070 1.647893 459s > plotTracks(fit) 459s > 459s > 459s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 459s > # Calling segments in allelic balance (AB) and 459s > # in loss-of-heterozygosity (LOH) 459s > # NOTE: Ideally, this should be done on whole-genome data 459s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 459s > fit <- callAB(fit, verbose=-10) 459s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 459s delta (offset adjusting for bias in DH): 0.3466649145302 459s alpha (CI quantile; significance level): 0.05 459s Calling segments... 459s Number of segments called allelic balance (AB): 2 (66.67%) of 3 459s Calling segments...done 459s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 459s > fit <- callLOH(fit, verbose=-10) 459s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals... 459s delta (offset adjusting for bias in C1): 0.771236438183453 459s alpha (CI quantile; significance level): 0.05 459s Calling segments... 459s Number of segments called low C1 (LowC1, "LOH_C1"): 1 (33.33%) of 3 459s Calling segments...done 459s Calling segments of allelic balance from one-sided DH bootstrap confidence intervals...done 459s > print(fit) 459s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 459s 1 1 1 1 554484 143926517 7599 1.3859 2111 459s 2 1 2 1 143926517 185449813 2668 2.0704 774 459s 3 1 3 1 185449813 247137334 4391 2.6341 1311 459s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean abCall lohCall 459s 1 2111 2111 0.5237 0.3300521 1.055848 FALSE TRUE 459s 2 774 774 0.1542 0.8755722 1.194828 TRUE FALSE 459s 3 1311 1311 0.2512 0.9862070 1.647893 TRUE FALSE 459s > plotTracks(fit) 459s > 459s > proc.time() 459s user system elapsed 459s 2.399 0.086 2.493 459s Test segmentByPairedPSCBS,noNormalBAFs passed 459s 0 459s Begin test segmentByPairedPSCBS,report 459s + [ 0 != 0 ] 459s + echo Test segmentByPairedPSCBS,noNormalBAFs passed 459s + echo 0 459s + echo Begin test segmentByPairedPSCBS,report 459s + exitcode=0 459s + R CMD BATCH segmentByPairedPSCBS,report.R 459s + cat segmentByPairedPSCBS,report.Rout 459s 459s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 459s Copyright (C) 2024 The R Foundation for Statistical Computing 459s Platform: s390x-ibm-linux-gnu (64-bit) 459s 459s R is free software and comes with ABSOLUTELY NO WARRANTY. 459s You are welcome to redistribute it under certain conditions. 459s Type 'license()' or 'licence()' for distribution details. 459s 459s R is a collaborative project with many contributors. 459s Type 'contributors()' for more information and 459s 'citation()' on how to cite R or R packages in publications. 459s 459s Type 'demo()' for some demos, 'help()' for on-line help, or 459s 'help.start()' for an HTML browser interface to help. 459s Type 'q()' to quit R. 459s 459s [Previously saved workspace restored] 459s 459s > # This test script calls a report generator which requires 459s > # the 'ggplot2' package, which in turn will require packages 459s > # 'colorspace', 'dichromat', 'munsell', 'reshape2' and 'scales'. 459s > 459s > # Only run this test in full testing mode 459s > if (Sys.getenv("_R_CHECK_FULL_") != "") { 459s + library("PSCBS") 459s + 459s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 459s + # Load SNP microarray data 459s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 459s + data <- PSCBS::exampleData("paired.chr01") 459s + str(data) 459s + 459s + 459s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 459s + # Paired PSCBS segmentation 459s + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 459s + # Drop single-locus outliers 459s + dataS <- dropSegmentationOutliers(data) 459s + 459s + # Speed up example by segmenting fewer loci 459s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 459s + 459s + str(dataS) 459s + 459s + gaps <- findLargeGaps(dataS, minLength=2e6) 459s + knownSegments <- gapsToSegments(gaps) 459s + 459s + # Paired PSCBS segmentation 459s + fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 459s + seed=0xBEEF, verbose=-10) 459s + 459s + # Fake a multi-chromosome segmentation 459s + fit1 <- fit 459s + fit2 <- renameChromosomes(fit, from=1, to=2) 459s + fit <- c(fit1, fit2) 459s + 459s + report(fit, sampleName="PairedPSCBS", studyName="PSCBS-Ex", verbose=-10) 459s + 459s + } # if (Sys.getenv("_R_CHECK_FULL_")) 459s > 459s > proc.time() 459s user system elapsed 459s 0.317 0.044 0.361 459s + [ 0 != 0 ] 459s + echo Test segmentByPairedPSCBS,report passed 459s + echo 0 459s + Test segmentByPairedPSCBS,report passed 459s 0 459s echo Begin test segmentByPairedPSCBS,seqOfSegmentsByDP 459s Begin test segmentByPairedPSCBS,seqOfSegmentsByDP 459s + exitcode=0 459s + R CMD BATCH segmentByPairedPSCBS,seqOfSegmentsByDP.R 464s + cat segmentByPairedPSCBS,seqOfSegmentsByDP.Rout 464s 464s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 464s Copyright (C) 2024 The R Foundation for Statistical Computing 464s Platform: s390x-ibm-linux-gnu (64-bit) 464s 464s R is free software and comes with ABSOLUTELY NO WARRANTY. 464s You are welcome to redistribute it under certain conditions. 464s Type 'license()' or 'licence()' for distribution details. 464s 464s R is a collaborative project with many contributors. 464s Type 'contributors()' for more information and 464s 'citation()' on how to cite R or R packages in publications. 464s 464s Type 'demo()' for some demos, 'help()' for on-line help, or 464s 'help.start()' for an HTML browser interface to help. 464s Type 'q()' to quit R. 464s 464s [Previously saved workspace restored] 464s 464s > library("PSCBS") 464s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 464s 464s Attaching package: 'PSCBS' 464s 464s The following objects are masked from 'package:base': 464s 464s append, load 464s 464s > subplots <- R.utils::subplots 464s > stext <- R.utils::stext 464s > 464s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 464s > # Load SNP microarray data 464s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 464s > data <- PSCBS::exampleData("paired.chr01") 464s > str(data) 464s 'data.frame': 73346 obs. of 6 variables: 464s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 464s $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ... 464s $ CT : num 1.625 1.071 1.406 1.18 0.856 ... 464s $ betaT : num 0.757 0.771 0.834 0.778 0.229 ... 464s $ CN : num 2.36 2.13 2.59 1.93 1.71 ... 464s $ betaN : num 0.827 0.875 0.887 0.884 0.103 ... 464s > 464s > 464s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 464s > # Paired PSCBS segmentation 464s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 464s > # Drop single-locus outliers 464s > dataS <- dropSegmentationOutliers(data) 464s > 464s > # Run light-weight tests by default 464s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 464s + # Use only every 5th data point 464s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 464s + # Number of segments (for assertion) 464s + nSegs <- 3L 464s + # Number of bootstrap samples (see below) 464s + B <- 100L 464s + } else { 464s + # Full tests 464s + nSegs <- 12L 464s + B <- 1000L 464s + } 464s > 464s > str(dataS) 464s 'data.frame': 14670 obs. of 6 variables: 464s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 464s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 464s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 464s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 464s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 464s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 464s > 464s > R.oo::attachLocally(dataS) 464s > 464s > 464s > gaps <- findLargeGaps(dataS, minLength=2e6) 464s > knownSegments <- gapsToSegments(gaps, dropGaps=TRUE) 464s > 464s > # Paired PSCBS segmentation 464s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 464s + seed=0xBEEF, verbose=-10) 464s Segmenting paired tumor-normal signals using Paired PSCBS... 464s Calling genotypes from normal allele B fractions... 464s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 464s Called genotypes: 464s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 464s - attr(*, "modelFit")=List of 1 464s ..$ :List of 7 464s .. ..$ flavor : chr "density" 464s .. ..$ cn : int 2 464s .. ..$ nbrOfGenotypeGroups: int 3 464s .. ..$ tau : num [1:2] 0.315 0.677 464s .. ..$ n : int 14640 464s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 464s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 464s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 464s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 464s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 464s .. .. ..$ type : chr [1:2] "valley" "valley" 464s .. .. ..$ x : num [1:2] 0.315 0.677 464s .. .. ..$ density: num [1:2] 0.522 0.552 464s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 464s muN 464s 0 0.5 1 464s 5221 4198 5251 464s Calling genotypes from normal allele B fractions...done 464s Normalizing betaT using betaN (TumorBoost)... 464s Normalized BAFs: 464s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 464s - attr(*, "modelFit")=List of 5 464s ..$ method : chr "normalizeTumorBoost" 464s ..$ flavor : chr "v4" 464s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 464s .. ..- attr(*, "modelFit")=List of 1 464s .. .. ..$ :List of 7 464s .. .. .. ..$ flavor : chr "density" 464s .. .. .. ..$ cn : int 2 464s .. .. .. ..$ nbrOfGenotypeGroups: int 3 464s .. .. .. ..$ tau : num [1:2] 0.315 0.677 464s .. .. .. ..$ n : int 14640 464s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 464s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 464s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 464s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 464s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 464s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 464s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 464s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 464s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 464s ..$ preserveScale: logi FALSE 464s ..$ scaleFactor : num NA 464s Normalizing betaT using betaN (TumorBoost)...done 464s Setup up data... 464s 'data.frame': 14670 obs. of 7 variables: 464s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 464s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 464s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 464s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 464s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 464s ..- attr(*, "modelFit")=List of 5 464s .. ..$ method : chr "normalizeTumorBoost" 464s .. ..$ flavor : chr "v4" 464s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 464s .. .. ..- attr(*, "modelFit")=List of 1 464s .. .. .. ..$ :List of 7 464s .. .. .. .. ..$ flavor : chr "density" 464s .. .. .. .. ..$ cn : int 2 464s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 464s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 464s .. .. .. .. ..$ n : int 14640 464s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 464s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 464s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 464s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 464s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 464s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 464s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 464s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 464s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 464s .. ..$ preserveScale: logi FALSE 464s .. ..$ scaleFactor : num NA 464s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 464s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 464s ..- attr(*, "modelFit")=List of 1 464s .. ..$ :List of 7 464s .. .. ..$ flavor : chr "density" 464s .. .. ..$ cn : int 2 464s .. .. ..$ nbrOfGenotypeGroups: int 3 464s .. .. ..$ tau : num [1:2] 0.315 0.677 464s .. .. ..$ n : int 14640 464s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 464s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 464s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 464s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 464s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 464s .. .. .. ..$ type : chr [1:2] "valley" "valley" 464s .. .. .. ..$ x : num [1:2] 0.315 0.677 464s .. .. .. ..$ density: num [1:2] 0.522 0.552 464s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 464s Setup up data...done 464s Dropping loci for which TCNs are missing... 464s Number of loci dropped: 12 464s Dropping loci for which TCNs are missing...done 464s Ordering data along genome... 464s 'data.frame': 14658 obs. of 7 variables: 464s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 464s $ x : num 554484 730720 782343 878522 916294 ... 464s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 464s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 464s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 464s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 464s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 464s Ordering data along genome...done 464s Keeping only current chromosome for 'knownSegments'... 464s Chromosome: 1 464s Known segments for this chromosome: 464s chromosome start end length 464s 1 1 -Inf 120908858 Inf 464s 2 1 142693888 Inf Inf 464s Keeping only current chromosome for 'knownSegments'...done 464s alphaTCN: 0.009 464s alphaDH: 0.001 464s Number of loci: 14658 464s Calculating DHs... 464s Number of SNPs: 14658 464s Number of heterozygous SNPs: 4196 (28.63%) 464s Normalized DHs: 464s num [1:14658] NA NA NA NA NA ... 464s Calculating DHs...done 464s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 464s Produced 2 seeds from this stream for future usage 464s Identification of change points by total copy numbers... 464s Segmenting by CBS... 464s Chromosome: 1 464s Segmenting multiple segments on current chromosome... 464s Number of segments: 2 464s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 464s Produced 2 seeds from this stream for future usage 464s Segmenting by CBS... 464s Chromosome: 1 464s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 464s Segmenting by CBS...done 464s Segmenting by CBS... 464s Chromosome: 1 464s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 464s Segmenting by CBS...done 464s Segmenting multiple segments on current chromosome...done 464s Segmenting by CBS...done 464s List of 4 464s $ data :'data.frame': 14658 obs. of 4 variables: 464s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 464s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 464s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 464s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 464s $ output :'data.frame': 3 obs. of 6 variables: 464s ..$ sampleName: chr [1:3] NA NA NA 464s ..$ chromosome: int [1:3] 1 1 1 464s ..$ start : num [1:3] 5.54e+05 1.43e+08 1.85e+08 464s ..$ end : num [1:3] 1.21e+08 1.85e+08 2.47e+08 464s ..$ nbrOfLoci : int [1:3] 7586 2681 4391 464s ..$ mean : num [1:3] 1.39 2.07 2.63 464s $ segRows:'data.frame': 3 obs. of 2 variables: 464s ..$ startRow: int [1:3] 1 7587 10268 464s ..$ endRow : int [1:3] 7586 10267 14658 464s $ params :List of 5 464s ..$ alpha : num 0.009 464s ..$ undo : num 0 464s ..$ joinSegments : logi TRUE 464s ..$ knownSegments:'data.frame': 2 obs. of 3 variables: 464s .. ..$ chromosome: int [1:2] 1 1 464s .. ..$ start : num [1:2] -Inf 1.43e+08 464s .. ..$ end : num [1:2] 1.21e+08 Inf 464s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 464s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 464s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.188 0 0.19 0 0 464s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 464s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 464s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 464s Identification of change points by total copy numbers...done 464s Restructure TCN segmentation results... 464s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 464s 1 1 554484 120908858 7586 1.3853 464s 2 1 142693888 185449813 2681 2.0689 464s 3 1 185449813 247137334 4391 2.6341 464s Number of TCN segments: 3 464s Restructure TCN segmentation results...done 464s Total CN segment #1 ([ 554484,1.20909e+08]) of 3... 464s Number of TCN loci in segment: 7586 464s Locus data for TCN segment: 464s 'data.frame': 7586 obs. of 9 variables: 464s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 464s $ x : num 554484 730720 782343 878522 916294 ... 464s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 464s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 464s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 464s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 464s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 464s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 464s $ rho : num NA NA NA NA NA ... 464s Number of loci: 7586 464s Number of SNPs: 2108 (27.79%) 464s Number of heterozygous SNPs: 2108 (100.00%) 464s Chromosome: 1 464s Segmenting DH signals... 464s Segmenting by CBS... 464s Chromosome: 1 464s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 464s Segmenting by CBS...done 464s List of 4 464s $ data :'data.frame': 7586 obs. of 4 variables: 464s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 464s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 464s ..$ y : num [1:7586] NA NA NA NA NA ... 464s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 464s $ output :'data.frame': 1 obs. of 6 variables: 464s ..$ sampleName: chr NA 464s ..$ chromosome: int 1 464s ..$ start : num 554484 464s ..$ end : num 1.21e+08 464s ..$ nbrOfLoci : int 2108 464s ..$ mean : num 0.512 464s $ segRows:'data.frame': 1 obs. of 2 variables: 464s ..$ startRow: int 10 464s ..$ endRow : int 7574 464s $ params :List of 5 464s ..$ alpha : num 0.001 464s ..$ undo : num 0 464s ..$ joinSegments : logi TRUE 464s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 464s .. ..$ chromosome: int 1 464s .. ..$ start : num 554484 464s .. ..$ end : num 1.21e+08 464s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 464s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 464s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.049 0.001 0.053 0 0 464s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 464s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 464s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 464s DH segmentation (locally-indexed) rows: 464s startRow endRow 464s 1 10 7574 464s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 464s DH segmentation rows: 464s startRow endRow 464s 1 10 7574 464s Segmenting DH signals...done 464s DH segmentation table: 464s dhStart dhEnd dhNbrOfLoci dhMean 464s 1 554484 120908858 2108 0.5116 464s startRow endRow 464s 1 10 7574 464s Rows: 464s [1] 1 464s TCN segmentation rows: 464s startRow endRow 464s 1 1 7586 464s TCN and DH segmentation rows: 464s startRow endRow 464s 1 1 7586 464s startRow endRow 464s 1 10 7574 464s NULL 464s TCN segmentation (expanded) rows: 464s startRow endRow 464s 1 1 7586 464s TCN and DH segmentation rows: 464s startRow endRow 464s 1 1 7586 464s 2 7587 10267 464s 3 10268 14658 464s startRow endRow 464s 1 10 7574 464s startRow endRow 464s 1 1 7586 464s Total CN segmentation table (expanded): 464s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 464s 1 1 554484 120908858 7586 1.3853 2108 2108 464s (TCN,DH) segmentation for one total CN segment: 464s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 464s 1 1 1 1 554484 120908858 7586 1.3853 2108 464s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 464s 1 2108 554484 120908858 2108 0.5116 464s Total CN segment #1 ([ 554484,1.20909e+08]) of 3...done 464s Total CN segment #2 ([1.42694e+08,1.8545e+08]) of 3... 464s Number of TCN loci in segment: 2681 464s Locus data for TCN segment: 464s 'data.frame': 2681 obs. of 9 variables: 464s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 464s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.4+ [ 0 != 0 ] 464s + echo Test segmentByPairedPSCBS,seqOfSegmentsByDP passed 464s + echo 0 464s + echo Begin test segmentByPairedPSCBS 464s + exitcode=0 464s + R CMD BATCH segmentByPairedPSCBS.R 464s 3e+08 1.44e+08 ... 464s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 464s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 464s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 464s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 464s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 464s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 464s $ rho : num 0.117 0.258 NA NA NA ... 464s Number of loci: 2681 464s Number of SNPs: 777 (28.98%) 464s Number of heterozygous SNPs: 777 (100.00%) 464s Chromosome: 1 464s Segmenting DH signals... 464s Segmenting by CBS... 464s Chromosome: 1 464s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 464s Segmenting by CBS...done 464s List of 4 464s $ data :'data.frame': 2681 obs. of 4 variables: 464s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 464s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 464s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 464s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 464s $ output :'data.frame': 1 obs. of 6 variables: 464s ..$ sampleName: chr NA 464s ..$ chromosome: int 1 464s ..$ start : num 1.43e+08 464s ..$ end : num 1.85e+08 464s ..$ nbrOfLoci : int 777 464s ..$ mean : num 0.0973 464s $ segRows:'data.frame': 1 obs. of 2 variables: 464s ..$ startRow: int 1 464s ..$ endRow : int 2677 464s $ params :List of 5 464s ..$ alpha : num 0.001 464s ..$ undo : num 0 464s ..$ joinSegments : logi TRUE 464s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 464s .. ..$ chromosome: int 1 464s .. ..$ start : num 1.43e+08 464s .. ..$ end : num 1.85e+08 464s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 464s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 464s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.01 0 0 464s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 464s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 464s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 464s DH segmentation (locally-indexed) rows: 464s startRow endRow 464s 1 1 2677 464s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 464s DH segmentation rows: 464s startRow endRow 464s 1 7587 10263 464s Segmenting DH signals...done 464s DH segmentation table: 464s dhStart dhEnd dhNbrOfLoci dhMean 464s 1 142693888 185449813 777 0.0973 464s startRow endRow 464s 1 7587 10263 464s Rows: 464s [1] 2 464s TCN segmentation rows: 464s startRow endRow 464s 2 7587 10267 464s TCN and DH segmentation rows: 464s startRow endRow 464s 2 7587 10267 464s startRow endRow 464s 1 7587 10263 464s startRow endRow 464s 1 1 7586 464s TCN segmentation (expanded) rows: 464s startRow endRow 464s 1 1 7586 464s 2 7587 10267 464s TCN and DH segmentation rows: 464s startRow endRow 464s 1 1 7586 464s 2 7587 10267 464s 3 10268 14658 464s startRow endRow 464s 1 10 7574 464s 2 7587 10263 464s startRow endRow 464s 1 1 7586 464s 2 7587 10267 464s Total CN segmentation table (expanded): 464s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 464s 2 1 142693888 185449813 2681 2.0689 777 777 464s (TCN,DH) segmentation for one total CN segment: 464s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 464s 2 2 1 1 142693888 185449813 2681 2.0689 777 464s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 464s 2 777 142693888 185449813 777 0.0973 464s Total CN segment #2 ([1.42694e+08,1.8545e+08]) of 3...done 464s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 464s Number of TCN loci in segment: 4391 464s Locus data for TCN segment: 464s 'data.frame': 4391 obs. of 9 variables: 464s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 464s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 464s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 464s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 464s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 464s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 464s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 464s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 464s $ rho : num NA 0.2186 NA 0.0503 NA ... 464s Number of loci: 4391 464s Number of SNPs: 1311 (29.86%) 464s Number of heterozygous SNPs: 1311 (100.00%) 464s Chromosome: 1 464s Segmenting DH signals... 464s Segmenting by CBS... 464s Chromosome: 1 464s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 464s Segmenting by CBS...done 464s List of 4 464s $ data :'data.frame': 4391 obs. of 4 variables: 464s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 464s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 464s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 464s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 464s $ output :'data.frame': 1 obs. of 6 variables: 464s ..$ sampleName: chr NA 464s ..$ chromosome: int 1 464s ..$ start : num 1.85e+08 464s ..$ end : num 2.47e+08 464s ..$ nbrOfLoci : int 1311 464s ..$ mean : num 0.23 464s $ segRows:'data.frame': 1 obs. of 2 variables: 464s ..$ startRow: int 2 464s ..$ endRow : int 4388 464s $ params :List of 5 464s ..$ alpha : num 0.001 464s ..$ undo : num 0 464s ..$ joinSegments : logi TRUE 464s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 464s .. ..$ chromosome: int 1 464s .. ..$ start : num 1.85e+08 464s .. ..$ end : num 2.47e+08 464s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 464s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 464s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.019 0 0.021 0 0 464s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 464s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 464s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 464s DH segmentation (locally-indexed) rows: 464s startRow endRow 464s 1 2 4388 464s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 464s DH segmentation rows: 464s startRow endRow 464s 1 10269 14655 464s Segmenting DH signals...done 464s DH segmentation table: 464s dhStart dhEnd dhNbrOfLoci dhMean 464s 1 185449813 247137334 1311 0.2295 464s startRow endRow 464s 1 10269 14655 464s Rows: 464s [1] 3 464s TCN segmentation rows: 464s startRow endRow 464s 3 10268 14658 464s TCN and DH segmentation rows: 464s startRow endRow 464s 3 10268 14658 464s startRow endRow 464s 1 10269 14655 464s startRow endRow 464s 1 1 7586 464s 2 7587 10267 464s TCN segmentation (expanded) rows: 464s startRow endRow 464s 1 1 7586 464s 2 7587 10267 464s 3 10268 14658 464s TCN and DH segmentation rows: 464s startRow endRow 464s 1 1 7586 464s 2 7587 10267 464s 3 10268 14658 464s startRow endRow 464s 1 10 7574 464s 2 7587 10263 464s 3 10269 14655 464s startRow endRow 464s 1 1 7586 464s 2 7587 10267 464s 3 10268 14658 464s Total CN segmentation table (expanded): 464s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 464s 3 1 185449813 247137334 4391 2.6341 1311 1311 464s (TCN,DH) segmentation for one total CN segment: 464s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 464s 3 3 1 1 185449813 247137334 4391 2.6341 1311 464s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 464s 3 1311 185449813 247137334 1311 0.2295 464s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 464s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 464s 1 1 1 1 554484 120908858 7586 1.3853 2108 464s 2 1 2 1 142693888 185449813 2681 2.0689 777 464s 3 1 3 1 185449813 247137334 4391 2.6341 1311 464s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 464s 1 2108 554484 120908858 2108 0.5116 464s 2 777 142693888 185449813 777 0.0973 464s 3 1311 185449813 247137334 1311 0.2295 464s Calculating (C1,C2) per segment... 464s Calculating (C1,C2) per segment...done 464s Number of segments: 3 464s Segmenting paired tumor-normal signals using Paired PSCBS...done 464s Post-segmenting TCNs... 464s Number of segments: 3 464s Number of chromosomes: 1 464s [1] 1 464s Chromosome 1 ('chr01') of 1... 464s Rows: 464s [1] 1 2 3 464s Number of segments: 3 464s TCN segment #1 ('1') of 3... 464s Nothing todo. Only one DH segmentation. Skipping. 464s TCN segment #1 ('1') of 3...done 464s TCN segment #2 ('2') of 3... 464s Nothing todo. Only one DH segmentation. Skipping. 464s TCN segment #2 ('2') of 3...done 464s TCN segment #3 ('3') of 3... 464s Nothing todo. Only one DH segmentation. Skipping. 464s TCN segment #3 ('3') of 3...done 464s Chromosome 1 ('chr01') of 1...done 464s Update (C1,C2) per segment... 464s Update (C1,C2) per segment...done 464s Post-segmenting TCNs...done 464s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 464s 1 1 1 1 554484 120908858 7586 1.3853 2108 464s 2 1 2 1 142693888 185449813 2681 2.0689 777 464s 3 1 3 1 185449813 247137334 4391 2.6341 1311 464s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 464s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 464s 2 777 142693888 185449813 777 0.0973 0.9337980 1.135102 464s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 464s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 464s 1 1 1 1 554484 120908858 7586 1.3853 2108 464s 2 1 2 1 142693888 185449813 2681 2.0689 777 464s 3 1 3 1 185449813 247137334 4391 2.6341 1311 464s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 464s 1 2108 554484 120908858 2108 0.5116 0.3382903 1.047010 464s 2 777 142693888 185449813 777 0.0973 0.9337980 1.135102 464s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 464s > print(fit) 464s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 464s 1 1 1 1 554484 120908858 7586 1.3853 2108 464s 2 1 2 1 142693888 185449813 2681 2.0689 777 464s 3 1 3 1 185449813 247137334 4391 2.6341 1311 464s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 464s 1 2108 2108 0.5116 0.3382903 1.047010 464s 2 777 777 0.0973 0.9337980 1.135102 464s 3 1311 1311 0.2295 1.0147870 1.619313 464s > 464s > fit1 <- fit 464s > fit2 <- renameChromosomes(fit1, from=1, to=2) 464s > fit <- c(fit1, fit2) 464s > knownSegments <- tileChromosomes(fit)$params$knownSegments 464s > 464s > segList <- seqOfSegmentsByDP(fit, verbose=-10) 464s Identifying optimal sets of segments via dynamic programming... 464s Shifting TCN levels for every second segment... 464s Split up into non-empty independent regions... 464s Chromosome #1 ('1') of 2... 464s Number of loci on chromosome: 14658 464s Known segments on chromosome: 464s chromosome start end 464s 1 1 -Inf 120908858 464s 2 1 142693888 Inf 464s Known segment #1 of 2... 464s chromosome start end 464s 1 1 -Inf 120908858 464s Known segment #1 of 2...done 464s Known segment #2 of 2... 464s chromosome start end 464s 2 1 142693888 Inf 464s Known segment #2 of 2...done 464s Chromosome #1 ('1') of 2...done 464s Chromosome #2 ('2') of 2... 464s Number of loci on chromosome: 14658 464s Known segments on chromosome: 464s chromosome start end 464s 3 2 -Inf 120908858 464s 4 2 142693888 Inf 464s Known segment #1 of 2... 464s chromosome start end 464s 3 2 -Inf 120908858 464s Known segment #1 of 2...done 464s Known segment #2 of 2... 464s chromosome start end 464s 4 2 142693888 Inf 464s Known segment #2 of 2...done 464s Chromosome #2 ('2') of 2...done 464s Number of independent non-empty regions: 4 464s Split up into non-empty independent regions...done 464s Shift every other region... 464s Shift every other region...done 464s Merge... 464s Merge...done 464s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 464s 1 1 1 1 554484 120908858 7586 101.3853 2108 464s 2 1 2 1 142693888 185449813 2681 2.0689 777 464s 3 1 3 1 185449813 247137334 4391 2.6341 1311 464s 4 2 1 1 554484 120908858 7586 101.3853 2108 464s 5 2 2 1 142693888 185449813 2681 2.0689 777 464s 6 2 3 1 185449813 247137334 4391 2.6341 1311 464s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 464s 1 2108 554484 120908858 2108 0.511612 24.757671 76.627587 464s 2 777 142693888 185449813 777 0.097300 0.933798 1.135102 464s 3 1311 185449813 247137334 1311 0.229500 1.014787 1.619313 464s 4 2108 554484 120908858 2108 0.511612 24.757671 76.627587 464s 5 777 142693888 185449813 777 0.097300 0.933798 1.135102 464s 6 1311 185449813 247137334 1311 0.229500 1.014787 1.619313 464s Shifting TCN levels for every second segment...done 464s Extracting signals for dynamic programming... 464s CT rho 464s Min. : 0.805 Min. :0.000 464s 1st Qu.: 2.407 1st Qu.:0.139 464s Median :100.927 Median :0.293 464s Mean : 53.638 Mean :0.347 464s 3rd Qu.:101.370 3rd Qu.:0.557 464s Max. :103.080 Max. :1.022 464s NA's :20924 464s Extracting signals for dynamic programming...done 464s Dynamic programming... 464s Number of "DP" change points: 5 464s int [1:5] 7586 10267 14658 22244 24925 464s List of 4 464s $ jump :List of 5 464s ..$ : num 22244 464s ..$ : num [1:2] 7586 14658 464s ..$ : num [1:3] 7586 14658 22244 464s ..$ : num [1:4] 7586 10267 14658 22244 464s ..$ : num [1:5] 7586 10267 14658 22244 24925 464s $ rse : num [1:6] 71699116 47249179 35852530 5945 5410 ... 464s $ kbest: num 4 464s $ V : num [1:6, 1:6] 1114 0 0 0 0 ... 464s Dynamic programming...done 464s Excluding cases where known segments no longer correct... 464s Number of independent non-empty regions: 4 464s List of 3 464s $ : num [1:3] 7586 14658 22244 464s $ : num [1:4] 7586 10267 14658 22244 464s $ : num [1:5] 7586 10267 14658 22244 24925 464s Excluding cases where known segments no longer correct...done 464s List of 3 464s $ :'data.frame': 4 obs. of 3 variables: 464s ..$ chromosome: int [1:4] 1 1 2 2 464s ..$ start : num [1:4] 5.54e+05 1.43e+08 5.54e+05 1.43e+08 464s ..$ end : num [1:4] 1.21e+08 2.47e+08 1.21e+08 2.47e+08 464s $ :'data.frame': 5 obs. of 3 variables: 464s ..$ chromosome: int [1:5] 1 1 1 2 2 464s ..$ start : num [1:5] 5.54e+05 1.43e+08 1.85e+08 5.54e+05 1.43e+08 464s ..$ end : num [1:5] 1.21e+08 1.85e+08 2.47e+08 1.21e+08 2.47e+08 464s $ :'data.frame': 6 obs. of 3 variables: 464s ..$ chromosome: int [1:6] 1 1 1 2 2 2 464s ..$ start : num [1:6] 5.54e+05 1.43e+08 1.85e+08 5.54e+05 1.43e+08 ... 464s ..$ end : num [1:6] 1.21e+08 1.85e+08 2.47e+08 1.21e+08 1.85e+08 ... 464s Sequence of number of "DP" change points: 464s [1] 3 4 5 464s Sequence of number of segments: 464s [1] 4 5 6 464s Sequence of number of "discovered" change points: 464s [1] 0 1 2 464s Identifying optimal sets of segments via dynamic programming...done 464s > K <- length(segList) 464s > ks <- seq(from=1, to=K, length.out=min(5,K)) 464s > subplots(length(ks), ncol=1, byrow=TRUE) 464s > par(mar=c(2,1,1,1)) 464s > for (kk in ks) { 464s + knownSegmentsKK <- segList[[kk]] 464s + fitKK <- resegment(fit, knownSegments=knownSegmentsKK, undoTCN=+Inf, undoDH=+Inf) 464s + plotTracks(fitKK, tracks="tcn,c1,c2", Clim=c(0,5), add=TRUE) 464s + abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 464s + stext(side=3, pos=0, sprintf("Number of segments: %d", nrow(knownSegmentsKK))) 464s + } # for (kk ...) 464s > 464s > proc.time() 464s user system elapsed 464s 3.913 0.094 4.036 464s Test segmentByPairedPSCBS,seqOfSegmentsByDP passed 464s 0 464s Begin test segmentByPairedPSCBS 471s + cat segmentByPairedPSCBS.Rout 471s 471s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 471s Copyright (C) 2024 The R Foundation for Statistical Computing 471s Platform: s390x-ibm-linux-gnu (64-bit) 471s 471s R is free software and comes with ABSOLUTELY NO WARRANTY. 471s You are welcome to redistribute it under certain conditions. 471s Type 'license()' or 'licence()' for distribution details. 471s 471s R is a collaborative project with many contributors. 471s Type 'contributors()' for more information and 471s 'citation()' on how to cite R or R packages in publications. 471s 471s Type 'demo()' for some demos, 'help()' for on-line help, or 471s 'help.start()' for an HTML browser interface to help. 471s Type 'q()' to quit R. 471s 471s [Previously saved workspace restored] 471s 471s > ########################################################### 471s > # This tests: 471s > # - segmentByPairedPSCBS(...) 471s > # - segmentByPairedPSCBS(..., knownSegments) 471s > # - tileChromosomes() 471s > # - plotTracks() 471s > ########################################################### 471s > library("PSCBS") 471s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 471s 471s Attaching package: 'PSCBS' 471s 471s The following objects are masked from 'package:base': 471s 471s append, load 471s 471s > 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > # Load SNP microarray data 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > data <- PSCBS::exampleData("paired.chr01") 471s > 471s > 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > # Paired PSCBS segmentation 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > # Drop single-locus outliers 471s > dataS <- dropSegmentationOutliers(data) 471s > 471s > # Run light-weight tests by default 471s > if (Sys.getenv("_R_CHECK_FULL_") == "") { 471s + # Use only every 5th data point 471s + dataS <- dataS[seq(from=1, to=nrow(data), by=5),] 471s + # Number of segments (for assertion) 471s + nSegs <- 4L 471s + } else { 471s + # Full tests 471s + nSegs <- 11L 471s + } 471s > 471s > str(dataS) 471s 'data.frame': 14670 obs. of 6 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : int 1145994 2941694 3710825 4240737 4276892 4464544 4714611 5095111 5034491 5158416 ... 471s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 471s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 471s $ CN : num 2.36 2.13 2.26 2.01 2.32 ... 471s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 471s > 471s > fig <- 1 471s > 471s > 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > # (a) Don't segment the centromere (and force a separator) 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > knownSegments <- data.frame( 471s + chromosome = c( 1, 1, 1), 471s + start = c( -Inf, NA, 141510003), 471s + end = c(120992603, NA, +Inf) 471s + ) 471s > 471s > 471s > # Paired PSCBS segmentation 471s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 471s + seed=0xBEEF, verbose=-10) 471s Segmenting paired tumor-normal signals using Paired PSCBS... 471s Calling genotypes from normal allele B fractions... 471s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 471s Called genotypes: 471s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 471s - attr(*, "modelFit")=List of 1 471s ..$ :List of 7 471s .. ..$ flavor : chr "density" 471s .. ..$ cn : int 2 471s .. ..$ nbrOfGenotypeGroups: int 3 471s .. ..$ tau : num [1:2] 0.315 0.677 471s .. ..$ n : int 14640 471s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. ..$ density: num [1:2] 0.522 0.552 471s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s muN 471s 0 0.5 1 471s 5221 4198 5251 471s Calling genotypes from normal allele B fractions...done 471s Normalizing betaT using betaN (TumorBoost)... 471s Normalized BAFs: 471s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 471s - attr(*, "modelFit")=List of 5 471s ..$ method : chr "normalizeTumorBoost" 471s ..$ flavor : chr "v4" 471s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 471s .. ..- attr(*, "modelFit")=List of 1 471s .. .. ..$ :List of 7 471s .. .. .. ..$ flavor : chr "density" 471s .. .. .. ..$ cn : int 2 471s .. .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. .. ..$ n : int 14640 471s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s ..$ preserveScale: logi FALSE 471s ..$ scaleFactor : num NA 471s Normalizing betaT using betaN (TumorBoost)...done 471s Setup up data... 471s 'data.frame': 14670 obs. of 7 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 471s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 471s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 471s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 471s ..- attr(*, "modelFit")=List of 5 471s .. ..$ method : chr "normalizeTumorBoost" 471s .. ..$ flavor : chr "v4" 471s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 471s .. .. ..- attr(*, "modelFit")=List of 1 471s .. .. .. ..$ :List of 7 471s .. .. .. .. ..$ flavor : chr "density" 471s .. .. .. .. ..$ cn : int 2 471s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. .. .. ..$ n : int 14640 471s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s .. ..$ preserveScale: logi FALSE 471s .. ..$ scaleFactor : num NA 471s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 471s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 471s ..- attr(*, "modelFit")=List of 1 471s .. ..$ :List of 7 471s .. .. ..$ flavor : chr "density" 471s .. .. ..$ cn : int 2 471s .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. ..$ n : int 14640 471s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s Setup up data...done 471s Dropping loci for which TCNs are missing... 471s Number of loci dropped: 12 471s Dropping loci for which TCNs are missing...done 471s Ordering data along genome... 471s 'data.frame': 14658 obs. of 7 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 554484 730720 782343 878522 916294 ... 471s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 471s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 471s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 471s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 471s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 471s Ordering data along genome...done 471s Keeping only current chromosome for 'knownSegments'... 471s Chromosome: 1 471s Known segments for this chromosome: 471s chromosome start end 471s 1 1 -Inf 120992603 471s 2 1 NA NA 471s 3 1 141510003 Inf 471s Keeping only current chromosome for 'knownSegments'...done 471s alphaTCN: 0.009 471s alphaDH: 0.001 471s Number of loci: 14658 471s Calculating DHs... 471s Number of SNPs: 14658 471s Number of heterozygous SNPs: 4196 (28.63%) 471s Normalized DHs: 471s num [1:14658] NA NA NA NA NA ... 471s Calculating DHs...done 471s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 471s Produced 2 seeds from this stream for future usage 471s Identification of change points by total copy numbers... 471s Segmenting by CBS... 471s Chromosome: 1 471s Segmenting multiple segments on current chromosome... 471s Number of segments: 3 471s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 471s Produced 3 seeds from this stream for future usage 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s Segmenting multiple segments on current chromosome...done 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 14658 obs. of 4 variables: 471s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 471s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 471s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 4 obs. of 6 variables: 471s ..$ sampleName: chr [1:4] NA NA NA NA 471s ..$ chromosome: int [1:4] 1 NA 1 1 471s ..$ start : num [1:4] 5.54e+05 NA 1.42e+08 1.85e+08 471s ..$ end : num [1:4] 1.21e+08 NA 1.85e+08 2.47e+08 471s ..$ nbrOfLoci : int [1:4] 7586 NA 2681 4391 471s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 471s $ segRows:'data.frame': 4 obs. of 2 variables: 471s ..$ startRow: int [1:4] 1 NA 7587 10268 471s ..$ endRow : int [1:4] 7586 NA 10267 14658 471s $ params :List of 5 471s ..$ alpha : num 0.009 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 471s .. ..$ chromosome: num [1:4] 1 1 2 1 471s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.42e+08 471s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 471s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.197 0.002 0.192 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s Identification of change points by total copy numbers...done 471s Restructure TCN segmentation results... 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 471s 1 1 554484 120992603 7586 1.3853 471s 2 NA NA NA NA NA 471s 3 1 141510003 185449813 2681 2.0689 471s 4 1 185449813 247137334 4391 2.6341 471s Number of TCN segments: 4 471s Restructure TCN segmentation results...done 471s Total CN segment #1 ([ 554484,1.20993e+08]) of 4... 471s Number of TCN loci in segment: 7586 471s Locus data for TCN segment: 471s 'data.frame': 7586 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 554484 730720 782343 878522 916294 ... 471s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 471s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 471s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 471s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 471s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 471s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 471s $ rho : num NA NA NA NA NA ... 471s Number of loci: 7586 471s Number of SNPs: 2108 (27.79%) 471s Number of heterozygous SNPs: 2108 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 7586 obs. of 4 variables: 471s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 471s ..$ y : num [1:7586] NA NA NA NA NA ... 471s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 554484 471s ..$ end : num 1.21e+08 471s ..$ nbrOfLoci : int 2108 471s ..$ mean : num 0.512 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 10 471s ..$ endRow : int 7574 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 554484 471s .. ..$ end : num 1.21e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.05 0.001 0.053 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 10 7574 471s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 10 7574 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 554484 120992603 2108 0.5116 471s startRow endRow 471s 1 10 7574 471s Rows: 471s [1] 1 471s TCN segmentation rows: 471s startRow endRow 471s 1 1 7586 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s startRow endRow 471s 1 10 7574 471s NULL 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s startRow endRow 471s 1 10 7574 471s startRow endRow 471s 1 1 7586 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 1 1 554484 120992603 7586 1.3853 2108 2108 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 1 2108 554484 120992603 2108 0.5116 471s Total CN segment #1 ([ 554484,1.20993e+08]) of 4...done 471s Total CN segment #2 ([ NA, NA]) of 4... 471s No signals to segment. Just a "splitter" segment. Skipping. 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s NA 2 1 NA NA NA NA NA 0 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s NA 0 NA NA 0 NA 471s Total CN segment #2 ([ NA, NA]) of 4...done 471s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4... 471s Number of TCN loci in segment: 2681 471s Locus data for TCN segment: 471s 'data.frame': 2681 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 471s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 471s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 471s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 471s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 471s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 471s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 471s $ rho : num 0.117 0.258 NA NA NA ... 471s Number of loci: 2681 471s Number of SNPs: 777 (28.98%) 471s Number of heterozygous SNPs: 777 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 2681 obs. of 4 variables: 471s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 471s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 471s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 1.42e+08 471s ..$ end : num 1.85e+08 471s ..$ nbrOfLoci : int 777 471s ..$ mean : num 0.0973 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 1 471s ..$ endRow : int 2677 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 1.42e+08 471s .. ..$ end : num 1.85e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.011 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 1 2677 471s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 7587 10263 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 141510003 185449813 777 0.0973 471s startRow endRow 471s 1 7587 10263 471s Rows: 471s [1] 3 471s TCN segmentation rows: 471s startRow endRow 471s 3 7587 10267 471s TCN and DH segmentation rows: 471s startRow endRow 471s 3 7587 10267 471s startRow endRow 471s 1 7587 10263 471s startRow endRow 471s 1 1 7586 471s NA NA NA 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s NA NA NA 471s 3 7587 10267 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s startRow endRow 471s 1 10 7574 471s 2 NA NA 471s 3 7587 10263 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 3 1 141510003 185449813 2681 2.0689 777 777 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 3 3 1 1 141510003 185449813 2681 2.0689 777 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 3 777 141510003 185449813 777 0.0973 471s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4...done 471s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 471s Number of TCN loci in segment: 4391 471s Locus data for TCN segment: 471s 'data.frame': 4391 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 471s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 471s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 471s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 471s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 471s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 471s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 471s $ rho : num NA 0.2186 NA 0.0503 NA ... 471s Number of loci: 4391 471s Number of SNPs: 1311 (29.86%) 471s Number of heterozygous SNPs: 1311 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 4391 obs. of 4 variables: 471s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 471s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 471s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 1.85e+08 471s ..$ end : num 2.47e+08 471s ..$ nbrOfLoci : int 1311 471s ..$ mean : num 0.23 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 2 471s ..$ endRow : int 4388 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 1.85e+08 471s .. ..$ end : num 2.47e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.02 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 2 4388 471s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 10269 14655 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 185449813 247137334 1311 0.2295 471s startRow endRow 471s 1 10269 14655 471s Rows: 471s [1] 4 471s TCN segmentation rows: 471s startRow endRow 471s 4 10268 14658 471s TCN and DH segmentation rows: 471s startRow endRow 471s 4 10268 14658 471s startRow endRow 471s 1 10269 14655 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s startRow endRow 471s 1 10 7574 471s 2 NA NA 471s 3 7587 10263 471s 4 10269 14655 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 4 1 185449813 247137334 4391 2.6341 1311 1311 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 4 4 1 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 4 1311 185449813 247137334 1311 0.2295 471s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 NA 2 1 NA NA NA NA 0 471s 3 1 3 1 141510003 185449813 2681 2.0689 777 471s 4 1 4 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 1 2108 554484 120992603 2108 0.5116 471s 2 0 NA NA 0 NA 471s 3 777 141510003 185449813 777 0.0973 471s 4 1311 185449813 247137334 1311 0.2295 471s Calculating (C1,C2) per segment... 471s Calculating (C1,C2) per segment...done 471s Number of segments: 4 471s Segmenting paired tumor-normal signals using Paired PSCBS...done 471s Post-segmenting TCNs... 471s Number of segments: 3 471s Number of chromosomes: 1 471s [1] 1 471s Chromosome 1 ('chr01') of 1... 471s Rows: 471s [1] 1 2 3 471s Number of segments: 3 471s TCN segment #1 ('1') of 3... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #1 ('1') of 3...done 471s TCN segment #2 ('3') of 3... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #2 ('3') of 3...done 471s TCN segment #3 ('4') of 3... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #3 ('4') of 3...done 471s Chromosome 1 ('chr01') of 1...done 471s Update (C1,C2) per segment... 471s Update (C1,C2) per segment...done 471s Post-segmenting TCNs...done 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 NA 2 1 NA NA NA NA 0 471s 3 1 3 1 141510003 185449813 2681 2.0689 777 471s 4 1 4 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 471s 2 0 NA NA 0 NA NA NA 471s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 471s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 NA 2 1 NA NA NA NA 0 471s 3 1 3 1 141510003 185449813 2681 2.0689 777 471s 4 1 4 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 471s 2 0 NA NA 0 NA NA NA 471s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 471s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 471s > print(fit) 471s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 NA 2 1 NA NA NA NA 0 471s 3 1 3 1 141510003 185449813 2681 2.0689 777 471s 4 1 4 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 2108 0.5116 0.3382903 1.047010 471s 2 0 0 NA NA NA 471s 3 777 777 0.0973 0.9337980 1.135102 471s 4 1311 1311 0.2295 1.0147870 1.619313 471s > 471s > # Plot results 471s > dev.set(2L) 471s null device 471s 1 471s > plotTracks(fit) 471s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 471s > 471s > # Sanity check 471s > stopifnot(nbrOfSegments(fit) == nSegs) 471s > 471s > fit1 <- fit 471s > 471s > 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > # (b) Segment also the centromere (which will become NAs) 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > knownSegments <- data.frame( 471s + chromosome = c( 1, 1, 1), 471s + start = c( -Inf, 120992604, 141510003), 471s + end = c(120992603, 141510002, +Inf) 471s + ) 471s > 471s > 471s > # Paired PSCBS segmentation 471s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 471s + seed=0xBEEF, verbose=-10) 471s Segmenting paired tumor-normal signals using Paired PSCBS... 471s Calling genotypes from normal allele B fractions... 471s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 471s Called genotypes: 471s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 471s - attr(*, "modelFit")=List of 1 471s ..$ :List of 7 471s .. ..$ flavor : chr "density" 471s .. ..$ cn : int 2 471s .. ..$ nbrOfGenotypeGroups: int 3 471s .. ..$ tau : num [1:2] 0.315 0.677 471s .. ..$ n : int 14640 471s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. ..$ density: num [1:2] 0.522 0.552 471s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s muN 471s 0 0.5 1 471s 5221 4198 5251 471s Calling genotypes from normal allele B fractions...done 471s Normalizing betaT using betaN (TumorBoost)... 471s Normalized BAFs: 471s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 471s - attr(*, "modelFit")=List of 5 471s ..$ method : chr "normalizeTumorBoost" 471s ..$ flavor : chr "v4" 471s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 471s .. ..- attr(*, "modelFit")=List of 1 471s .. .. ..$ :List of 7 471s .. .. .. ..$ flavor : chr "density" 471s .. .. .. ..$ cn : int 2 471s .. .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. .. ..$ n : int 14640 471s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s ..$ preserveScale: logi FALSE 471s ..$ scaleFactor : num NA 471s Normalizing betaT using betaN (TumorBoost)...done 471s Setup up data... 471s 'data.frame': 14670 obs. of 7 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 471s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 471s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 471s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 471s ..- attr(*, "modelFit")=List of 5 471s .. ..$ method : chr "normalizeTumorBoost" 471s .. ..$ flavor : chr "v4" 471s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 471s .. .. ..- attr(*, "modelFit")=List of 1 471s .. .. .. ..$ :List of 7 471s .. .. .. .. ..$ flavor : chr "density" 471s .. .. .. .. ..$ cn : int 2 471s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. .. .. ..$ n : int 14640 471s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s .. ..$ preserveScale: logi FALSE 471s .. ..$ scaleFactor : num NA 471s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 471s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 471s ..- attr(*, "modelFit")=List of 1 471s .. ..$ :List of 7 471s .. .. ..$ flavor : chr "density" 471s .. .. ..$ cn : int 2 471s .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. ..$ n : int 14640 471s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s Setup up data...done 471s Dropping loci for which TCNs are missing... 471s Number of loci dropped: 12 471s Dropping loci for which TCNs are missing...done 471s Ordering data along genome... 471s 'data.frame': 14658 obs. of 7 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 554484 730720 782343 878522 916294 ... 471s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 471s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 471s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 471s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 471s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 471s Ordering data along genome...done 471s Keeping only current chromosome for 'knownSegments'... 471s Chromosome: 1 471s Known segments for this chromosome: 471s chromosome start end 471s 1 1 -Inf 120992603 471s 2 1 120992604 141510002 471s 3 1 141510003 Inf 471s Keeping only current chromosome for 'knownSegments'...done 471s alphaTCN: 0.009 471s alphaDH: 0.001 471s Number of loci: 14658 471s Calculating DHs... 471s Number of SNPs: 14658 471s Number of heterozygous SNPs: 4196 (28.63%) 471s Normalized DHs: 471s num [1:14658] NA NA NA NA NA ... 471s Calculating DHs...done 471s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 471s Produced 2 seeds from this stream for future usage 471s Identification of change points by total copy numbers... 471s Segmenting by CBS... 471s Chromosome: 1 471s Segmenting multiple segments on current chromosome... 471s Number of segments: 3 471s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 471s Produced 3 seeds from this stream for future usage 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, -1924040949, -1632234809, -437763632, -1464377300, 676654412, 2080370711), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s Segmenting multiple segments on current chromosome...done 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 14658 obs. of 4 variables: 471s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 471s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 471s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 4 obs. of 6 variables: 471s ..$ sampleName: chr [1:4] NA NA NA NA 471s ..$ chromosome: num [1:4] 1 1 1 1 471s ..$ start : num [1:4] 5.54e+05 1.21e+08 1.42e+08 1.85e+08 471s ..$ end : num [1:4] 1.21e+08 1.42e+08 1.85e+08 2.47e+08 471s ..$ nbrOfLoci : int [1:4] 7586 0 2681 4391 471s ..$ mean : num [1:4] 1.39 NA 2.07 2.63 471s $ segRows:'data.frame': 4 obs. of 2 variables: 471s ..$ startRow: int [1:4] 1 NA 7587 10268 471s ..$ endRow : int [1:4] 7586 NA 10267 14658 471s $ params :List of 5 471s ..$ alpha : num 0.009 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 4 obs. of 3 variables: 471s .. ..$ chromosome: num [1:4] 1 1 2 1 471s .. ..$ start : num [1:4] -Inf -Inf -Inf 1.42e+08 471s .. ..$ end : num [1:4] 1.21e+08 Inf Inf Inf 471s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.189 0 0.19 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s Identification of change points by total copy numbers...done 471s Restructure TCN segmentation results... 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 471s 1 1 554484 120992603 7586 1.3853 471s 2 1 120992604 141510002 0 NA 471s 3 1 141510003 185449813 2681 2.0689 471s 4 1 185449813 247137334 4391 2.6341 471s Number of TCN segments: 4 471s Restructure TCN segmentation results...done 471s Total CN segment #1 ([ 554484,1.20993e+08]) of 4... 471s Number of TCN loci in segment: 7586 471s Locus data for TCN segment: 471s 'data.frame': 7586 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 554484 730720 782343 878522 916294 ... 471s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 471s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 471s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 471s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 471s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 471s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 471s $ rho : num NA NA NA NA NA ... 471s Number of loci: 7586 471s Number of SNPs: 2108 (27.79%) 471s Number of heterozygous SNPs: 2108 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 7586 obs. of 4 variables: 471s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 471s ..$ y : num [1:7586] NA NA NA NA NA ... 471s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 554484 471s ..$ end : num 1.21e+08 471s ..$ nbrOfLoci : int 2108 471s ..$ mean : num 0.512 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 10 471s ..$ endRow : int 7574 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 554484 471s .. ..$ end : num 1.21e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.049 0.001 0.053 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 10 7574 471s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 10 7574 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 554484 120992603 2108 0.5116 471s startRow endRow 471s 1 10 7574 471s Rows: 471s [1] 1 471s TCN segmentation rows: 471s startRow endRow 471s 1 1 7586 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s startRow endRow 471s 1 10 7574 471s NULL 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s startRow endRow 471s 1 10 7574 471s startRow endRow 471s 1 1 7586 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 1 1 554484 120992603 7586 1.3853 2108 2108 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 1 2108 554484 120992603 2108 0.5116 471s Total CN segment #1 ([ 554484,1.20993e+08]) of 4...done 471s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4... 471s Number of TCN loci in segment: 0 471s Locus data for TCN segment: 471s 'data.frame': 0 obs. of 9 variables: 471s $ chromosome: int 471s $ x : num 471s $ CT : num 471s $ betaT : num 471s $ betaTN : num 471s $ betaN : num 471s $ muN : num 471s $ index : int 471s $ rho : num 471s Number of loci: 0 471s Number of SNPs: 0 (NaN%) 471s Number of heterozygous SNPs: 0 (NaN%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: NA 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 0 obs. of 4 variables: 471s ..$ chromosome: int(0) 471s ..$ x : num(0) 471s ..$ y : num(0) 471s ..$ index : int(0) 471s $ output :'data.frame': 0 obs. of 6 variables: 471s ..$ sampleName: chr(0) 471s ..$ chromosome: num(0) 471s ..$ start : num(0) 471s ..$ end : num(0) 471s ..$ nbrOfLoci : int(0) 471s ..$ mean : num(0) 471s $ segRows:'data.frame': 0 obs. of 2 variables: 471s ..$ startRow: int(0) 471s ..$ endRow : int(0) 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 0 obs. of 3 variables: 471s .. ..$ chromosome: int(0) 471s .. ..$ start : num(0) 471s .. ..$ end : num(0) 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.001 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s [1] startRow endRow 471s <0 rows> (or 0-length row.names) 471s int(0) 471s DH segmentation rows: 471s [1] startRow endRow 471s <0 rows> (or 0-length row.names) 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s NA NA NA NA NA 471s startRow endRow 471s NA NA NA 471s Rows: 471s [1] 2 471s TCN segmentation rows: 471s startRow endRow 471s 2 NA NA 471s TCN and DH segmentation rows: 471s startRow endRow 471s 2 NA NA 471s startRow endRow 471s NA NA NA 471s startRow endRow 471s 1 1 7586 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s startRow endRow 471s 1 10 7574 471s 2 NA NA 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 2 1 120992604 141510002 0 NA 0 0 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 2 2 1 1 120992604 141510002 0 NA 0 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 2 0 NA NA NA NA 471s Total CN segment #2 ([1.20993e+08,1.4151e+08]) of 4...done 471s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4... 471s Number of TCN loci in segment: 2681 471s Locus data for TCN segment: 471s 'data.frame': 2681 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 471s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 471s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 471s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 471s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 471s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 471s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 471s $ rho : num 0.117 0.258 NA NA NA ... 471s Number of loci: 2681 471s Number of SNPs: 777 (28.98%) 471s Number of heterozygous SNPs: 777 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 2681 obs. of 4 variables: 471s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 471s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 471s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 1.42e+08 471s ..$ end : num 1.85e+08 471s ..$ nbrOfLoci : int 777 471s ..$ mean : num 0.0973 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 1 471s ..$ endRow : int 2677 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 1.42e+08 471s .. ..$ end : num 1.85e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.011 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 1 2677 471s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 7587 10263 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 141510003 185449813 777 0.0973 471s startRow endRow 471s 1 7587 10263 471s Rows: 471s [1] 3 471s TCN segmentation rows: 471s startRow endRow 471s 3 7587 10267 471s TCN and DH segmentation rows: 471s startRow endRow 471s 3 7587 10267 471s startRow endRow 471s 1 7587 10263 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s startRow endRow 471s 1 10 7574 471s 2 NA NA 471s 3 7587 10263 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 3 1 141510003 185449813 2681 2.0689 777 777 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 3 3 1 1 141510003 185449813 2681 2.0689 777 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 3 777 141510003 185449813 777 0.0973 471s Total CN segment #3 ([1.4151e+08,1.8545e+08]) of 4...done 471s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4... 471s Number of TCN loci in segment: 4391 471s Locus data for TCN segment: 471s 'data.frame': 4391 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 471s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 471s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 471s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 471s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 471s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 471s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 471s $ rho : num NA 0.2186 NA 0.0503 NA ... 471s Number of loci: 4391 471s Number of SNPs: 1311 (29.86%) 471s Number of heterozygous SNPs: 1311 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 4391 obs. of 4 variables: 471s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 471s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 471s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 1.85e+08 471s ..$ end : num 2.47e+08 471s ..$ nbrOfLoci : int 1311 471s ..$ mean : num 0.23 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 2 471s ..$ endRow : int 4388 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 1.85e+08 471s .. ..$ end : num 2.47e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0 0.022 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 2 4388 471s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 10269 14655 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 185449813 247137334 1311 0.2295 471s startRow endRow 471s 1 10269 14655 471s Rows: 471s [1] 4 471s TCN segmentation rows: 471s startRow endRow 471s 4 10268 14658 471s TCN and DH segmentation rows: 471s startRow endRow 471s 4 10268 14658 471s startRow endRow 471s 1 10269 14655 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s startRow endRow 471s 1 10 7574 471s 2 NA NA 471s 3 7587 10263 471s 4 10269 14655 471s startRow endRow 471s 1 1 7586 471s 2 NA NA 471s 3 7587 10267 471s 4 10268 14658 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 4 1 185449813 247137334 4391 2.6341 1311 1311 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 4 4 1 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 4 1311 185449813 247137334 1311 0.2295 471s Total CN segment #4 ([1.8545e+08,2.47137e+08]) of 4...done 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 1 2 1 120992604 141510002 0 NA 0 471s 3 1 3 1 141510003 185449813 2681 2.0689 777 471s 4 1 4 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 1 2108 554484 120992603 2108 0.5116 471s 2 0 NA NA NA NA 471s 3 777 141510003 185449813 777 0.0973 471s 4 1311 185449813 247137334 1311 0.2295 471s Calculating (C1,C2) per segment... 471s Calculating (C1,C2) per segment...done 471s Number of segments: 4 471s Segmenting paired tumor-normal signals using Paired PSCBS...done 471s Post-segmenting TCNs... 471s Number of segments: 4 471s Number of chromosomes: 1 471s [1] 1 471s Chromosome 1 ('chr01') of 1... 471s Rows: 471s [1] 1 2 3 4 471s Number of segments: 4 471s TCN segment #1 ('1') of 4... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #1 ('1') of 4...done 471s TCN segment #2 ('2') of 4... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #2 ('2') of 4...done 471s TCN segment #3 ('3') of 4... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #3 ('3') of 4...done 471s TCN segment #4 ('4') of 4... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #4 ('4') of 4...done 471s Chromosome 1 ('chr01') of 1...done 471s Update (C1,C2) per segment... 471s Update (C1,C2) per segment...done 471s Post-segmenting TCNs...done 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 1 2 1 120992604 141510002 0 NA 0 471s 3 1 3 1 141510003 185449813 2681 2.0689 777 471s 4 1 4 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 471s 2 0 NA NA NA NA NA NA 471s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 471s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 1 2 1 120992604 141510002 0 NA 0 471s 3 1 3 1 141510003 185449813 2681 2.0689 777 471s 4 1 4 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 471s 2 0 NA NA NA NA NA NA 471s 3 777 141510003 185449813 777 0.0973 0.9337980 1.135102 471s 4 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 471s > print(fit) 471s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 1 2 1 120992604 141510002 0 NA 0 471s 3 1 3 1 141510003 185449813 2681 2.0689 777 471s 4 1 4 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 2108 0.5116 0.3382903 1.047010 471s 2 0 NA NA NA NA 471s 3 777 777 0.0973 0.9337980 1.135102 471s 4 1311 1311 0.2295 1.0147870 1.619313 471s > 471s > # Plot results 471s > dev.set(3L) 471s pdf 471s 2 471s > plotTracks(fit) 471s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 471s > 471s > # Sanity check [TO FIX: See above] 471s > stopifnot(nbrOfSegments(fit) == nSegs) 471s > 471s > fit2 <- fit 471s > 471s > 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > # (c) Do not segment the centromere (without a separator) 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > knownSegments <- data.frame( 471s + chromosome = c( 1, 1), 471s + start = c( -Inf, 141510003), 471s + end = c(120992603, +Inf) 471s + ) 471s > 471s > # Paired PSCBS segmentation 471s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 471s + seed=0xBEEF, verbose=-10) 471s Segmenting paired tumor-normal signals using Paired PSCBS... 471s Calling genotypes from normal allele B fractions... 471s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 471s Called genotypes: 471s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 471s - attr(*, "modelFit")=List of 1 471s ..$ :List of 7 471s .. ..$ flavor : chr "density" 471s .. ..$ cn : int 2 471s .. ..$ nbrOfGenotypeGroups: int 3 471s .. ..$ tau : num [1:2] 0.315 0.677 471s .. ..$ n : int 14640 471s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. ..$ density: num [1:2] 0.522 0.552 471s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s muN 471s 0 0.5 1 471s 5221 4198 5251 471s Calling genotypes from normal allele B fractions...done 471s Normalizing betaT using betaN (TumorBoost)... 471s Normalized BAFs: 471s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 471s - attr(*, "modelFit")=List of 5 471s ..$ method : chr "normalizeTumorBoost" 471s ..$ flavor : chr "v4" 471s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 471s .. ..- attr(*, "modelFit")=List of 1 471s .. .. ..$ :List of 7 471s .. .. .. ..$ flavor : chr "density" 471s .. .. .. ..$ cn : int 2 471s .. .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. .. ..$ n : int 14640 471s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s ..$ preserveScale: logi FALSE 471s ..$ scaleFactor : num NA 471s Normalizing betaT using betaN (TumorBoost)...done 471s Setup up data... 471s 'data.frame': 14670 obs. of 7 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 471s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 471s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 471s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 471s ..- attr(*, "modelFit")=List of 5 471s .. ..$ method : chr "normalizeTumorBoost" 471s .. ..$ flavor : chr "v4" 471s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 471s .. .. ..- attr(*, "modelFit")=List of 1 471s .. .. .. ..$ :List of 7 471s .. .. .. .. ..$ flavor : chr "density" 471s .. .. .. .. ..$ cn : int 2 471s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. .. .. ..$ n : int 14640 471s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s .. ..$ preserveScale: logi FALSE 471s .. ..$ scaleFactor : num NA 471s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 471s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 471s ..- attr(*, "modelFit")=List of 1 471s .. ..$ :List of 7 471s .. .. ..$ flavor : chr "density" 471s .. .. ..$ cn : int 2 471s .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. ..$ n : int 14640 471s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s Setup up data...done 471s Dropping loci for which TCNs are missing... 471s Number of loci dropped: 12 471s Dropping loci for which TCNs are missing...done 471s Ordering data along genome... 471s 'data.frame': 14658 obs. of 7 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 554484 730720 782343 878522 916294 ... 471s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 471s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 471s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 471s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 471s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 471s Ordering data along genome...done 471s Keeping only current chromosome for 'knownSegments'... 471s Chromosome: 1 471s Known segments for this chromosome: 471s chromosome start end 471s 1 1 -Inf 120992603 471s 2 1 141510003 Inf 471s Keeping only current chromosome for 'knownSegments'...done 471s alphaTCN: 0.009 471s alphaDH: 0.001 471s Number of loci: 14658 471s Calculating DHs... 471s Number of SNPs: 14658 471s Number of heterozygous SNPs: 4196 (28.63%) 471s Normalized DHs: 471s num [1:14658] NA NA NA NA NA ... 471s Calculating DHs...done 471s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 471s Produced 2 seeds from this stream for future usage 471s Identification of change points by total copy numbers... 471s Segmenting by CBS... 471s Chromosome: 1 471s Segmenting multiple segments on current chromosome... 471s Number of segments: 2 471s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 471s Produced 2 seeds from this stream for future usage 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s Segmenting multiple segments on current chromosome...done 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 14658 obs. of 4 variables: 471s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 471s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 471s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 3 obs. of 6 variables: 471s ..$ sampleName: chr [1:3] NA NA NA 471s ..$ chromosome: int [1:3] 1 1 1 471s ..$ start : num [1:3] 5.54e+05 1.42e+08 1.85e+08 471s ..$ end : num [1:3] 1.21e+08 1.85e+08 2.47e+08 471s ..$ nbrOfLoci : int [1:3] 7586 2681 4391 471s ..$ mean : num [1:3] 1.39 2.07 2.63 471s $ segRows:'data.frame': 3 obs. of 2 variables: 471s ..$ startRow: int [1:3] 1 7587 10268 471s ..$ endRow : int [1:3] 7586 10267 14658 471s $ params :List of 5 471s ..$ alpha : num 0.009 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 2 obs. of 3 variables: 471s .. ..$ chromosome: num [1:2] 1 1 471s .. ..$ start : num [1:2] -Inf 1.42e+08 471s .. ..$ end : num [1:2] 1.21e+08 Inf 471s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.19 0 0.19 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s Identification of change points by total copy numbers...done 471s Restructure TCN segmentation results... 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 471s 1 1 554484 120992603 7586 1.3853 471s 2 1 141510003 185449813 2681 2.0689 471s 3 1 185449813 247137334 4391 2.6341 471s Number of TCN segments: 3 471s Restructure TCN segmentation results...done 471s Total CN segment #1 ([ 554484,1.20993e+08]) of 3... 471s Number of TCN loci in segment: 7586 471s Locus data for TCN segment: 471s 'data.frame': 7586 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 554484 730720 782343 878522 916294 ... 471s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 471s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 471s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 471s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 471s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 471s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 471s $ rho : num NA NA NA NA NA ... 471s Number of loci: 7586 471s Number of SNPs: 2108 (27.79%) 471s Number of heterozygous SNPs: 2108 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 7586 obs. of 4 variables: 471s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 471s ..$ y : num [1:7586] NA NA NA NA NA ... 471s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 554484 471s ..$ end : num 1.21e+08 471s ..$ nbrOfLoci : int 2108 471s ..$ mean : num 0.512 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 10 471s ..$ endRow : int 7574 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 554484 471s .. ..$ end : num 1.21e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.059 0.001 0.055 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 10 7574 471s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 10 7574 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 554484 120992603 2108 0.5116 471s startRow endRow 471s 1 10 7574 471s Rows: 471s [1] 1 471s TCN segmentation rows: 471s startRow endRow 471s 1 1 7586 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s startRow endRow 471s 1 10 7574 471s NULL 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 7587 10267 471s 3 10268 14658 471s startRow endRow 471s 1 10 7574 471s startRow endRow 471s 1 1 7586 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 1 1 554484 120992603 7586 1.3853 2108 2108 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 1 2108 554484 120992603 2108 0.5116 471s Total CN segment #1 ([ 554484,1.20993e+08]) of 3...done 471s Total CN segment #2 ([1.4151e+08,1.8545e+08]) of 3... 471s Number of TCN loci in segment: 2681 471s Locus data for TCN segment: 471s 'data.frame': 2681 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 471s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 471s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 471s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 471s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 471s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 471s $ index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 471s $ rho : num 0.117 0.258 NA NA NA ... 471s Number of loci: 2681 471s Number of SNPs: 777 (28.98%) 471s Number of heterozygous SNPs: 777 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 2681 obs. of 4 variables: 471s ..$ chromosome: int [1:2681] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:2681] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 471s ..$ y : num [1:2681] 0.117 0.258 NA NA NA ... 471s ..$ index : int [1:2681] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 1.42e+08 471s ..$ end : num 1.85e+08 471s ..$ nbrOfLoci : int 777 471s ..$ mean : num 0.0973 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 1 471s ..$ endRow : int 2677 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 1.42e+08 471s .. ..$ end : num 1.85e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.011 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 1 2677 471s int [1:2681] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 7587 10263 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 141510003 185449813 777 0.0973 471s startRow endRow 471s 1 7587 10263 471s Rows: 471s [1] 2 471s TCN segmentation rows: 471s startRow endRow 471s 2 7587 10267 471s TCN and DH segmentation rows: 471s startRow endRow 471s 2 7587 10267 471s startRow endRow 471s 1 7587 10263 471s startRow endRow 471s 1 1 7586 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s 2 7587 10267 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 7587 10267 471s 3 10268 14658 471s startRow endRow 471s 1 10 7574 471s 2 7587 10263 471s startRow endRow 471s 1 1 7586 471s 2 7587 10267 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 2 1 141510003 185449813 2681 2.0689 777 777 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 2 2 1 1 141510003 185449813 2681 2.0689 777 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 2 777 141510003 185449813 777 0.0973 471s Total CN segment #2 ([1.4151e+08,1.8545e+08]) of 3...done 471s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3... 471s Number of TCN loci in segment: 4391 471s Locus data for TCN segment: 471s 'data.frame': 4391 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 471s $ CT : num 2.93 2.15 2.82 2.93 2.46 ... 471s $ betaT : num 0.0811 0.5154 0.9473 0.3734 0.7506 ... 471s $ betaTN : num -0.169 0.609 1.028 0.525 0.968 ... 471s $ betaN : num 0.25 0.38 0.919 0.34 0.783 ... 471s $ muN : num 0 0.5 1 0.5 1 1 0 1 0 1 ... 471s $ index : int 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 471s $ rho : num NA 0.2186 NA 0.0503 NA ... 471s Number of loci: 4391 471s Number of SNPs: 1311 (29.86%) 471s Number of heterozygous SNPs: 1311 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 4391 obs. of 4 variables: 471s ..$ chromosome: int [1:4391] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:4391] 1.85e+08 1.85e+08 1.85e+08 1.86e+08 1.86e+08 ... 471s ..$ y : num [1:4391] NA 0.2186 NA 0.0503 NA ... 471s ..$ index : int [1:4391] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 1.85e+08 471s ..$ end : num 2.47e+08 471s ..$ nbrOfLoci : int 1311 471s ..$ mean : num 0.23 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 2 471s ..$ endRow : int 4388 471s $ params :List of 5 471s ..$ alpha : num 0.001 471s ..$ undo : num 0 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 1.85e+08 471s .. ..$ end : num 2.47e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.02 0.001 0.021 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 2 4388 471s int [1:4391] 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 10269 14655 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 185449813 247137334 1311 0.2295 471s startRow endRow 471s 1 10269 14655 471s Rows: 471s [1] 3 471s TCN segmentation rows: 471s startRow endRow 471s 3 10268 14658 471s TCN and DH segmentation rows: 471s startRow endRow 471s 3 10268 14658 471s startRow endRow 471s 1 10269 14655 471s startRow endRow 471s 1 1 7586 471s 2 7587 10267 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s 2 7587 10267 471s 3 10268 14658 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 7587 10267 471s 3 10268 14658 471s startRow endRow 471s 1 10 7574 471s 2 7587 10263 471s 3 10269 14655 471s startRow endRow 471s 1 1 7586 471s 2 7587 10267 471s 3 10268 14658 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 3 1 185449813 247137334 4391 2.6341 1311 1311 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 3 3 1 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 3 1311 185449813 247137334 1311 0.2295 471s Total CN segment #3 ([1.8545e+08,2.47137e+08]) of 3...done 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 1 2 1 141510003 185449813 2681 2.0689 777 471s 3 1 3 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 1 2108 554484 120992603 2108 0.5116 471s 2 777 141510003 185449813 777 0.0973 471s 3 1311 185449813 247137334 1311 0.2295 471s Calculating (C1,C2) per segment... 471s Calculating (C1,C2) per segment...done 471s Number of segments: 3 471s Segmenting paired tumor-normal signals using Paired PSCBS...done 471s Post-segmenting TCNs... 471s Number of segments: 3 471s Number of chromosomes: 1 471s [1] 1 471s Chromosome 1 ('chr01') of 1... 471s Rows: 471s [1] 1 2 3 471s Number of segments: 3 471s TCN segment #1 ('1') of 3... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #1 ('1') of 3...done 471s TCN segment #2 ('2') of 3... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #2 ('2') of 3...done 471s TCN segment #3 ('3') of 3... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #3 ('3') of 3...done 471s Chromosome 1 ('chr01') of 1...done 471s Update (C1,C2) per segment... 471s Update (C1,C2) per segment...done 471s Post-segmenting TCNs...done 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 1 2 1 141510003 185449813 2681 2.0689 777 471s 3 1 3 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 471s 2 777 141510003 185449813 777 0.0973 0.9337980 1.135102 471s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 1 2 1 141510003 185449813 2681 2.0689 777 471s 3 1 3 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 554484 120992603 2108 0.5116 0.3382903 1.047010 471s 2 777 141510003 185449813 777 0.0973 0.9337980 1.135102 471s 3 1311 185449813 247137334 1311 0.2295 1.0147870 1.619313 471s > print(fit) 471s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.3853 2108 471s 2 1 2 1 141510003 185449813 2681 2.0689 777 471s 3 1 3 1 185449813 247137334 4391 2.6341 1311 471s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 2108 0.5116 0.3382903 1.047010 471s 2 777 777 0.0973 0.9337980 1.135102 471s 3 1311 1311 0.2295 1.0147870 1.619313 471s > 471s > # Plot results 471s > dev.set(4L) 471s pdf 471s 2 471s > plotTracks(fit) 471s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 471s > 471s > # Sanity check 471s > stopifnot(nbrOfSegments(fit) == nSegs-1L) 471s > 471s > fit3 <- fit 471s > 471s > 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > # (d) Skip the identification of new change points 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > knownSegments <- data.frame( 471s + chromosome = c( 1, 1), 471s + start = c( -Inf, 141510003), 471s + end = c(120992603, +Inf) 471s + ) 471s > 471s > # Paired PSCBS segmentation 471s > fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments, 471s + undoTCN=Inf, undoDH=Inf, 471s + seed=0xBEEF, verbose=-10) 471s Segmenting paired tumor-normal signals using Paired PSCBS... 471s Calling genotypes from normal allele B fractions... 471s num [1:14670] 0.8274 0.5072 0.1671 0.1609 0.0421 ... 471s Called genotypes: 471s num [1:14670] 1 0.5 0 0 0 0 1 0 1 0.5 ... 471s - attr(*, "modelFit")=List of 1 471s ..$ :List of 7 471s .. ..$ flavor : chr "density" 471s .. ..$ cn : int 2 471s .. ..$ nbrOfGenotypeGroups: int 3 471s .. ..$ tau : num [1:2] 0.315 0.677 471s .. ..$ n : int 14640 471s .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. ..$ density: num [1:2] 0.522 0.552 471s ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s muN 471s 0 0.5 1 471s 5221 4198 5251 471s Calling genotypes from normal allele B fractions...done 471s Normalizing betaT using betaN (TumorBoost)... 471s Normalized BAFs: 471s num [1:14670] 0.9301 0.1667 0.0685 0.0995 0.0155 ... 471s - attr(*, "modelFit")=List of 5 471s ..$ method : chr "normalizeTumorBoost" 471s ..$ flavor : chr "v4" 471s ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 471s .. ..- attr(*, "modelFit")=List of 1 471s .. .. ..$ :List of 7 471s .. .. .. ..$ flavor : chr "density" 471s .. .. .. ..$ cn : int 2 471s .. .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. .. ..$ n : int 14640 471s .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s ..$ preserveScale: logi FALSE 471s ..$ scaleFactor : num NA 471s Normalizing betaT using betaN (TumorBoost)...done 471s Setup up data... 471s 'data.frame': 14670 obs. of 7 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1145994 2941694 3710825 4240737 4276892 ... 471s $ CT : num 1.63 1.4 1.41 1.17 1.16 ... 471s $ betaT : num 0.7574 0.169 0.2357 0.2604 0.0576 ... 471s $ betaTN : num 0.9301 0.1667 0.0685 0.0995 0.0155 ... 471s ..- attr(*, "modelFit")=List of 5 471s .. ..$ method : chr "normalizeTumorBoost" 471s .. ..$ flavor : chr "v4" 471s .. ..$ delta : num [1:14670] -0.17264 0.00239 0.1671 0.16085 0.04213 ... 471s .. .. ..- attr(*, "modelFit")=List of 1 471s .. .. .. ..$ :List of 7 471s .. .. .. .. ..$ flavor : chr "density" 471s .. .. .. .. ..$ cn : int 2 471s .. .. .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. .. .. ..$ n : int 14640 471s .. .. .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. .. .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s .. ..$ preserveScale: logi FALSE 471s .. ..$ scaleFactor : num NA 471s $ betaN : num 0.8274 0.5072 0.1671 0.1609 0.0421 ... 471s $ muN : num 1 0.5 0 0 0 0 1 0 1 0.5 ... 471s ..- attr(*, "modelFit")=List of 1 471s .. ..$ :List of 7 471s .. .. ..$ flavor : chr "density" 471s .. .. ..$ cn : int 2 471s .. .. ..$ nbrOfGenotypeGroups: int 3 471s .. .. ..$ tau : num [1:2] 0.315 0.677 471s .. .. ..$ n : int 14640 471s .. .. ..$ fit :Classes 'PeaksAndValleys' and 'data.frame': 5 obs. of 3 variables: 471s .. .. .. ..$ type : chr [1:5] "peak" "valley" "peak" "valley" ... 471s .. .. .. ..$ x : num [1:5] 0.104 0.315 0.499 0.677 0.885 471s .. .. .. ..$ density: num [1:5] 1.48 0.522 1.056 0.552 1.454 471s .. .. ..$ fitValleys :Classes 'PeaksAndValleys' and 'data.frame': 2 obs. of 3 variables: 471s .. .. .. ..$ type : chr [1:2] "valley" "valley" 471s .. .. .. ..$ x : num [1:2] 0.315 0.677 471s .. .. .. ..$ density: num [1:2] 0.522 0.552 471s .. ..- attr(*, "class")= chr [1:2] "NaiveGenotypeModelFit" "list" 471s Setup up data...done 471s Dropping loci for which TCNs are missing... 471s Number of loci dropped: 12 471s Dropping loci for which TCNs are missing...done 471s Ordering data along genome... 471s 'data.frame': 14658 obs. of 7 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 554484 730720 782343 878522 916294 ... 471s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 471s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 471s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 471s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 471s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 471s Ordering data along genome...done 471s Keeping only current chromosome for 'knownSegments'... 471s Chromosome: 1 471s Known segments for this chromosome: 471s chromosome start end 471s 1 1 -Inf 120992603 471s 2 1 141510003 Inf 471s Keeping only current chromosome for 'knownSegments'...done 471s alphaTCN: 0.009 471s alphaDH: 0.001 471s Number of loci: 14658 471s Calculating DHs... 471s Number of SNPs: 14658 471s Number of heterozygous SNPs: 4196 (28.63%) 471s Normalized DHs: 471s num [1:14658] NA NA NA NA NA ... 471s Calculating DHs...done 471s Random seed temporarily set (seed=c(48879), kind="L'Ecuyer-CMRG") 471s Produced 2 seeds from this stream for future usage 471s Identification of change points by total copy numbers... 471s Segmenting by CBS... 471s Chromosome: 1 471s Segmenting multiple segments on current chromosome... 471s Number of segments: 2 471s Random seed temporarily set (seed=c(10407, 1066287653, -51199871, 161854402, -1995183193, 1503453565, -747102133), kind="L'Ecuyer-CMRG") 471s Produced 2 seeds from this stream for future usage 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, -821273412, -52578226, 1415511586, 721384351, -665928286, 1316562960), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s Segmenting multiple segments on current chromosome...done 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 14658 obs. of 4 variables: 471s ..$ chromosome: int [1:14658] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:14658] 554484 730720 782343 878522 916294 ... 471s ..$ y : num [1:14658] 1.88 1.8 1.59 1.64 1.53 ... 471s ..$ index : int [1:14658] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 2 obs. of 6 variables: 471s ..$ sampleName: chr [1:2] NA NA 471s ..$ chromosome: num [1:2] 1 1 471s ..$ start : num [1:2] 5.54e+05 1.42e+08 471s ..$ end : num [1:2] 1.21e+08 2.47e+08 471s ..$ nbrOfLoci : int [1:2] 7586 7072 471s ..$ mean : num [1:2] 1.39 2.42 471s $ segRows:'data.frame': 2 obs. of 2 variables: 471s ..$ startRow: int [1:2] 1 7587 471s ..$ endRow : int [1:2] 7586 14658 471s $ params :List of 7 471s ..$ undo.splits : chr "sdundo" 471s ..$ undo.SD : num Inf 471s ..$ alpha : num 0.009 471s ..$ undo : num Inf 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 2 obs. of 3 variables: 471s .. ..$ chromosome: num [1:2] 1 1 471s .. ..$ start : num [1:2] -Inf 1.42e+08 471s .. ..$ end : num [1:2] 1.21e+08 Inf 471s ..$ seed : int [1:7] 10407 1066287653 -51199871 161854402 -1995183193 1503453565 -747102133 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0 0 0.002 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s Identification of change points by total copy numbers...done 471s Restructure TCN segmentation results... 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean 471s 1 1 554484 120992603 7586 1.385258 471s 2 1 141510003 247137334 7072 2.419824 471s Number of TCN segments: 2 471s Restructure TCN segmentation results...done 471s Total CN segment #1 ([ 554484,1.20993e+08]) of 2... 471s Number of TCN loci in segment: 7586 471s Locus data for TCN segment: 471s 'data.frame': 7586 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 554484 730720 782343 878522 916294 ... 471s $ CT : num 1.88 1.8 1.59 1.64 1.53 ... 471s $ betaT : num 0.0646 0.1672 0.9284 0.113 0.7209 ... 471s $ betaTN : num -0.0515 -0.1172 1.0194 0.031 0.8604 ... 471s $ betaN : num 0.116 0.284 0.909 0.082 0.86 ... 471s $ muN : num 0 0 1 0 1 1 1 0 1 0.5 ... 471s $ index : int 1 2 3 4 5 6 7 8 9 10 ... 471s $ rho : num NA NA NA NA NA ... 471s Number of loci: 7586 471s Number of SNPs: 2108 (27.79%) 471s Number of heterozygous SNPs: 2108 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 7586 obs. of 4 variables: 471s ..$ chromosome: int [1:7586] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:7586] 554484 730720 782343 878522 916294 ... 471s ..$ y : num [1:7586] NA NA NA NA NA ... 471s ..$ index : int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 554484 471s ..$ end : num 1.21e+08 471s ..$ nbrOfLoci : int 7586 471s ..$ mean : num 0.512 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 1 471s ..$ endRow : int 7586 471s $ params :List of 7 471s ..$ undo.splits : chr "sdundo" 471s ..$ undo.SD : num Inf 471s ..$ alpha : num 0.001 471s ..$ undo : num Inf 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 554484 471s .. ..$ end : num 1.21e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0 0 0.002 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 1 7586 471s int [1:7586] 1 2 3 4 5 6 7 8 9 10 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 554484 120992603 7586 0.511612 471s startRow endRow 471s 1 1 7586 471s Rows: 471s [1] 1 471s TCN segmentation rows: 471s startRow endRow 471s 1 1 7586 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s startRow endRow 471s 1 1 7586 471s NULL 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 7587 14658 471s startRow endRow 471s 1 1 7586 471s startRow endRow 471s 1 1 7586 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets 471s 1 1 554484 120992603 7586 1.385258 2108 2108 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.385258 2108 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 1 2108 554484 120992603 7586 0.511612 471s Total CN segment #1 ([ 554484,1.20993e+08]) of 2...done 471s Total CN segment #2 ([1.4151e+08,2.47137e+08]) of 2... 471s Number of TCN loci in segment: 7072 471s Locus data for TCN segment: 471s 'data.frame': 7072 obs. of 9 variables: 471s $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ... 471s $ x : num 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 471s $ CT : num 2.27 1.55 1.47 1.5 1.81 ... 471s $ betaT : num 0.34 0.55 0.048 0.813 0.575 ... 471s $ betaTN : num 0.441 0.629 -0.05 0.958 0.872 ... 471s $ betaN : num 0.3851 0.3933 0.0981 0.8552 0.7028 ... 471s $ muN : num 0.5 0.5 0 1 1 1 1 0.5 1 1 ... 471s $ + [ 0 != 0 ] 471s + echo Test segmentByPairedPSCBS passed 471s + echo 0 471s + echo Begin test weightedQuantile 471s + exitcode=0 471s + R CMD BATCH weightedQuantile.R 471s index : int 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 471s $ rho : num 0.117 0.258 NA NA NA ... 471s Number of loci: 7072 471s Number of SNPs: 2088 (29.52%) 471s Number of heterozygous SNPs: 2088 (100.00%) 471s Chromosome: 1 471s Segmenting DH signals... 471s Segmenting by CBS... 471s Chromosome: 1 471s Random seed temporarily set (seed=c(10407, 1797822437, 388243314, 91406689, -519578635, -1381924756, 1089253019), kind="L'Ecuyer-CMRG") 471s Segmenting by CBS...done 471s List of 4 471s $ data :'data.frame': 7072 obs. of 4 variables: 471s ..$ chromosome: int [1:7072] 1 1 1 1 1 1 1 1 1 1 ... 471s ..$ x : num [1:7072] 1.43e+08 1.43e+08 1.43e+08 1.43e+08 1.44e+08 ... 471s ..$ y : num [1:7072] 0.117 0.258 NA NA NA ... 471s ..$ index : int [1:7072] 1 2 3 4 5 6 7 8 9 10 ... 471s $ output :'data.frame': 1 obs. of 6 variables: 471s ..$ sampleName: chr NA 471s ..$ chromosome: int 1 471s ..$ start : num 1.42e+08 471s ..$ end : num 2.47e+08 471s ..$ nbrOfLoci : int 7072 471s ..$ mean : num 0.18 471s $ segRows:'data.frame': 1 obs. of 2 variables: 471s ..$ startRow: int 1 471s ..$ endRow : int 7072 471s $ params :List of 7 471s ..$ undo.splits : chr "sdundo" 471s ..$ undo.SD : num Inf 471s ..$ alpha : num 0.001 471s ..$ undo : num Inf 471s ..$ joinSegments : logi TRUE 471s ..$ knownSegments:'data.frame': 1 obs. of 3 variables: 471s .. ..$ chromosome: int 1 471s .. ..$ start : num 1.42e+08 471s .. ..$ end : num 2.47e+08 471s ..$ seed : int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s - attr(*, "class")= chr [1:2] "CBS" "AbstractCBS" 471s - attr(*, "processingTime")= 'proc_time' Named num [1:5] 0.01 0 0.001 0 0 471s ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ... 471s - attr(*, "pkgDetails")= chr "DNAcopy v1.76.0" 471s - attr(*, "randomSeed")= int [1:7] 10407 1797822437 388243314 91406689 -519578635 -1381924756 1089253019 471s DH segmentation (locally-indexed) rows: 471s startRow endRow 471s 1 1 7072 471s int [1:7072] 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 ... 471s DH segmentation rows: 471s startRow endRow 471s 1 7587 14658 471s Segmenting DH signals...done 471s DH segmentation table: 471s dhStart dhEnd dhNbrOfLoci dhMean 471s 1 141510003 247137334 7072 0.1803011 471s startRow endRow 471s 1 7587 14658 471s Rows: 471s [1] 2 471s TCN segmentation rows: 471s startRow endRow 471s 2 7587 14658 471s TCN and DH segmentation rows: 471s startRow endRow 471s 2 7587 14658 471s startRow endRow 471s 1 7587 14658 471s startRow endRow 471s 1 1 7586 471s TCN segmentation (expanded) rows: 471s startRow endRow 471s 1 1 7586 471s 2 7587 14658 471s TCN and DH segmentation rows: 471s startRow endRow 471s 1 1 7586 471s 2 7587 14658 471s startRow endRow 471s 1 1 7586 471s 2 7587 14658 471s startRow endRow 471s 1 1 7586 471s 2 7587 14658 471s Total CN segmentation table (expanded): 471s chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 2 1 141510003 247137334 7072 2.419824 2088 471s tcnNbrOfHets 471s 2 2088 471s (TCN,DH) segmentation for one total CN segment: 471s tcnId dhId chromosome tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 2 2 1 1 141510003 247137334 7072 2.419824 2088 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 2 2088 141510003 247137334 7072 0.1803011 471s Total CN segment #2 ([1.4151e+08,2.47137e+08]) of 2...done 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.385258 2108 471s 2 1 2 1 141510003 247137334 7072 2.419824 2088 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean 471s 1 2108 554484 120992603 7586 0.5116120 471s 2 2088 141510003 247137334 7072 0.1803011 471s Calculating (C1,C2) per segment... 471s Calculating (C1,C2) per segment...done 471s Number of segments: 2 471s Segmenting paired tumor-normal signals using Paired PSCBS...done 471s Post-segmenting TCNs... 471s Number of segments: 2 471s Number of chromosomes: 1 471s [1] 1 471s Chromosome 1 ('chr01') of 1... 471s Rows: 471s [1] 1 2 471s Number of segments: 2 471s TCN segment #1 ('1') of 2... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #1 ('1') of 2...done 471s TCN segment #2 ('2') of 2... 471s Nothing todo. Only one DH segmentation. Skipping. 471s TCN segment #2 ('2') of 2...done 471s Chromosome 1 ('chr01') of 1...done 471s Update (C1,C2) per segment... 471s Update (C1,C2) per segment...done 471s Post-segmenting TCNs...done 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.385258 2108 471s 2 1 2 1 141510003 247137334 7072 2.419824 2088 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 554484 120992603 7586 0.5116120 0.3382717 1.046986 471s 2 2088 141510003 247137334 7072 0.1803011 0.9917635 1.428060 471s chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.385258 2108 471s 2 1 2 1 141510003 247137334 7072 2.419824 2088 471s tcnNbrOfHets dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 554484 120992603 7586 0.5116120 0.3382717 1.046986 471s 2 2088 141510003 247137334 7072 0.1803011 0.9917635 1.428060 471s > print(fit) 471s chromosome tcnId dhId start end tcnNbrOfLoci tcnMean tcnNbrOfSNPs 471s 1 1 1 1 554484 120992603 7586 1.385258 2108 471s 2 1 2 1 141510003 247137334 7072 2.419824 2088 471s tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean 471s 1 2108 7586 0.5116120 0.3382717 1.046986 471s 2 2088 7072 0.1803011 0.9917635 1.428060 471s > 471s > # Plot results 471s > dev.set(5L) 471s pdf 471s 2 471s > plotTracks(fit) 471s > abline(v=c(knownSegments$start, knownSegments$end)/1e6, lty=3) 471s > 471s > # Sanity check 471s > stopifnot(nbrOfSegments(fit) == nrow(knownSegments)) 471s > 471s > fit4 <- fit 471s > 471s > 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > # Tiling multiple chromosomes 471s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 471s > # Simulate multiple chromosomes 471s > fit1 <- fit 471s > fit2 <- renameChromosomes(fit, from=1, to=2) 471s > fitM <- c(fit1, fit2) 471s > 471s > # Tile chromosomes 471s > fitT <- tileChromosomes(fitM) 471s > fitTb <- tileChromosomes(fitT) 471s > stopifnot(identical(fitTb, fitT)) 471s > 471s > # Plotting multiple chromosomes 471s > plotTracks(fitT) 471s > 471s > proc.time() 471s user system elapsed 471s 5.666 0.105 5.799 471s Test segmentByPairedPSCBS passed 471s 0 471s Begin test weightedQuantile 474s + cat weightedQuantile.Rout 474s 474s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 474s Copyright (C) 2024 The R Foundation for Statistical Computing 474s Platform: s390x-ibm-linux-gnu (64-bit) 474s 474s R is free software and comes with ABSOLUTELY NO WARRANTY. 474s You are welcome to redistribute it under certain conditions. 474s Type 'license()' or 'licence()' for distribution details. 474s 474s R is a collaborative project with many contributors. 474s Type 'contributors()' for more information and 474s 'citation()' on how to cite R or R packages in publications. 474s 474s Type 'demo()' for some demos, 'help()' for on-line help, or 474s 'help.start()' for an HTML browser interface to help. 474s Type 'q()' to quit R. 474s 474s [Previously saved workspace restored] 474s 474s > library("PSCBS") 474s PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help. 474s 474s Attaching package: 'PSCBS' 474s 474s The following objects are masked from 'package:base': 474s 474s append, load 474s 474s > library("stats") 474s > 474s > message("weightedQuantile() ...") 474s weightedQuantile() ... 474s > 474s > if (requireNamespace("Hmisc")) { 474s + message(" - assert identical results to Hmisc::wtd.quantile()") 474s + wtd.quantile <- Hmisc::wtd.quantile 474s + for (kk in 1:100) { 474s + n <- 5L + sample.int(995, size = 1L) 474s + x <- rnorm(n, mean = 0.0, sd = 1.0) 474s + w <- runif(n, min = 0.5, max = 2.0) ## Non-normalized weights 474s + probs <- c(0.0, 0.25, 0.50, 0.75, 1.0) 474s + q0 <- wtd.quantile(x, weights = w, probs = probs, normwt = TRUE) 474s + q <- weightedQuantile(x, w = w, probs = probs) 474s + if (!isTRUE(all.equal(q, q0))) { 474s + print(q0) 474s + print(q) 474s + stopifnot(all.equal(q, q0)) 474s + } 474s + } 474s + } 474s Loading required namespace: Hmisc 474s - assert identical results to Hmisc::wtd.quantile() 474s > 474s > message("weightedQuantile() ... DONE") 474s weightedQuantile() ... DONE 474s > 474s > proc.time() 474s user system elapsed 474s 1.379 0.094 1.483 474s Test weightedQuantile passed 474s 0 474s + [ 0 != 0 ] 474s + echo Test weightedQuantile passed 474s + echo 0 474s + rm -f /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/PairedPSCBS,boot.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/PairedPSCBS,boot.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/Rplots.pdf /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/findLargeGaps.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/findLargeGaps.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/randomSeed.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/randomSeed.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,calls.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,calls.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,futures.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,futures.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,median.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,median.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,prune.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,prune.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,report.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,report.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,shiftTCN.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,shiftTCN.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,weights.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS,weights.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByCBS.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByNonPairedPSCBS,medianDH.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByNonPairedPSCBS,medianDH.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,DH.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,DH.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,calls.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,calls.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,futures.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,futures.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,noNormalBAFs.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,noNormalBAFs.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,report.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,report.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,seqOfSegmentsByDP.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS,seqOfSegmentsByDP.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/segmentByPairedPSCBS.Rout /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/weightedQuantile.R /tmp/autopkgtest.iuHVDJ/autopkgtest_tmp/weightedQuantile.Rout 474s autopkgtest [01:32:20]: test run-unit-test: -----------------------] 475s run-unit-test PASS 475s autopkgtest [01:32:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 475s autopkgtest [01:32:21]: @@@@@@@@@@@@@@@@@@@@ summary 475s run-unit-test PASS 490s Creating nova instance adt-noble-s390x-r-cran-pscbs-20240328-012426-juju-7f2275-prod-proposed-migration-environment-2-9ea40968-96ef-4947-8f9b-7a3063c31717 from image adt/ubuntu-noble-s390x-server-20240327.img (UUID 4dc0c4c2-a3ae-40cd-8411-e7fc228c10ae)...