0s autopkgtest [12:18:09]: starting date and time: 2024-03-26 12:18:09+0000
  0s autopkgtest [12:18:09]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [12:18:09]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k5z5w4ip/out --timeout-copy=6000 --setup-commands 'dhclient || true; ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed --apt-upgrade r-cran-mcmc --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 -- lxd -r lxd-armhf-10.44.124.111 lxd-armhf-10.44.124.111:autopkgtest/ubuntu/noble/armhf
 47s autopkgtest [12:18:56]: testbed dpkg architecture: armhf
 49s autopkgtest [12:18:58]: testbed apt version: 2.7.12
 49s autopkgtest [12:18:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 51s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 51s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB]
 51s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB]
 51s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B]
 51s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4019 kB]
 52s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [669 kB]
 52s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B]
 52s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B]
 52s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B]
 52s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [4075 kB]
 52s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B]
 52s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [49.1 kB]
 52s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B]
 59s Fetched 9502 kB in 2s (3900 kB/s)
 59s Reading package lists...
 65s Get:1 http://ports.ubuntu.com/ubuntu-ports noble-proposed InRelease [117 kB]
 65s Get:2 http://ports.ubuntu.com/ubuntu-ports noble-proposed/main armhf Packages [669 kB]
 65s Get:3 http://ports.ubuntu.com/ubuntu-ports noble-proposed/main armhf c-n-f Metadata [2492 B]
 65s Get:4 http://ports.ubuntu.com/ubuntu-ports noble-proposed/universe armhf Packages [4073 kB]
 66s Get:5 http://ports.ubuntu.com/ubuntu-ports noble-proposed/universe armhf c-n-f Metadata [7776 B]
 66s Get:6 http://ports.ubuntu.com/ubuntu-ports noble-proposed/restricted armhf Packages [1372 B]
 66s Get:7 http://ports.ubuntu.com/ubuntu-ports noble-proposed/restricted armhf c-n-f Metadata [116 B]
 66s Get:8 http://ports.ubuntu.com/ubuntu-ports noble-proposed/multiverse armhf Packages [49.1 kB]
 66s Get:9 http://ports.ubuntu.com/ubuntu-ports noble-proposed/multiverse armhf c-n-f Metadata [116 B]
 72s Fetched 4919 kB in 2s (2919 kB/s)
 72s Reading package lists...
 79s sh: 1: dhclient: not found
 81s tee: /proc/self/fd/2: Permission denied
109s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble-proposed InRelease
109s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
109s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble InRelease
109s Hit:4 http://ftpmaster.internal/ubuntu noble-updates InRelease
109s Hit:5 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease
109s Hit:6 http://ftpmaster.internal/ubuntu noble-security InRelease
109s Hit:7 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease
109s Hit:8 http://ftpmaster.internal/ubuntu noble-proposed InRelease
109s Hit:9 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease
113s Reading package lists...
114s Reading package lists...
114s Building dependency tree...
114s Reading state information...
116s Calculating upgrade...
117s The following packages were automatically installed and are no longer required:
117s   linux-headers-6.8.0-11 python3-distutils python3-lib2to3
117s Use 'apt autoremove' to remove them.
119s The following packages will be REMOVED:
119s   libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1
119s   libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11
119s   libhogweed6 libmagic1 libnetplan0 libnettle8 libnpth0 libnvme1 libparted2
119s   libpcap0.8 libperl5.38 libpng16-16 libpsl5 libreadline8 libreiserfscore0
119s   libssl3 libtirpc3 libuv1 linux-headers-6.8.0-11-generic
119s The following NEW packages will be installed:
119s   libapt-pkg6.0t64 libarchive13t64 libatm1t64 libcurl3t64-gnutls libcurl4t64
119s   libdb5.3t64 libelf1t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64
119s   libglib2.0-0t64 libgnutls30t64 libgpgme11t64 libhogweed6t64 libmagic1t64
119s   libnetplan1 libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64
119s   libpcap0.8t64 libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64
119s   libreiserfscore0t64 libssl3t64 libtirpc3t64 libuv1t64 linux-headers-6.8.0-20
119s   linux-headers-6.8.0-20-generic xdg-user-dirs
119s The following packages have been kept back:
119s   multipath-tools
119s The following packages will be upgraded:
119s   apparmor apt apt-utils base-files bind9-dnsutils bind9-host bind9-libs
119s   binutils binutils-arm-linux-gnueabihf binutils-common bolt bsdextrautils
119s   bsdutils btrfs-progs cloud-init coreutils cryptsetup-bin curl dbus dbus-bin
119s   dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session
119s   debianutils dhcpcd-base dirmngr dmsetup dpkg dpkg-dev e2fsprogs
119s   e2fsprogs-l10n eject fdisk file fonts-ubuntu-console ftp fwupd gawk
119s   gcc-13-base gcc-14-base gir1.2-girepository-2.0 gir1.2-glib-2.0 gnupg
119s   gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv
119s   groff-base ibverbs-providers inetutils-telnet info initramfs-tools
119s   initramfs-tools-bin initramfs-tools-core install-info iproute2 jq keyboxd
119s   kmod kpartx krb5-locales libapparmor1 libaudit-common libaudit1 libbinutils
119s   libblkid1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3
119s   libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3
119s   libblockdev-utils3 libblockdev3 libbpf1 libbrotli1 libbsd0 libc-bin libc6
119s   libcap-ng0 libcom-err2 libcryptsetup12 libctf-nobfd0 libctf0 libdbus-1-3
119s   libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libevent-core-2.1-7
119s   libexpat1 libfdisk1 libfido2-1 libftdi1-2 libfwupd2 libgcc-s1
119s   libgirepository-1.0-1 libglib2.0-data libgssapi-krb5-2 libgudev-1.0-0
119s   libgusb2 libibverbs1 libjcat1 libjq1 libjson-glib-1.0-0
119s   libjson-glib-1.0-common libk5crypto3 libkmod2 libkrb5-3 libkrb5support0
119s   libldap-common libldap2 liblocale-gettext-perl liblzma5 libmagic-mgc
119s   libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 libnghttp2-14 libnsl2
119s   libnss-systemd libpam-modules libpam-modules-bin libpam-runtime
119s   libpam-systemd libpam0g libplymouth5 libpolkit-agent-1-0
119s   libpolkit-gobject-1-0 libproc2-0 libprotobuf-c1 libpython3-stdlib
119s   libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal
119s   libpython3.12-stdlib libqmi-glib5 libqmi-proxy libqrtr-glib0 librtmp1
119s   libsasl2-2 libsasl2-modules libsasl2-modules-db libseccomp2 libselinux1
119s   libsemanage-common libsemanage2 libsframe1 libslang2 libsmartcols1
119s   libsqlite3-0 libss2 libssh-4 libstdc++6 libsystemd-shared libsystemd0
119s   libtext-charwidth-perl libtext-iconv-perl libtirpc-common libudev1
119s   libudisks2-0 libusb-1.0-0 libuuid1 libvolume-key1 libxml2 libxmlb2 libxmuu1
119s   linux-headers-generic locales logsave lshw lsof man-db motd-news-config
119s   mount mtr-tiny netplan-generator netplan.io openssh-client openssh-server
119s   openssh-sftp-server openssl parted perl perl-base perl-modules-5.38
119s   pinentry-curses plymouth plymouth-theme-ubuntu-text procps psmisc
119s   python-apt-common python3 python3-apt python3-cryptography python3-dbus
119s   python3-distutils python3-gdbm python3-gi python3-lib2to3 python3-markupsafe
119s   python3-minimal python3-netplan python3-pkg-resources python3-pyrsistent
119s   python3-setuptools python3-typing-extensions python3-yaml python3.11
119s   python3.11-minimal python3.12 python3.12-minimal readline-common rsync
119s   rsyslog shared-mime-info sudo systemd systemd-dev systemd-resolved
119s   systemd-sysv systemd-timesyncd tcpdump telnet tnftp ubuntu-minimal
119s   ubuntu-pro-client ubuntu-pro-client-l10n ubuntu-standard udev udisks2
119s   usb.ids util-linux uuid-runtime vim-common vim-tiny wget xxd xz-utils zlib1g
119s 246 upgraded, 32 newly installed, 30 to remove and 1 not upgraded.
119s Need to get 109 MB of archives.
119s After this operation, 85.0 MB of additional disk space will be used.
119s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf motd-news-config all 13ubuntu8 [5098 B]
119s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240315-1ubuntu1 [47.0 kB]
119s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240315-1ubuntu1 [41.5 kB]
119s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240315-1ubuntu1 [714 kB]
119s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libc6 armhf 2.39-0ubuntu6 [2827 kB]
119s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf base-files armhf 13ubuntu8 [73.9 kB]
119s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu2 [102 kB]
119s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.13-0ubuntu2 [975 kB]
120s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu1 [49.2 kB]
120s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build6 [51.3 kB]
120s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12 armhf 3.12.2-4build3 [645 kB]
120s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libexpat1 armhf 2.6.1-2 [65.9 kB]
120s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12-minimal armhf 3.12.2-4build3 [1942 kB]
120s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-stdlib armhf 3.12.2-4build3 [1906 kB]
120s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-minimal armhf 3.12.2-4build3 [816 kB]
120s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf parted armhf 3.6-3.1build2 [39.4 kB]
120s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu2 [160 kB]
120s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2ubuntu1 [70.9 kB]
120s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.4-1ubuntu5 [103 kB]
120s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-timesyncd armhf 255.4-1ubuntu5 [36.0 kB]
120s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB]
120s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit-common all 1:3.1.2-2.1 [5674 B]
120s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.4-2build1 [13.5 kB]
120s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit1 armhf 1:3.1.2-2.1 [44.3 kB]
120s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.3-5ubuntu3 [62.0 kB]
120s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma5 armhf 5.6.0-0.2 [117 kB]
120s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap2 armhf 2.6.7+dfsg-1~exp1ubuntu6 [172 kB]
120s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudisks2-0 armhf 2.10.1-6 [143 kB]
120s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udisks2 armhf 2.10.1-6 [276 kB]
120s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf shared-mime-info armhf 2.4-1build1 [470 kB]
120s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-girepository-2.0 armhf 1.79.1-1ubuntu6 [24.8 kB]
120s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-glib-2.0 armhf 2.79.3-3ubuntu5 [182 kB]
120s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgirepository-1.0-1 armhf 1.79.1-1ubuntu6 [106 kB]
120s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gi armhf 3.47.0-3build1 [219 kB]
120s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dbus armhf 1.3.2-5build2 [94.7 kB]
120s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpgme11t64 armhf 1.18.0-4.1ubuntu3 [120 kB]
120s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libvolume-key1 armhf 0.3.12-7build1 [38.4 kB]
120s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnetplan1 armhf 1.0-1 [113 kB]
120s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-netplan armhf 1.0-1 [22.5 kB]
120s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan-generator armhf 1.0-1 [58.7 kB]
120s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-bin armhf 0.142ubuntu23 [20.3 kB]
120s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-core all 0.142ubuntu23 [50.1 kB]
120s Get:43 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-minimal armhf 1.536build1 [10.7 kB]
120s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools all 0.142ubuntu23 [9058 B]
120s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan.io armhf 1.0-1 [64.3 kB]
120s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmlb2 armhf 0.3.15-1build1 [57.0 kB]
120s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqrtr-glib0 armhf 1.2.2-1ubuntu3 [15.4 kB]
120s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-glib5 armhf 1.35.2-0ubuntu1 [908 kB]
120s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-proxy armhf 1.35.2-0ubuntu1 [5732 B]
120s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-agent-1-0 armhf 124-1ubuntu1 [15.3 kB]
120s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-gobject-1-0 armhf 124-1ubuntu1 [44.1 kB]
120s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-0t64 armhf 2.79.3-3ubuntu5 [1414 kB]
120s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjcat1 armhf 0.2.0-2build2 [30.4 kB]
120s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libarchive13t64 armhf 3.7.2-1.1ubuntu2 [330 kB]
120s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fwupd armhf 1.9.15-2 [4350 kB]
120s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client-l10n armhf 31.2.2 [19.4 kB]
120s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client armhf 31.2.2 [216 kB]
120s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11 armhf 3.11.8-1build4 [589 kB]
120s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11-minimal armhf 3.11.8-1build4 [1795 kB]
120s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-minimal armhf 3.11.8-1build4 [826 kB]
120s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-5ubuntu1 [19.0 kB]
120s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build2 [12.7 kB]
121s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build2 [8962 B]
121s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3.2 [1671 kB]
121s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu4 [15.0 kB]
121s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3.2 [3110 kB]
121s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gdbm armhf 3.12.2-3ubuntu1.1 [17.1 kB]
121s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf man-db armhf 2.12.0-3build4 [1196 kB]
121s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm6t64 armhf 1.23-5.1 [30.3 kB]
121s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm-compat4t64 armhf 1.23-5.1 [6208 B]
121s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38t64 armhf 5.38.2-3.2 [4101 kB]
121s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3.2 [231 kB]
121s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-6 [661 kB]
121s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-stdlib armhf 3.11.8-1build4 [1810 kB]
121s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf keyboxd armhf 2.4.4-2ubuntu15 [111 kB]
121s Get:76 http://ftpmaster.internal/ubuntu noble/main armhf libnpth0t64 armhf 1.6-3.1 [6940 B]
121s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu15 [224 kB]
121s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu15 [524 kB]
121s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-wks-client armhf 2.4.4-2ubuntu15 [87.4 kB]
121s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-utils armhf 2.4.4-2ubuntu15 [158 kB]
121s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu15 [235 kB]
121s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgsm armhf 2.4.4-2ubuntu15 [241 kB]
121s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreadline8t64 armhf 8.2-4 [129 kB]
121s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gawk armhf 1:5.2.1-2build2 [415 kB]
121s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fdisk armhf 2.39.3-9ubuntu2 [135 kB]
121s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu15 [115 kB]
121s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dirmngr armhf 2.4.4-2ubuntu15 [346 kB]
121s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg all 2.4.4-2ubuntu15 [359 kB]
121s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-apt armhf 2.7.7 [162 kB]
121s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.14 [210 kB]
121s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0t64 armhf 2.7.14 [986 kB]
121s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnettle8t64 armhf 3.9.1-2.2 [187 kB]
121s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libhogweed6t64 armhf 3.9.1-2.2 [187 kB]
121s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu2 [1046 kB]
121s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.14 [1368 kB]
121s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu8 [290 kB]
121s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfwupd2 armhf 1.9.15-2 [123 kB]
122s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.7 kB]
122s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main armhf wget armhf 1.21.4-1ubuntu2 [317 kB]
122s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tnftp armhf 20230507-2build1 [98.6 kB]
122s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpcap0.8t64 armhf 1.10.4-4.1ubuntu2 [137 kB]
122s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tcpdump armhf 4.99.4-3ubuntu2 [425 kB]
122s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.4-1ubuntu5 [2009 kB]
123s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-resolved armhf 255.4-1ubuntu5 [289 kB]
123s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sudo armhf 1.9.15p5-3ubuntu3 [936 kB]
123s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main armhf rsync armhf 3.2.7-1build1 [413 kB]
123s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-cryptography armhf 41.0.7-4build2 [788 kB]
123s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu11 [35.5 kB]
123s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-client armhf 1:9.6p1-3ubuntu11 [890 kB]
123s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-server armhf 1:9.6p1-3ubuntu11 [503 kB]
123s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20 all 6.8.0-20.20 [13.6 MB]
124s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20-generic armhf 6.8.0-20.20 [1287 kB]
124s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-generic armhf 6.8.0-20.20+1 [9610 B]
124s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3t64 armhf 3.0.13-0ubuntu2 [1558 kB]
124s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.4-1ubuntu5 [166 kB]
124s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.4-1ubuntu5 [3502 kB]
125s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udev armhf 255.4-1ubuntu5 [1852 kB]
125s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.4-1ubuntu5 [11.9 kB]
125s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnss-systemd armhf 255.4-1ubuntu5 [148 kB]
125s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-systemd armhf 255.4-1ubuntu5 [216 kB]
125s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.4-1ubuntu5 [410 kB]
125s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu3 [47.0 kB]
125s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.3-5ubuntu3 [261 kB]
125s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB]
125s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-user-session armhf 1.14.10-4ubuntu2 [9962 B]
125s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapparmor1 armhf 4.0.0-beta3-0ubuntu2 [45.0 kB]
125s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-bin armhf 1.14.10-4ubuntu2 [37.1 kB]
125s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB]
125s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus armhf 1.14.10-4ubuntu2 [28.1 kB]
125s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-daemon armhf 1.14.10-4ubuntu2 [109 kB]
125s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdbus-1-3 armhf 1.14.10-4ubuntu2 [190 kB]
125s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kmod armhf 31+20240202-2ubuntu4 [91.8 kB]
125s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu4 [44.9 kB]
125s Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu2 [171 kB]
125s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.5-1ubuntu2 [49.5 kB]
125s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu2 [34.4 kB]
125s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu2 [238 kB]
125s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu2 [196 kB]
125s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu2 [134 kB]
125s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu2 [135 kB]
125s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libparted2t64 armhf 3.6-3.1build2 [143 kB]
125s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu1 [599 kB]
125s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf pinentry-curses armhf 1.2.1-3ubuntu4 [36.7 kB]
125s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu2 [117 kB]
125s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-4 [56.4 kB]
125s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-yaml armhf 6.0.1-2build1 [117 kB]
125s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python-apt-common all 2.7.7 [19.8 kB]
125s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-setuptools all 68.1.2-2ubuntu1 [396 kB]
125s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB]
125s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.6ubuntu4 [1229 kB]
125s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-minimal armhf 3.12.2-0ubuntu1 [27.1 kB]
125s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3 armhf 3.12.2-0ubuntu1 [24.1 kB]
125s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-stdlib armhf 3.12.2-0ubuntu1 [9802 B]
125s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu2 [78.7 kB]
125s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main armhf groff-base armhf 1.23.0-3build1 [946 kB]
125s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-2 armhf 2.1.28+dfsg1-5ubuntu1 [49.7 kB]
125s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-utils3 armhf 3.1.0-1build1 [16.9 kB]
125s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-crypto3 armhf 3.1.0-1build1 [20.3 kB]
125s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB]
125s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dhcpcd-base armhf 1:10.0.6-1ubuntu2 [186 kB]
125s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main armhf eject armhf 2.39.3-9ubuntu2 [43.2 kB]
125s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbpf1 armhf 1:1.3.0-2build1 [146 kB]
125s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf iproute2 armhf 6.1.0-1ubuntu5 [1060 kB]
125s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libelf1t64 armhf 0.190-1.1build2 [49.9 kB]
125s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1 [8018 B]
125s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lsof armhf 4.95.0-1build2 [248 kB]
125s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl2 armhf 1.3.0-3build2 [36.5 kB]
125s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-6ubuntu1 [119 kB]
125s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5-3 armhf 1.20.1-6ubuntu1 [320 kB]
125s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5support0 armhf 1.20.1-6ubuntu1 [31.5 kB]
125s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libk5crypto3 armhf 1.20.1-6ubuntu1 [78.6 kB]
125s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB]
125s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1 [73.2 kB]
125s Get:174 http://ftpmaster.internal/ubuntu noble/main armhf libc-bin armhf 2.39-0ubuntu6 [530 kB]
125s Get:175 http://ftpmaster.internal/ubuntu noble/main armhf locales all 2.39-0ubuntu6 [4232 kB]
125s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libproc2-0 armhf 2:4.0.4-4ubuntu2 [49.0 kB]
125s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main armhf procps armhf 2:4.0.4-4ubuntu2 [700 kB]
125s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-tiny armhf 2:9.1.0016-1ubuntu6 [665 kB]
126s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-common all 2:9.1.0016-1ubuntu6 [385 kB]
126s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B]
126s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-fs3 armhf 3.1.0-1build1 [34.4 kB]
126s Get:182 http://ftpmaster.internal/ubuntu noble/main armhf libreiserfscore0t64 armhf 1:3.6.27-7.1 [66.2 kB]
126s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main armhf btrfs-progs armhf 6.6.3-1.1build1 [852 kB]
126s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu2 [201 kB]
126s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu2 [571 kB]
126s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-loop3 armhf 3.1.0-1build1 [6502 B]
126s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-mdraid3 armhf 3.1.0-1build1 [13.3 kB]
126s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-nvme3 armhf 3.1.0-1build1 [17.5 kB]
126s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnvme1t64 armhf 1.8-3 [67.5 kB]
126s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-part3 armhf 3.1.0-1build1 [16.4 kB]
126s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-swap3 armhf 3.1.0-1build1 [8894 B]
126s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev3 armhf 3.1.0-1build1 [42.9 kB]
126s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgudev-1.0-0 armhf 1:238-3ubuntu2 [13.6 kB]
126s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.3ubuntu2 [595 kB]
126s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-proxy armhf 1.31.2-0ubuntu2 [5748 B]
126s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-glib4 armhf 1.31.2-0ubuntu2 [216 kB]
126s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-common all 1.8.0-2build1 [4210 B]
126s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-0 armhf 1.8.0-2build1 [61.2 kB]
126s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libusb-1.0-0 armhf 2:1.0.27-1 [48.7 kB]
126s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgusb2 armhf 0.4.8-1build1 [34.6 kB]
126s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmm-glib0 armhf 1.23.4-0ubuntu1 [214 kB]
126s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libprotobuf-c1 armhf 1.4.1-1ubuntu3 [17.7 kB]
126s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbrotli1 armhf 1.1.0-2build1 [319 kB]
126s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnghttp2-14 armhf 1.59.0-1build1 [68.1 kB]
126s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssh-4 armhf 0.10.6-2build1 [169 kB]
126s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libibverbs1 armhf 50.0-2build1 [57.9 kB]
126s Get:207 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfido2-1 armhf 1.14.0-1build1 [75.8 kB]
126s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-3ubuntu3 [1280 kB]
126s Get:209 http://ftpmaster.internal/ubuntu noble/main armhf debianutils armhf 5.17 [88.9 kB]
126s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu2 [1216 kB]
126s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main armhf curl armhf 8.5.0-2ubuntu8 [219 kB]
126s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl4t64 armhf 8.5.0-2ubuntu8 [296 kB]
126s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main armhf file armhf 1:5.45-3 [21.1 kB]
126s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic-mgc armhf 1:5.45-3 [307 kB]
126s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic1t64 armhf 1:5.45-3 [81.4 kB]
126s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libplymouth5 armhf 24.004.60-1ubuntu6 [140 kB]
126s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng16-16t64 armhf 1.6.43-3 [166 kB]
126s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-host armhf 1:9.18.24-0ubuntu3 [47.4 kB]
126s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-dnsutils armhf 1:9.18.24-0ubuntu3 [149 kB]
127s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-libs armhf 1:9.18.24-0ubuntu3 [1148 kB]
127s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuv1t64 armhf 1.48.0-1.1 [82.9 kB]
127s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu2 [41.7 kB]
127s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebconfclient0 armhf 0.271ubuntu2 [10.8 kB]
127s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage-common all 3.5-1build4 [10.1 kB]
127s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage2 armhf 3.5-1build4 [84.5 kB]
127s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main armhf install-info armhf 7.1-3build1 [60.5 kB]
127s Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-21ubuntu1 [48.3 kB]
127s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu2 [14.7 kB]
127s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dmsetup armhf 2:1.02.185-3ubuntu2 [81.1 kB]
127s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/main armhf krb5-locales all 1.20.1-6ubuntu1 [13.8 kB]
127s Get:231 http://ftpmaster.internal/ubuntu noble/main armhf libbsd0 armhf 0.12.1-1 [36.6 kB]
127s Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB]
127s Get:233 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libslang2 armhf 2.3.3-3build1 [478 kB]
127s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main armhf rsyslog armhf 8.2312.0-3ubuntu7 [460 kB]
127s Get:235 http://ftpmaster.internal/ubuntu noble/main armhf xdg-user-dirs armhf 0.18-1 [17.3 kB]
127s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xxd armhf 2:9.1.0016-1ubuntu6 [62.5 kB]
127s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apparmor armhf 4.0.0-beta3-0ubuntu2 [562 kB]
127s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ftp all 20230507-2build1 [4724 B]
127s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main armhf inetutils-telnet armhf 2:2.5-3ubuntu3 [90.7 kB]
127s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main armhf info armhf 7.1-3build1 [127 kB]
127s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmuu1 armhf 2:1.1.3-3build1 [8004 B]
127s Get:242 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lshw armhf 02.19.git.2021.06.19.996aaad9c7-2build2 [310 kB]
127s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mtr-tiny armhf 0.95-1.1build1 [51.7 kB]
127s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu6 [9818 B]
127s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth armhf 24.004.60-1ubuntu6 [142 kB]
127s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.7-1 [176 kB]
127s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main armhf telnet all 0.17+2.5-3ubuntu3 [3682 B]
127s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xz-utils armhf 5.6.0-0.2 [271 kB]
127s Get:249 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-standard armhf 1.536build1 [10.7 kB]
127s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main armhf usb.ids all 2024.03.18-1 [223 kB]
127s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf-nobfd0 armhf 2.42-4ubuntu1 [88.0 kB]
127s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf0 armhf 2.42-4ubuntu1 [87.7 kB]
127s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.42-4ubuntu1 [2925 kB]
127s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbinutils armhf 2.42-4ubuntu1 [464 kB]
127s Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils armhf 2.42-4ubuntu1 [3078 B]
127s Get:256 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-common armhf 2.42-4ubuntu1 [217 kB]
127s Get:257 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsframe1 armhf 2.42-4ubuntu1 [13.1 kB]
127s Get:258 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bolt armhf 0.9.6-2build1 [138 kB]
127s Get:259 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cryptsetup-bin armhf 2:2.7.0-1ubuntu2 [214 kB]
127s Get:260 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.6ubuntu4 [1074 kB]
127s Get:261 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.6ubuntu4 [268 kB]
127s Get:262 http://ftpmaster.internal/ubuntu noble/main armhf fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB]
127s Get:263 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB]
127s Get:264 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ibverbs-providers armhf 50.0-2build1 [27.4 kB]
127s Get:265 http://ftpmaster.internal/ubuntu noble-proposed/main armhf jq armhf 1.7.1-3 [65.2 kB]
127s Get:266 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjq1 armhf 1.7.1-3 [156 kB]
127s Get:267 http://ftpmaster.internal/ubuntu noble/main armhf libatm1t64 armhf 1:2.5.1-5.1 [20.0 kB]
127s Get:268 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB]
127s Get:269 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libftdi1-2 armhf 1.5-6build4 [25.7 kB]
127s Get:270 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB]
127s Get:271 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules armhf 2.1.28+dfsg1-5ubuntu1 [61.3 kB]
127s Get:272 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-distutils all 3.12.2-3ubuntu1.1 [133 kB]
127s Get:273 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-lib2to3 all 3.12.2-3ubuntu1.1 [79.1 kB]
127s Get:274 http://ftpmaster.internal/ubuntu noble/main armhf python3-markupsafe armhf 2.1.5-1build1 [12.1 kB]
127s Get:275 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pyrsistent armhf 0.20.0-1build1 [53.0 kB]
127s Get:276 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-typing-extensions all 4.10.0-1 [60.7 kB]
127s Get:277 http://ftpmaster.internal/ubuntu noble/main armhf cloud-init all 24.1.2-0ubuntu1 [597 kB]
127s Get:278 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kpartx armhf 0.9.4-5ubuntu6 [31.5 kB]
143s Preconfiguring packages ...
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144s Preparing to unpack .../motd-news-config_13ubuntu8_all.deb ...
144s Unpacking motd-news-config (13ubuntu8) over (13ubuntu7) ...
144s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_armhf.deb ...
144s Unpacking gcc-14-base:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
144s Setting up gcc-14-base:armhf (14-20240315-1ubuntu1) ...
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144s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_armhf.deb ...
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144s Setting up libgcc-s1:armhf (14-20240315-1ubuntu1) ...
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144s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_armhf.deb ...
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145s Setting up libstdc++6:armhf (14-20240315-1ubuntu1) ...
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145s Preparing to unpack .../libc6_2.39-0ubuntu6_armhf.deb ...
145s Unpacking libc6:armhf (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
145s Setting up libc6:armhf (2.39-0ubuntu6) ...
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146s Preparing to unpack .../base-files_13ubuntu8_armhf.deb ...
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148s motd-news.service is a disabled or a static unit not running, not starting it.
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148s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_armhf.deb ...
148s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ...
148s Setting up bsdutils (1:2.39.3-9ubuntu2) ...
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148s Preparing to unpack .../openssl_3.0.13-0ubuntu2_armhf.deb ...
148s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
148s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_armhf.deb ...
148s Unpacking zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ...
148s Setting up zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) ...
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148s Preparing to unpack .../0-librtmp1_2.4+20151223.gitfa8646d.1-2build6_armhf.deb ...
148s Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ...
148s Preparing to unpack .../1-python3.12_3.12.2-4build3_armhf.deb ...
149s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ...
149s Preparing to unpack .../2-libexpat1_2.6.1-2_armhf.deb ...
149s Unpacking libexpat1:armhf (2.6.1-2) over (2.6.0-1) ...
149s Preparing to unpack .../3-python3.12-minimal_3.12.2-4build3_armhf.deb ...
149s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ...
149s Preparing to unpack .../4-libpython3.12-stdlib_3.12.2-4build3_armhf.deb ...
149s Unpacking libpython3.12-stdlib:armhf (3.12.2-4build3) over (3.12.2-1) ...
149s Preparing to unpack .../5-libpython3.12-minimal_3.12.2-4build3_armhf.deb ...
149s Unpacking libpython3.12-minimal:armhf (3.12.2-4build3) over (3.12.2-1) ...
150s Preparing to unpack .../6-parted_3.6-3.1build2_armhf.deb ...
150s Unpacking parted (3.6-3.1build2) over (3.6-3) ...
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150s Removing libparted2:armhf (3.6-3) ...
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150s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_armhf.deb ...
150s Unpacking libblkid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
150s Setting up libblkid1:armhf (2.39.3-9ubuntu2) ...
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150s Preparing to unpack .../libselinux1_3.5-2ubuntu1_armhf.deb ...
150s Unpacking libselinux1:armhf (3.5-2ubuntu1) over (3.5-2build1) ...
150s Setting up libselinux1:armhf (3.5-2ubuntu1) ...
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150s Preparing to unpack .../systemd-dev_255.4-1ubuntu5_all.deb ...
150s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
150s Preparing to unpack .../systemd-timesyncd_255.4-1ubuntu5_armhf.deb ...
150s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
150s Preparing to unpack .../dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ...
150s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
151s Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ...
151s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ...
151s Setting up libaudit-common (1:3.1.2-2.1) ...
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151s Preparing to unpack .../libcap-ng0_0.8.4-2build1_armhf.deb ...
151s Unpacking libcap-ng0:armhf (0.8.4-2build1) over (0.8.4-2) ...
151s Setting up libcap-ng0:armhf (0.8.4-2build1) ...
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151s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_armhf.deb ...
151s Unpacking libaudit1:armhf (1:3.1.2-2.1) over (1:3.1.2-2) ...
151s Setting up libaudit1:armhf (1:3.1.2-2.1) ...
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151s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_armhf.deb ...
151s Unpacking libpam0g:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
151s Setting up libpam0g:armhf (1.5.3-5ubuntu3) ...
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151s Preparing to unpack .../liblzma5_5.6.0-0.2_armhf.deb ...
151s Unpacking liblzma5:armhf (5.6.0-0.2) over (5.4.5-0.3) ...
151s Setting up liblzma5:armhf (5.6.0-0.2) ...
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152s Preparing to unpack .../0-libldap2_2.6.7+dfsg-1~exp1ubuntu6_armhf.deb ...
152s Unpacking libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ...
152s Preparing to unpack .../1-libudisks2-0_2.10.1-6_armhf.deb ...
152s Unpacking libudisks2-0:armhf (2.10.1-6) over (2.10.1-1ubuntu2) ...
152s Preparing to unpack .../2-udisks2_2.10.1-6_armhf.deb ...
152s Unpacking udisks2 (2.10.1-6) over (2.10.1-1ubuntu2) ...
152s Preparing to unpack .../3-shared-mime-info_2.4-1build1_armhf.deb ...
152s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ...
152s Preparing to unpack .../4-gir1.2-girepository-2.0_1.79.1-1ubuntu6_armhf.deb ...
152s Unpacking gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ...
152s Preparing to unpack .../5-gir1.2-glib-2.0_2.79.3-3ubuntu5_armhf.deb ...
152s Unpacking gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
152s Preparing to unpack .../6-libgirepository-1.0-1_1.79.1-1ubuntu6_armhf.deb ...
152s Unpacking libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ...
152s Preparing to unpack .../7-python3-gi_3.47.0-3build1_armhf.deb ...
153s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ...
153s Preparing to unpack .../8-python3-dbus_1.3.2-5build2_armhf.deb ...
153s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ...
153s dpkg: libgpgme11:armhf: dependency problems, but removing anyway as you requested:
153s  libvolume-key1:armhf depends on libgpgme11 (>= 1.4.1).
153s  libjcat1:armhf depends on libgpgme11 (>= 1.2.0).
153s 
153s (Reading database ... 
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153s Removing libgpgme11:armhf (1.18.0-4ubuntu1) ...
153s Selecting previously unselected package libgpgme11t64:armhf.
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153s Preparing to unpack .../00-libgpgme11t64_1.18.0-4.1ubuntu3_armhf.deb ...
153s Unpacking libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ...
153s Preparing to unpack .../01-libvolume-key1_0.3.12-7build1_armhf.deb ...
153s Unpacking libvolume-key1:armhf (0.3.12-7build1) over (0.3.12-5build2) ...
153s Selecting previously unselected package libnetplan1:armhf.
153s Preparing to unpack .../02-libnetplan1_1.0-1_armhf.deb ...
153s Unpacking libnetplan1:armhf (1.0-1) ...
154s Preparing to unpack .../03-python3-netplan_1.0-1_armhf.deb ...
154s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ...
154s Preparing to unpack .../04-netplan-generator_1.0-1_armhf.deb ...
154s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
154s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ...
154s Preparing to unpack .../05-initramfs-tools-bin_0.142ubuntu23_armhf.deb ...
154s Unpacking initramfs-tools-bin (0.142ubuntu23) over (0.142ubuntu20) ...
154s Preparing to unpack .../06-initramfs-tools-core_0.142ubuntu23_all.deb ...
154s Unpacking initramfs-tools-core (0.142ubuntu23) over (0.142ubuntu20) ...
154s Preparing to unpack .../07-ubuntu-minimal_1.536build1_armhf.deb ...
154s Unpacking ubuntu-minimal (1.536build1) over (1.536) ...
154s Preparing to unpack .../08-initramfs-tools_0.142ubuntu23_all.deb ...
154s Unpacking initramfs-tools (0.142ubuntu23) over (0.142ubuntu20) ...
154s Preparing to unpack .../09-netplan.io_1.0-1_armhf.deb ...
154s Unpacking netplan.io (1.0-1) over (0.107.1-3) ...
154s Preparing to unpack .../10-libxmlb2_0.3.15-1build1_armhf.deb ...
154s Unpacking libxmlb2:armhf (0.3.15-1build1) over (0.3.15-1) ...
154s Preparing to unpack .../11-libqrtr-glib0_1.2.2-1ubuntu3_armhf.deb ...
154s Unpacking libqrtr-glib0:armhf (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ...
154s Preparing to unpack .../12-libqmi-glib5_1.35.2-0ubuntu1_armhf.deb ...
154s Unpacking libqmi-glib5:armhf (1.35.2-0ubuntu1) over (1.34.0-2) ...
154s Preparing to unpack .../13-libqmi-proxy_1.35.2-0ubuntu1_armhf.deb ...
154s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ...
154s Preparing to unpack .../14-libpolkit-agent-1-0_124-1ubuntu1_armhf.deb ...
154s Unpacking libpolkit-agent-1-0:armhf (124-1ubuntu1) over (124-1) ...
154s Preparing to unpack .../15-libpolkit-gobject-1-0_124-1ubuntu1_armhf.deb ...
154s Unpacking libpolkit-gobject-1-0:armhf (124-1ubuntu1) over (124-1) ...
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155s Removing libnetplan0:armhf (0.107.1-3) ...
155s dpkg: libglib2.0-0:armhf: dependency problems, but removing anyway as you requested:
155s  libmm-glib0:armhf depends on libglib2.0-0 (>= 2.62.0).
155s  libmbim-proxy depends on libglib2.0-0 (>= 2.56).
155s  libmbim-glib4:armhf depends on libglib2.0-0 (>= 2.56).
155s  libjson-glib-1.0-0:armhf depends on libglib2.0-0 (>= 2.75.3).
155s  libjcat1:armhf depends on libglib2.0-0 (>= 2.75.3).
155s  libgusb2:armhf depends on libglib2.0-0 (>= 2.75.3).
155s  libgudev-1.0-0:armhf depends on libglib2.0-0 (>= 2.38.0).
155s  libfwupd2:armhf depends on libglib2.0-0 (>= 2.79.0).
155s  libblockdev3:armhf depends on libglib2.0-0 (>= 2.42.2).
155s  libblockdev-utils3:armhf depends on libglib2.0-0 (>= 2.75.3).
155s  libblockdev-swap3:armhf depends on libglib2.0-0 (>= 2.42.2).
155s  libblockdev-part3:armhf depends on libglib2.0-0 (>= 2.42.2).
155s  libblockdev-nvme3:armhf depends on libglib2.0-0 (>= 2.42.2).
155s  libblockdev-mdraid3:armhf depends on libglib2.0-0 (>= 2.42.2).
155s  libblockdev-loop3:armhf depends on libglib2.0-0 (>= 2.42.2).
155s  libblockdev-fs3:armhf depends on libglib2.0-0 (>= 2.42.2).
155s  libblockdev-crypto3:armhf depends on libglib2.0-0 (>= 2.42.2).
155s  fwupd depends on libglib2.0-0 (>= 2.79.0).
155s  bolt depends on libglib2.0-0 (>= 2.56.0).
155s 
155s Removing libglib2.0-0:armhf (2.79.2-1~ubuntu1) ...
155s Selecting previously unselected package libglib2.0-0t64:armhf.
155s (Reading database ... 
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155s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_armhf.deb ...
155s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:armhf.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled...
155s removed '/var/lib/dpkg/info/libglib2.0-0:armhf.postrm'
155s Unpacking libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ...
155s Preparing to unpack .../libjcat1_0.2.0-2build2_armhf.deb ...
155s Unpacking libjcat1:armhf (0.2.0-2build2) over (0.2.0-2) ...
177s dpkg: libarchive13:armhf: dependency problems, but removing anyway as you requested:
177s  fwupd depends on libarchive13 (>= 3.2.1).
177s 
177s (Reading database ... 
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177s Removing libarchive13:armhf (3.7.2-1ubuntu2) ...
177s Selecting previously unselected package libarchive13t64:armhf.
177s (Reading database ... 
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177s Preparing to unpack .../00-libarchive13t64_3.7.2-1.1ubuntu2_armhf.deb ...
177s Unpacking libarchive13t64:armhf (3.7.2-1.1ubuntu2) ...
177s Preparing to unpack .../01-fwupd_1.9.15-2_armhf.deb ...
177s Unpacking fwupd (1.9.15-2) over (1.9.14-1) ...
178s Preparing to unpack .../02-ubuntu-pro-client-l10n_31.2.2_armhf.deb ...
178s Unpacking ubuntu-pro-client-l10n (31.2.2) over (31.1) ...
178s Preparing to unpack .../03-ubuntu-pro-client_31.2.2_armhf.deb ...
178s Unpacking ubuntu-pro-client (31.2.2) over (31.1) ...
178s Preparing to unpack .../04-python3.11_3.11.8-1build4_armhf.deb ...
178s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ...
178s Preparing to unpack .../05-python3.11-minimal_3.11.8-1build4_armhf.deb ...
178s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ...
179s Preparing to unpack .../06-libpython3.11-minimal_3.11.8-1build4_armhf.deb ...
179s Unpacking libpython3.11-minimal:armhf (3.11.8-1build4) over (3.11.8-1) ...
179s Preparing to unpack .../07-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu1_armhf.deb ...
179s Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
179s Preparing to unpack .../08-libtext-iconv-perl_1.7-8build2_armhf.deb ...
179s Unpacking libtext-iconv-perl:armhf (1.7-8build2) over (1.7-8build1) ...
179s Preparing to unpack .../09-libtext-charwidth-perl_0.04-11build2_armhf.deb ...
179s Unpacking libtext-charwidth-perl:armhf (0.04-11build2) over (0.04-11build1) ...
179s Preparing to unpack .../10-perl-base_5.38.2-3.2_armhf.deb ...
179s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ...
180s Setting up perl-base (5.38.2-3.2) ...
180s (Reading database ... 
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180s Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu4_armhf.deb ...
180s Unpacking liblocale-gettext-perl (1.07-6ubuntu4) over (1.07-6build1) ...
180s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ...
180s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ...
181s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu1.1_armhf.deb ...
181s Unpacking python3-gdbm:armhf (3.12.2-3ubuntu1.1) over (3.11.5-1) ...
181s Preparing to unpack .../man-db_2.12.0-3build4_armhf.deb ...
181s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ...
181s dpkg: libgdbm-compat4:armhf: dependency problems, but removing anyway as you requested:
181s  libperl5.38:armhf depends on libgdbm-compat4 (>= 1.18-3).
181s 
181s (Reading database ... 
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181s Removing libgdbm-compat4:armhf (1.23-5) ...
181s dpkg: libgdbm6:armhf: dependency problems, but removing anyway as you requested:
181s  libperl5.38:armhf depends on libgdbm6 (>= 1.21).
181s 
181s Removing libgdbm6:armhf (1.23-5) ...
181s Selecting previously unselected package libgdbm6t64:armhf.
181s (Reading database ... 
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181s Preparing to unpack .../libgdbm6t64_1.23-5.1_armhf.deb ...
181s Unpacking libgdbm6t64:armhf (1.23-5.1) ...
181s Selecting previously unselected package libgdbm-compat4t64:armhf.
182s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_armhf.deb ...
182s Unpacking libgdbm-compat4t64:armhf (1.23-5.1) ...
182s dpkg: libperl5.38:armhf: dependency problems, but removing anyway as you requested:
182s  perl depends on libperl5.38 (= 5.38.2-3).
182s 
182s (Reading database ... 
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182s Removing libperl5.38:armhf (5.38.2-3) ...
182s Selecting previously unselected package libperl5.38t64:armhf.
182s (Reading database ... 
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182s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_armhf.deb ...
182s Unpacking libperl5.38t64:armhf (5.38.2-3.2) ...
182s Preparing to unpack .../perl_5.38.2-3.2_armhf.deb ...
182s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ...
182s dpkg: libdb5.3:armhf: dependency problems, but removing anyway as you requested:
182s  libpython3.11-stdlib:armhf depends on libdb5.3.
182s  libpam-modules:armhf depends on libdb5.3.
182s  iproute2 depends on libdb5.3.
182s  apt-utils depends on libdb5.3.
182s 
182s (Reading database ... 
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182s Removing libdb5.3:armhf (5.3.28+dfsg2-4) ...
183s Selecting previously unselected package libdb5.3t64:armhf.
183s (Reading database ... 
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183s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_armhf.deb ...
183s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-6) ...
183s Preparing to unpack .../libpython3.11-stdlib_3.11.8-1build4_armhf.deb ...
183s Unpacking libpython3.11-stdlib:armhf (3.11.8-1build4) over (3.11.8-1) ...
183s Preparing to unpack .../keyboxd_2.4.4-2ubuntu15_armhf.deb ...
183s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
183s dpkg: libnpth0:armhf: dependency problems, but removing anyway as you requested:
183s  gpgv depends on libnpth0 (>= 0.90).
183s  gpgsm depends on libnpth0 (>= 0.90).
183s  gpg-agent depends on libnpth0 (>= 0.90).
183s  gpg depends on libnpth0 (>= 0.90).
183s  dirmngr depends on libnpth0 (>= 0.90).
183s 
183s (Reading database ... 
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183s Removing libnpth0:armhf (1.6-3build2) ...
183s Selecting previously unselected package libnpth0t64:armhf.
183s (Reading database ... 
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183s Preparing to unpack .../libnpth0t64_1.6-3.1_armhf.deb ...
183s Unpacking libnpth0t64:armhf (1.6-3.1) ...
183s Setting up libnpth0t64:armhf (1.6-3.1) ...
183s (Reading database ... 
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183s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_armhf.deb ...
183s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
183s Setting up gpgv (2.4.4-2ubuntu15) ...
184s (Reading database ... 
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184s Preparing to unpack .../gpg_2.4.4-2ubuntu15_armhf.deb ...
184s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
184s Preparing to unpack .../gpg-wks-client_2.4.4-2ubuntu15_armhf.deb ...
184s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
184s Preparing to unpack .../gnupg-utils_2.4.4-2ubuntu15_armhf.deb ...
184s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
184s Preparing to unpack .../gpg-agent_2.4.4-2ubuntu15_armhf.deb ...
184s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
184s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_armhf.deb ...
184s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
184s dpkg: libreadline8:armhf: dependency problems, but removing anyway as you requested:
184s  gpgconf depends on libreadline8 (>= 6.0).
184s  gawk depends on libreadline8 (>= 6.0).
184s  fdisk depends on libreadline8 (>= 6.0).
184s 
184s (Reading database ... 
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184s Removing libreadline8:armhf (8.2-3) ...
184s Selecting previously unselected package libreadline8t64:armhf.
184s (Reading database ... 
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184s Preparing to unpack .../libreadline8t64_8.2-4_armhf.deb ...
184s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64'
184s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64'
184s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64'
184s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64'
184s Unpacking libreadline8t64:armhf (8.2-4) ...
184s Setting up libreadline8t64:armhf (8.2-4) ...
184s (Reading database ... 
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184s Preparing to unpack .../0-gawk_1%3a5.2.1-2build2_armhf.deb ...
184s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ...
184s Preparing to unpack .../1-fdisk_2.39.3-9ubuntu2_armhf.deb ...
184s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
185s Preparing to unpack .../2-gpgconf_2.4.4-2ubuntu15_armhf.deb ...
185s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
185s Preparing to unpack .../3-dirmngr_2.4.4-2ubuntu15_armhf.deb ...
185s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
185s Preparing to unpack .../4-gnupg_2.4.4-2ubuntu15_all.deb ...
185s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
185s Preparing to unpack .../5-python3-apt_2.7.7_armhf.deb ...
185s Unpacking python3-apt (2.7.7) over (2.7.6) ...
185s Preparing to unpack .../6-apt-utils_2.7.14_armhf.deb ...
185s Unpacking apt-utils (2.7.14) over (2.7.12) ...
185s dpkg: libapt-pkg6.0:armhf: dependency problems, but removing anyway as you requested:
185s  apt depends on libapt-pkg6.0 (>= 2.7.12).
185s 
185s (Reading database ... 
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185s Removing libapt-pkg6.0:armhf (2.7.12) ...
185s dpkg: libnettle8:armhf: dependency problems, but removing anyway as you requested:
185s  libhogweed6:armhf depends on libnettle8.
185s  libgnutls30:armhf depends on libnettle8 (>= 3.9~).
185s  libcurl3-gnutls:armhf depends on libnettle8.
185s 
185s Removing libnettle8:armhf (3.9.1-2) ...
185s Selecting previously unselected package libapt-pkg6.0t64:armhf.
185s (Reading database ... 
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185s Preparing to unpack .../libapt-pkg6.0t64_2.7.14_armhf.deb ...
185s Unpacking libapt-pkg6.0t64:armhf (2.7.14) ...
186s Setting up libapt-pkg6.0t64:armhf (2.7.14) ...
186s Selecting previously unselected package libnettle8t64:armhf.
186s (Reading database ... 
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186s Preparing to unpack .../libnettle8t64_3.9.1-2.2_armhf.deb ...
186s Unpacking libnettle8t64:armhf (3.9.1-2.2) ...
186s Setting up libnettle8t64:armhf (3.9.1-2.2) ...
186s dpkg: libhogweed6:armhf: dependency problems, but removing anyway as you requested:
186s  libgnutls30:armhf depends on libhogweed6 (>= 3.6).
186s 
186s (Reading database ... 
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186s Removing libhogweed6:armhf (3.9.1-2) ...
186s Selecting previously unselected package libhogweed6t64:armhf.
186s (Reading database ... 
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186s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_armhf.deb ...
186s Unpacking libhogweed6t64:armhf (3.9.1-2.2) ...
186s Setting up libhogweed6t64:armhf (3.9.1-2.2) ...
186s dpkg: libgnutls30:armhf: dependency problems, but removing anyway as you requested:
186s  libcurl3-gnutls:armhf depends on libgnutls30 (>= 3.8.2).
186s  apt depends on libgnutls30 (>= 3.8.1).
186s 
186s (Reading database ... 
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186s Removing libgnutls30:armhf (3.8.3-1ubuntu1) ...
186s Selecting previously unselected package libgnutls30t64:armhf.
186s (Reading database ... 
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186s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_armhf.deb ...
186s Unpacking libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ...
186s Setting up libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ...
186s (Reading database ... 
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186s Preparing to unpack .../archives/apt_2.7.14_armhf.deb ...
186s Unpacking apt (2.7.14) over (2.7.12) ...
187s Setting up apt (2.7.14) ...
188s dpkg: libcurl3-gnutls:armhf: dependency problems, but removing anyway as you requested:
188s  libfwupd2:armhf depends on libcurl3-gnutls (>= 7.63.0).
188s 
188s (Reading database ... 
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188s Removing libcurl3-gnutls:armhf (8.5.0-2ubuntu2) ...
188s Selecting previously unselected package libcurl3t64-gnutls:armhf.
188s (Reading database ... 
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188s Preparing to unpack .../libcurl3t64-gnutls_8.5.0-2ubuntu8_armhf.deb ...
188s Unpacking libcurl3t64-gnutls:armhf (8.5.0-2ubuntu8) ...
188s Preparing to unpack .../libfwupd2_1.9.15-2_armhf.deb ...
188s Unpacking libfwupd2:armhf (1.9.15-2) over (1.9.14-1) ...
188s dpkg: libpsl5:armhf: dependency problems, but removing anyway as you requested:
188s  wget depends on libpsl5 (>= 0.16.0).
188s  libcurl4:armhf depends on libpsl5 (>= 0.16.0).
188s 
188s (Reading database ... 
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188s Removing libpsl5:armhf (0.21.2-1build1) ...
188s Selecting previously unselected package libpsl5t64:armhf.
188s (Reading database ... 
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188s Preparing to unpack .../libpsl5t64_0.21.2-1.1_armhf.deb ...
188s Unpacking libpsl5t64:armhf (0.21.2-1.1) ...
188s Preparing to unpack .../wget_1.21.4-1ubuntu2_armhf.deb ...
188s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ...
188s Preparing to unpack .../tnftp_20230507-2build1_armhf.deb ...
188s Unpacking tnftp (20230507-2build1) over (20230507-2) ...
188s dpkg: libpcap0.8:armhf: dependency problems, but removing anyway as you requested:
188s  tcpdump depends on libpcap0.8 (>= 1.9.1).
188s 
188s (Reading database ... 
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188s Removing libpcap0.8:armhf (1.10.4-4ubuntu3) ...
189s Selecting previously unselected package libpcap0.8t64:armhf.
189s (Reading database ... 
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189s Preparing to unpack .../00-libpcap0.8t64_1.10.4-4.1ubuntu2_armhf.deb ...
189s Unpacking libpcap0.8t64:armhf (1.10.4-4.1ubuntu2) ...
189s Preparing to unpack .../01-tcpdump_4.99.4-3ubuntu2_armhf.deb ...
189s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ...
189s Preparing to unpack .../02-libsystemd-shared_255.4-1ubuntu5_armhf.deb ...
189s Unpacking libsystemd-shared:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
189s Preparing to unpack .../03-systemd-resolved_255.4-1ubuntu5_armhf.deb ...
189s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
189s Preparing to unpack .../04-sudo_1.9.15p5-3ubuntu3_armhf.deb ...
189s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ...
189s Preparing to unpack .../05-rsync_3.2.7-1build1_armhf.deb ...
189s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ...
189s Preparing to unpack .../06-python3-cryptography_41.0.7-4build2_armhf.deb ...
189s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ...
189s Preparing to unpack .../07-openssh-sftp-server_1%3a9.6p1-3ubuntu11_armhf.deb ...
189s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
190s Preparing to unpack .../08-openssh-client_1%3a9.6p1-3ubuntu11_armhf.deb ...
190s Unpacking openssh-client (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
190s Preparing to unpack .../09-openssh-server_1%3a9.6p1-3ubuntu11_armhf.deb ...
211s Unpacking openssh-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
211s Selecting previously unselected package linux-headers-6.8.0-20.
211s Preparing to unpack .../10-linux-headers-6.8.0-20_6.8.0-20.20_all.deb ...
211s Unpacking linux-headers-6.8.0-20 (6.8.0-20.20) ...
217s Selecting previously unselected package linux-headers-6.8.0-20-generic.
217s Preparing to unpack .../11-linux-headers-6.8.0-20-generic_6.8.0-20.20_armhf.deb ...
217s Unpacking linux-headers-6.8.0-20-generic (6.8.0-20.20) ...
221s Preparing to unpack .../12-linux-headers-generic_6.8.0-20.20+1_armhf.deb ...
221s Unpacking linux-headers-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ...
221s (Reading database ... 
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221s Removing linux-headers-6.8.0-11-generic (6.8.0-11.11) ...
222s dpkg: libssl3:armhf: dependency problems, but removing anyway as you requested:
222s  systemd depends on libssl3 (>= 3.0.0).
222s  libssh-4:armhf depends on libssl3 (>= 3.0.0).
222s  libsasl2-modules:armhf depends on libssl3 (>= 3.0.0).
222s  libsasl2-2:armhf depends on libssl3 (>= 3.0.0).
222s  libnvme1 depends on libssl3 (>= 3.0.0).
222s  libkrb5-3:armhf depends on libssl3 (>= 3.0.0).
222s  libkmod2:armhf depends on libssl3 (>= 3.0.0).
222s  libfido2-1:armhf depends on libssl3 (>= 3.0.0).
222s  libcurl4:armhf depends on libssl3 (>= 3.0.0).
222s  libcryptsetup12:armhf depends on libssl3 (>= 3.0.0).
222s  kmod depends on libssl3 (>= 3.0.0).
222s  dhcpcd-base depends on libssl3 (>= 3.0.0).
222s  bind9-libs:armhf depends on libssl3 (>= 3.0.0).
222s 
222s Removing libssl3:armhf (3.0.10-1ubuntu4) ...
222s Selecting previously unselected package libssl3t64:armhf.
222s (Reading database ... 
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222s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_armhf.deb ...
222s Unpacking libssl3t64:armhf (3.0.13-0ubuntu2) ...
222s Setting up libssl3t64:armhf (3.0.13-0ubuntu2) ...
222s (Reading database ... 
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222s Preparing to unpack .../libudev1_255.4-1ubuntu5_armhf.deb ...
222s Unpacking libudev1:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
223s Setting up libudev1:armhf (255.4-1ubuntu5) ...
223s (Reading database ... 
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223s Preparing to unpack .../systemd_255.4-1ubuntu5_armhf.deb ...
223s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
223s Preparing to unpack .../udev_255.4-1ubuntu5_armhf.deb ...
223s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
224s Preparing to unpack .../libsystemd0_255.4-1ubuntu5_armhf.deb ...
224s Unpacking libsystemd0:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
224s Setting up libsystemd0:armhf (255.4-1ubuntu5) ...
224s Setting up libsystemd-shared:armhf (255.4-1ubuntu5) ...
224s Setting up systemd-dev (255.4-1ubuntu5) ...
224s Setting up systemd (255.4-1ubuntu5) ...
250s (Reading database ... 
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250s Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_armhf.deb ...
250s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
250s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_armhf.deb ...
250s Unpacking libnss-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
250s Preparing to unpack .../libpam-systemd_255.4-1ubuntu5_armhf.deb ...
250s Unpacking libpam-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
250s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_armhf.deb ...
250s Unpacking libpam-modules-bin (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
250s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ...
251s pam_namespace.service is a disabled or a static unit not running, not starting it.
251s (Reading database ... 
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251s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu3_armhf.deb ...
251s Unpacking libpam-modules:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
251s Setting up libpam-modules:armhf (1.5.3-5ubuntu3) ...
251s Installing new version of config file /etc/security/namespace.init ...
252s (Reading database ... 
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252s Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu3_all.deb ...
252s Unpacking libpam-runtime (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
252s Setting up libpam-runtime (1.5.3-5ubuntu3) ...
252s (Reading database ... 
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252s Preparing to unpack .../0-dbus-user-session_1.14.10-4ubuntu2_armhf.deb ...
252s Unpacking dbus-user-session (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
252s Preparing to unpack .../1-libapparmor1_4.0.0-beta3-0ubuntu2_armhf.deb ...
252s Unpacking libapparmor1:armhf (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ...
252s Preparing to unpack .../2-dbus-bin_1.14.10-4ubuntu2_armhf.deb ...
252s Unpacking dbus-bin (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
252s Preparing to unpack .../3-dbus-system-bus-common_1.14.10-4ubuntu2_all.deb ...
252s Unpacking dbus-system-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
252s Preparing to unpack .../4-dbus_1.14.10-4ubuntu2_armhf.deb ...
252s Unpacking dbus (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
253s Preparing to unpack .../5-dbus-daemon_1.14.10-4ubuntu2_armhf.deb ...
253s Unpacking dbus-daemon (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
253s Preparing to unpack .../6-libdbus-1-3_1.14.10-4ubuntu2_armhf.deb ...
253s Unpacking libdbus-1-3:armhf (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
253s Preparing to unpack .../7-kmod_31+20240202-2ubuntu4_armhf.deb ...
253s Unpacking kmod (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ...
253s dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty
253s Preparing to unpack .../8-libkmod2_31+20240202-2ubuntu4_armhf.deb ...
253s Unpacking libkmod2:armhf (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ...
253s Preparing to unpack .../9-libmount1_2.39.3-9ubuntu2_armhf.deb ...
253s Unpacking libmount1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
253s Setting up libmount1:armhf (2.39.3-9ubuntu2) ...
253s (Reading database ... 
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253s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu2_armhf.deb ...
253s Unpacking libseccomp2:armhf (2.5.5-1ubuntu2) over (2.5.5-1ubuntu1) ...
253s Setting up libseccomp2:armhf (2.5.5-1ubuntu2) ...
253s (Reading database ... 
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253s Preparing to unpack .../libuuid1_2.39.3-9ubuntu2_armhf.deb ...
253s Unpacking libuuid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
253s Setting up libuuid1:armhf (2.39.3-9ubuntu2) ...
254s (Reading database ... 
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254s Preparing to unpack .../0-libcryptsetup12_2%3a2.7.0-1ubuntu2_armhf.deb ...
254s Unpacking libcryptsetup12:armhf (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ...
254s Preparing to unpack .../1-libfdisk1_2.39.3-9ubuntu2_armhf.deb ...
254s Unpacking libfdisk1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
254s Preparing to unpack .../2-mount_2.39.3-9ubuntu2_armhf.deb ...
254s Unpacking mount (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
254s Preparing to unpack .../3-libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_armhf.deb ...
254s Unpacking libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ...
254s Selecting previously unselected package libparted2t64:armhf.
254s Preparing to unpack .../4-libparted2t64_3.6-3.1build2_armhf.deb ...
254s Unpacking libparted2t64:armhf (3.6-3.1build2) ...
254s Preparing to unpack .../5-libsqlite3-0_3.45.1-1ubuntu1_armhf.deb ...
254s Unpacking libsqlite3-0:armhf (3.45.1-1ubuntu1) over (3.45.1-1) ...
254s Preparing to unpack .../6-pinentry-curses_1.2.1-3ubuntu4_armhf.deb ...
254s Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-3ubuntu1) ...
254s Preparing to unpack .../7-libsmartcols1_2.39.3-9ubuntu2_armhf.deb ...
254s Unpacking libsmartcols1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
254s Setting up libsmartcols1:armhf (2.39.3-9ubuntu2) ...
255s (Reading database ... 
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255s Preparing to unpack .../0-readline-common_8.2-4_all.deb ...
255s Unpacking readline-common (8.2-4) over (8.2-3) ...
255s Preparing to unpack .../1-python3-yaml_6.0.1-2build1_armhf.deb ...
255s Unpacking python3-yaml (6.0.1-2build1) over (6.0.1-2) ...
255s Preparing to unpack .../2-python-apt-common_2.7.7_all.deb ...
255s Unpacking python-apt-common (2.7.7) over (2.7.6) ...
255s Preparing to unpack .../3-python3-setuptools_68.1.2-2ubuntu1_all.deb ...
255s Unpacking python3-setuptools (68.1.2-2ubuntu1) over (68.1.2-2) ...
256s Preparing to unpack .../4-python3-pkg-resources_68.1.2-2ubuntu1_all.deb ...
256s Unpacking python3-pkg-resources (68.1.2-2ubuntu1) over (68.1.2-2) ...
256s Preparing to unpack .../5-dpkg_1.22.6ubuntu4_armhf.deb ...
256s Unpacking dpkg (1.22.6ubuntu4) over (1.22.4ubuntu5) ...
256s Setting up dpkg (1.22.6ubuntu4) ...
257s Setting up libpython3.12-minimal:armhf (3.12.2-4build3) ...
257s Setting up libexpat1:armhf (2.6.1-2) ...
257s Setting up python3.12-minimal (3.12.2-4build3) ...
260s (Reading database ... 
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260s Preparing to unpack .../python3-minimal_3.12.2-0ubuntu1_armhf.deb ...
260s Unpacking python3-minimal (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ...
260s Setting up python3-minimal (3.12.2-0ubuntu1) ...
260s (Reading database ... 
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260s Preparing to unpack .../00-python3_3.12.2-0ubuntu1_armhf.deb ...
261s Unpacking python3 (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ...
261s Preparing to unpack .../01-libpython3-stdlib_3.12.2-0ubuntu1_armhf.deb ...
261s Unpacking libpython3-stdlib:armhf (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ...
261s Preparing to unpack .../02-bsdextrautils_2.39.3-9ubuntu2_armhf.deb ...
261s Unpacking bsdextrautils (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
261s Preparing to unpack .../03-groff-base_1.23.0-3build1_armhf.deb ...
261s Unpacking groff-base (1.23.0-3build1) over (1.23.0-3) ...
261s Preparing to unpack .../04-libsasl2-2_2.1.28+dfsg1-5ubuntu1_armhf.deb ...
261s Unpacking libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
261s Preparing to unpack .../05-libblockdev-utils3_3.1.0-1build1_armhf.deb ...
261s Unpacking libblockdev-utils3:armhf (3.1.0-1build1) over (3.1.0-1) ...
261s Preparing to unpack .../06-libblockdev-crypto3_3.1.0-1build1_armhf.deb ...
261s Unpacking libblockdev-crypto3:armhf (3.1.0-1build1) over (3.1.0-1) ...
261s Preparing to unpack .../07-logsave_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
261s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
261s Preparing to unpack .../08-dhcpcd-base_1%3a10.0.6-1ubuntu2_armhf.deb ...
261s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ...
262s Preparing to unpack .../09-eject_2.39.3-9ubuntu2_armhf.deb ...
262s Unpacking eject (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
262s Preparing to unpack .../10-libbpf1_1%3a1.3.0-2build1_armhf.deb ...
262s Unpacking libbpf1:armhf (1:1.3.0-2build1) over (1:1.3.0-2) ...
262s Preparing to unpack .../11-iproute2_6.1.0-1ubuntu5_armhf.deb ...
262s Unpacking iproute2 (6.1.0-1ubuntu5) over (6.1.0-1ubuntu2) ...
262s (Reading database ... 
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262s Removing libelf1:armhf (0.190-1) ...
262s Selecting previously unselected package libelf1t64:armhf.
262s (Reading database ... 
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262s Preparing to unpack .../libelf1t64_0.190-1.1build2_armhf.deb ...
262s Unpacking libelf1t64:armhf (0.190-1.1build2) ...
262s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ...
262s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ...
262s Preparing to unpack .../lsof_4.95.0-1build2_armhf.deb ...
262s Unpacking lsof (4.95.0-1build2) over (4.95.0-1build1) ...
262s Preparing to unpack .../libnsl2_1.3.0-3build2_armhf.deb ...
262s Unpacking libnsl2:armhf (1.3.0-3build2) over (1.3.0-3) ...
263s (Reading database ... 
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263s Removing libtirpc3:armhf (1.3.4+ds-1build1) ...
263s (Reading database ... 
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263s Preparing to unpack .../0-libgssapi-krb5-2_1.20.1-6ubuntu1_armhf.deb ...
263s Unpacking libgssapi-krb5-2:armhf (1.20.1-6ubuntu1) over (1.20.1-5build1) ...
263s Preparing to unpack .../1-libkrb5-3_1.20.1-6ubuntu1_armhf.deb ...
263s Unpacking libkrb5-3:armhf (1.20.1-6ubuntu1) over (1.20.1-5build1) ...
263s Preparing to unpack .../2-libkrb5support0_1.20.1-6ubuntu1_armhf.deb ...
263s Unpacking libkrb5support0:armhf (1.20.1-6ubuntu1) over (1.20.1-5build1) ...
263s Preparing to unpack .../3-libk5crypto3_1.20.1-6ubuntu1_armhf.deb ...
263s Unpacking libk5crypto3:armhf (1.20.1-6ubuntu1) over (1.20.1-5build1) ...
263s Preparing to unpack .../4-libcom-err2_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
263s Unpacking libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
263s Selecting previously unselected package libtirpc3t64:armhf.
263s Preparing to unpack .../5-libtirpc3t64_1.3.4+ds-1.1_armhf.deb ...
263s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64'
263s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
263s Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1) ...
263s Preparing to unpack .../6-libc-bin_2.39-0ubuntu6_armhf.deb ...
263s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
264s Setting up libc-bin (2.39-0ubuntu6) ...
264s (Reading database ... 
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264s Preparing to unpack .../0-locales_2.39-0ubuntu6_all.deb ...
264s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
265s Preparing to unpack .../1-libproc2-0_2%3a4.0.4-4ubuntu2_armhf.deb ...
265s Unpacking libproc2-0:armhf (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ...
265s Preparing to unpack .../2-procps_2%3a4.0.4-4ubuntu2_armhf.deb ...
265s Unpacking procps (2:4.0.4-4ubuntu2) over (2:4.0.4-4ubuntu1) ...
265s Preparing to unpack .../3-vim-tiny_2%3a9.1.0016-1ubuntu6_armhf.deb ...
265s Unpacking vim-tiny (2:9.1.0016-1ubuntu6) over (2:9.1.0016-1ubuntu2) ...
265s Preparing to unpack .../4-vim-common_2%3a9.1.0016-1ubuntu6_all.deb ...
265s Unpacking vim-common (2:9.1.0016-1ubuntu6) over (2:9.1.0016-1ubuntu2) ...
265s Preparing to unpack .../5-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ...
265s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
265s Preparing to unpack .../6-libblockdev-fs3_3.1.0-1build1_armhf.deb ...
265s Unpacking libblockdev-fs3:armhf (3.1.0-1build1) over (3.1.0-1) ...
265s dpkg: libreiserfscore0: dependency problems, but removing anyway as you requested:
265s  btrfs-progs depends on libreiserfscore0 (>= 1:3.6.27).
265s 
266s (Reading database ... 
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266s Removing libreiserfscore0 (1:3.6.27-7) ...
266s Selecting previously unselected package libreiserfscore0t64.
266s (Reading database ... 
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266s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_armhf.deb ...
266s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ...
266s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_armhf.deb ...
266s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ...
266s dpkg: libext2fs2:armhf: dependency problems, but removing anyway as you requested:
266s  e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1).
266s 
266s (Reading database ... 
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266s Removing libext2fs2:armhf (1.47.0-2ubuntu1) ...
266s Selecting previously unselected package libext2fs2t64:armhf.
266s (Reading database ... 
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266s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
266s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64'
266s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64'
266s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64'
266s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64'
266s Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ...
266s Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) ...
266s Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ...
267s (Reading database ... 
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267s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
267s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
267s Preparing to unpack .../libblockdev-loop3_3.1.0-1build1_armhf.deb ...
267s Unpacking libblockdev-loop3:armhf (3.1.0-1build1) over (3.1.0-1) ...
267s Preparing to unpack .../libblockdev-mdraid3_3.1.0-1build1_armhf.deb ...
267s Unpacking libblockdev-mdraid3:armhf (3.1.0-1build1) over (3.1.0-1) ...
267s Preparing to unpack .../libblockdev-nvme3_3.1.0-1build1_armhf.deb ...
267s Unpacking libblockdev-nvme3:armhf (3.1.0-1build1) over (3.1.0-1) ...
267s (Reading database ... 
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267s Removing libnvme1 (1.8-2) ...
267s Selecting previously unselected package libnvme1t64.
267s (Reading database ... 
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267s Preparing to unpack .../00-libnvme1t64_1.8-3_armhf.deb ...
267s Unpacking libnvme1t64 (1.8-3) ...
267s Preparing to unpack .../01-libblockdev-part3_3.1.0-1build1_armhf.deb ...
267s Unpacking libblockdev-part3:armhf (3.1.0-1build1) over (3.1.0-1) ...
268s Preparing to unpack .../02-libblockdev-swap3_3.1.0-1build1_armhf.deb ...
268s Unpacking libblockdev-swap3:armhf (3.1.0-1build1) over (3.1.0-1) ...
268s Preparing to unpack .../03-libblockdev3_3.1.0-1build1_armhf.deb ...
268s Unpacking libblockdev3:armhf (3.1.0-1build1) over (3.1.0-1) ...
268s Preparing to unpack .../04-libgudev-1.0-0_1%3a238-3ubuntu2_armhf.deb ...
268s Unpacking libgudev-1.0-0:armhf (1:238-3ubuntu2) over (1:238-3) ...
268s Preparing to unpack .../05-libxml2_2.9.14+dfsg-1.3ubuntu2_armhf.deb ...
268s Unpacking libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) over (2.9.14+dfsg-1.3ubuntu1) ...
268s Preparing to unpack .../06-libmbim-proxy_1.31.2-0ubuntu2_armhf.deb ...
268s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ...
268s Preparing to unpack .../07-libmbim-glib4_1.31.2-0ubuntu2_armhf.deb ...
268s Unpacking libmbim-glib4:armhf (1.31.2-0ubuntu2) over (1.30.0-1) ...
268s Preparing to unpack .../08-libjson-glib-1.0-common_1.8.0-2build1_all.deb ...
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268s Preparing to unpack .../09-libjson-glib-1.0-0_1.8.0-2build1_armhf.deb ...
268s Unpacking libjson-glib-1.0-0:armhf (1.8.0-2build1) over (1.8.0-2) ...
268s Preparing to unpack .../10-libusb-1.0-0_2%3a1.0.27-1_armhf.deb ...
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269s Preparing to unpack .../13-libprotobuf-c1_1.4.1-1ubuntu3_armhf.deb ...
269s Unpacking libprotobuf-c1:armhf (1.4.1-1ubuntu3) over (1.4.1-1ubuntu2) ...
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269s Preparing to unpack .../15-libnghttp2-14_1.59.0-1build1_armhf.deb ...
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269s Preparing to unpack .../16-libssh-4_0.10.6-2build1_armhf.deb ...
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269s Preparing to unpack .../19-coreutils_9.4-3ubuntu3_armhf.deb ...
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269s Setting up coreutils (9.4-3ubuntu3) ...
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270s Preparing to unpack .../debianutils_5.17_armhf.deb ...
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270s Preparing to unpack .../util-linux_2.39.3-9ubuntu2_armhf.deb ...
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272s fstrim.service is a disabled or a static unit not running, not starting it.
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272s Removing libatm1:armhf (1:2.5.1-5) ...
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273s Preparing to unpack .../curl_8.5.0-2ubuntu8_armhf.deb ...
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273s Removing libcurl4:armhf (8.5.0-2ubuntu2) ...
273s Selecting previously unselected package libcurl4t64:armhf.
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273s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu8_armhf.deb ...
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273s Preparing to unpack .../file_1%3a5.45-3_armhf.deb ...
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273s Removing libmagic1:armhf (1:5.45-2) ...
273s (Reading database ... 
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273s Preparing to unpack .../libmagic-mgc_1%3a5.45-3_armhf.deb ...
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273s Selecting previously unselected package libmagic1t64:armhf.
273s Preparing to unpack .../libmagic1t64_1%3a5.45-3_armhf.deb ...
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274s Preparing to unpack .../libplymouth5_24.004.60-1ubuntu6_armhf.deb ...
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274s (Reading database ... 
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274s Removing libpng16-16:armhf (1.6.43-1) ...
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274s (Reading database ... 
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274s Preparing to unpack .../libpng16-16t64_1.6.43-3_armhf.deb ...
274s Unpacking libpng16-16t64:armhf (1.6.43-3) ...
274s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_armhf.deb ...
274s Unpacking bind9-host (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ...
274s Preparing to unpack .../bind9-dnsutils_1%3a9.18.24-0ubuntu3_armhf.deb ...
274s Unpacking bind9-dnsutils (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ...
274s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_armhf.deb ...
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274s (Reading database ... 
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274s Removing libuv1:armhf (1.48.0-1) ...
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275s (Reading database ... 
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275s Preparing to unpack .../libuv1t64_1.48.0-1.1_armhf.deb ...
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275s Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu2_armhf.deb ...
275s Unpacking uuid-runtime (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
275s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_armhf.deb ...
275s Unpacking libdebconfclient0:armhf (0.271ubuntu2) over (0.271ubuntu1) ...
275s Setting up libdebconfclient0:armhf (0.271ubuntu2) ...
275s (Reading database ... 
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275s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ...
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275s Setting up libsemanage-common (3.5-1build4) ...
275s (Reading database ... 
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275s Preparing to unpack .../libsemanage2_3.5-1build4_armhf.deb ...
275s Unpacking libsemanage2:armhf (3.5-1build4) over (3.5-1build2) ...
275s Setting up libsemanage2:armhf (3.5-1build4) ...
275s (Reading database ... 
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275s Preparing to unpack .../install-info_7.1-3build1_armhf.deb ...
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275s Setting up install-info (7.1-3build1) ...
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276s Preparing to unpack .../00-gcc-13-base_13.2.0-21ubuntu1_armhf.deb ...
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276s Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
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276s Preparing to unpack .../02-dmsetup_2%3a1.02.185-3ubuntu2_armhf.deb ...
276s Unpacking dmsetup (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ...
276s Preparing to unpack .../03-krb5-locales_1.20.1-6ubuntu1_all.deb ...
276s Unpacking krb5-locales (1.20.1-6ubuntu1) over (1.20.1-5build1) ...
276s Preparing to unpack .../04-libbsd0_0.12.1-1_armhf.deb ...
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276s Preparing to unpack .../05-libglib2.0-data_2.79.3-3ubuntu5_all.deb ...
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276s Preparing to unpack .../06-libslang2_2.3.3-3build1_armhf.deb ...
276s Unpacking libslang2:armhf (2.3.3-3build1) over (2.3.3-3) ...
276s Preparing to unpack .../07-rsyslog_8.2312.0-3ubuntu7_armhf.deb ...
276s Unpacking rsyslog (8.2312.0-3ubuntu7) over (8.2312.0-3ubuntu3) ...
276s Selecting previously unselected package xdg-user-dirs.
276s Preparing to unpack .../08-xdg-user-dirs_0.18-1_armhf.deb ...
276s Unpacking xdg-user-dirs (0.18-1) ...
276s Preparing to unpack .../09-xxd_2%3a9.1.0016-1ubuntu6_armhf.deb ...
276s Unpacking xxd (2:9.1.0016-1ubuntu6) over (2:9.1.0016-1ubuntu2) ...
276s Preparing to unpack .../10-apparmor_4.0.0-beta3-0ubuntu2_armhf.deb ...
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278s Preparing to unpack .../11-ftp_20230507-2build1_all.deb ...
278s Unpacking ftp (20230507-2build1) over (20230507-2) ...
279s Preparing to unpack .../12-inetutils-telnet_2%3a2.5-3ubuntu3_armhf.deb ...
279s Unpacking inetutils-telnet (2:2.5-3ubuntu3) over (2:2.5-3ubuntu1) ...
279s Preparing to unpack .../13-info_7.1-3build1_armhf.deb ...
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279s Preparing to unpack .../14-libxmuu1_2%3a1.1.3-3build1_armhf.deb ...
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279s Preparing to unpack .../15-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_armhf.deb ...
279s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ...
279s Preparing to unpack .../16-mtr-tiny_0.95-1.1build1_armhf.deb ...
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279s Preparing to unpack .../17-plymouth-theme-ubuntu-text_24.004.60-1ubuntu6_armhf.deb ...
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279s Preparing to unpack .../18-plymouth_24.004.60-1ubuntu6_armhf.deb ...
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279s Preparing to unpack .../19-psmisc_23.7-1_armhf.deb ...
279s Unpacking psmisc (23.7-1) over (23.6-2) ...
279s Preparing to unpack .../20-telnet_0.17+2.5-3ubuntu3_all.deb ...
279s Unpacking telnet (0.17+2.5-3ubuntu3) over (0.17+2.5-3ubuntu1) ...
280s Preparing to unpack .../21-xz-utils_5.6.0-0.2_armhf.deb ...
280s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ...
280s Preparing to unpack .../22-ubuntu-standard_1.536build1_armhf.deb ...
280s Unpacking ubuntu-standard (1.536build1) over (1.536) ...
280s Preparing to unpack .../23-usb.ids_2024.03.18-1_all.deb ...
280s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ...
280s Preparing to unpack .../24-libctf-nobfd0_2.42-4ubuntu1_armhf.deb ...
280s Unpacking libctf-nobfd0:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
280s Preparing to unpack .../25-libctf0_2.42-4ubuntu1_armhf.deb ...
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280s Preparing to unpack .../26-binutils-arm-linux-gnueabihf_2.42-4ubuntu1_armhf.deb ...
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280s Preparing to unpack .../27-libbinutils_2.42-4ubuntu1_armhf.deb ...
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280s Preparing to unpack .../28-binutils_2.42-4ubuntu1_armhf.deb ...
280s Unpacking binutils (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
280s Preparing to unpack .../29-binutils-common_2.42-4ubuntu1_armhf.deb ...
280s Unpacking binutils-common:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
280s Preparing to unpack .../30-libsframe1_2.42-4ubuntu1_armhf.deb ...
280s Unpacking libsframe1:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
280s Preparing to unpack .../31-bolt_0.9.6-2build1_armhf.deb ...
280s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ...
281s Preparing to unpack .../32-cryptsetup-bin_2%3a2.7.0-1ubuntu2_armhf.deb ...
281s Unpacking cryptsetup-bin (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ...
281s Preparing to unpack .../33-dpkg-dev_1.22.6ubuntu4_all.deb ...
281s Unpacking dpkg-dev (1.22.6ubuntu4) over (1.22.4ubuntu5) ...
281s Preparing to unpack .../34-libdpkg-perl_1.22.6ubuntu4_all.deb ...
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291s Preparing to unpack .../35-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ...
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291s Preparing to unpack .../36-gnupg-l10n_2.4.4-2ubuntu15_all.deb ...
291s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
291s Preparing to unpack .../37-ibverbs-providers_50.0-2build1_armhf.deb ...
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291s Preparing to unpack .../38-jq_1.7.1-3_armhf.deb ...
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292s Preparing to unpack .../39-libjq1_1.7.1-3_armhf.deb ...
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292s Selecting previously unselected package libatm1t64:armhf.
292s Preparing to unpack .../40-libatm1t64_1%3a2.5.1-5.1_armhf.deb ...
292s Unpacking libatm1t64:armhf (1:2.5.1-5.1) ...
292s Preparing to unpack .../41-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ...
292s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ...
292s Preparing to unpack .../42-libftdi1-2_1.5-6build4_armhf.deb ...
292s Unpacking libftdi1-2:armhf (1.5-6build4) over (1.5-6build3) ...
292s Preparing to unpack .../43-libldap-common_2.6.7+dfsg-1~exp1ubuntu6_all.deb ...
292s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ...
292s Preparing to unpack .../44-libsasl2-modules_2.1.28+dfsg1-5ubuntu1_armhf.deb ...
292s Unpacking libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
292s Preparing to unpack .../45-python3-distutils_3.12.2-3ubuntu1.1_all.deb ...
292s Unpacking python3-distutils (3.12.2-3ubuntu1.1) over (3.11.5-1) ...
292s Preparing to unpack .../46-python3-lib2to3_3.12.2-3ubuntu1.1_all.deb ...
292s Unpacking python3-lib2to3 (3.12.2-3ubuntu1.1) over (3.11.5-1) ...
293s Preparing to unpack .../47-python3-markupsafe_2.1.5-1build1_armhf.deb ...
293s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ...
293s Preparing to unpack .../48-python3-pyrsistent_0.20.0-1build1_armhf.deb ...
293s Unpacking python3-pyrsistent:armhf (0.20.0-1build1) over (0.20.0-1) ...
293s Preparing to unpack .../49-python3-typing-extensions_4.10.0-1_all.deb ...
293s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ...
293s Preparing to unpack .../50-cloud-init_24.1.2-0ubuntu1_all.deb ...
294s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ...
294s Preparing to unpack .../51-kpartx_0.9.4-5ubuntu6_armhf.deb ...
294s Unpacking kpartx (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ...
294s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ...
294s Setting up pinentry-curses (1.2.1-3ubuntu4) ...
294s Setting up motd-news-config (13ubuntu8) ...
294s Setting up libtext-iconv-perl:armhf (1.7-8build2) ...
294s Setting up libtext-charwidth-perl:armhf (0.04-11build2) ...
294s Setting up libibverbs1:armhf (50.0-2build1) ...
294s Setting up systemd-sysv (255.4-1ubuntu5) ...
294s Setting up libapparmor1:armhf (4.0.0-beta3-0ubuntu2) ...
294s Setting up libatm1t64:armhf (1:2.5.1-5.1) ...
294s Setting up libgdbm6t64:armhf (1.23-5.1) ...
294s Setting up bsdextrautils (2.39.3-9ubuntu2) ...
294s Setting up libgdbm-compat4t64:armhf (1.23-5.1) ...
294s Setting up xdg-user-dirs (0.18-1) ...
294s Setting up ibverbs-providers:armhf (50.0-2build1) ...
295s Setting up linux-headers-6.8.0-20 (6.8.0-20.20) ...
295s Setting up libmagic-mgc (1:5.45-3) ...
295s Setting up gawk (1:5.2.1-2build2) ...
295s Setting up psmisc (23.7-1) ...
295s Setting up libjq1:armhf (1.7.1-3) ...
295s Setting up libtirpc-common (1.3.4+ds-1.1) ...
295s Setting up libbrotli1:armhf (1.1.0-2build1) ...
295s Setting up libsqlite3-0:armhf (3.45.1-1ubuntu1) ...
295s Setting up libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) ...
295s Setting up libuv1t64:armhf (1.48.0-1.1) ...
295s Setting up libmagic1t64:armhf (1:5.45-3) ...
295s Setting up rsyslog (8.2312.0-3ubuntu7) ...
295s info: The user `syslog' is already a member of `adm'.
295s apparmor_parser: Unable to replace "rsyslogd".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
295s 
297s Setting up binutils-common:armhf (2.42-4ubuntu1) ...
297s Setting up libpsl5t64:armhf (0.21.2-1.1) ...
297s Setting up libnghttp2-14:armhf (1.59.0-1build1) ...
297s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ...
297s Setting up libctf-nobfd0:armhf (2.42-4ubuntu1) ...
297s Setting up libnss-systemd:armhf (255.4-1ubuntu5) ...
297s Setting up krb5-locales (1.20.1-6ubuntu1) ...
297s Setting up file (1:5.45-3) ...
297s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ...
297s Setting up locales (2.39-0ubuntu6) ...
299s Generating locales (this might take a while)...
304s   en_US.UTF-8... done
304s Generation complete.
304s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ...
304s Setting up libprotobuf-c1:armhf (1.4.1-1ubuntu3) ...
304s Setting up xxd (2:9.1.0016-1ubuntu6) ...
304s Setting up libsframe1:armhf (2.42-4ubuntu1) ...
304s Setting up libelf1t64:armhf (0.190-1.1build2) ...
304s Setting up libkrb5support0:armhf (1.20.1-6ubuntu1) ...
304s Setting up linux-headers-6.8.0-20-generic (6.8.0-20.20) ...
304s Setting up eject (2.39.3-9ubuntu2) ...
304s Setting up apparmor (4.0.0-beta3-0ubuntu2) ...
304s Installing new version of config file /etc/apparmor.d/abstractions/authentication ...
304s Installing new version of config file /etc/apparmor.d/abstractions/crypto ...
304s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ...
304s Installing new version of config file /etc/apparmor.d/abstractions/openssl ...
305s Installing new version of config file /etc/apparmor.d/code ...
305s Installing new version of config file /etc/apparmor.d/firefox ...
305s apparmor_parser: Unable to replace "lsb_release".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
305s 
305s apparmor_parser: Unable to replace "kmod".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
305s 
305s apparmor_parser: Unable to replace "nvidia_modprobe".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
305s 
307s sysctl: cannot stat /proc/sys/kernel/apparmor_restrict_unprivileged_userns: No such file or directory
307s Reloading AppArmor profiles 
307s /sbin/apparmor_parser: Unable to replace "1password".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "Discord".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "MongoDB Compass".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "brave".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "buildah".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "busybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "cam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "ch-checkns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "ch-run".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "chrome".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "vscode".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "crun".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "element-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "devhelp".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "epiphany".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "evolution".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "firefox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "flatpak".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "geary".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "github-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "goldendict".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "ipa_verify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "keybase".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "lc-compliance".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "libcamerify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "linux-sandbox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "loupe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "kchmviewer".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "lxc-attach".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "lxc-create".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "lxc-destroy".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "lxc-execute".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "lxc-stop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "lxc-unshare".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "mmdebstrap".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "nautilus".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "msedge".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "notepadqq".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "opam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "obsidian".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "opera".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "podman".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "pageedit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "privacybrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "polypane".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "qmapshack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "qcam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "rpm".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "rssguard".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "runc".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "rootlesskit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "plasmashell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-abort".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-clean".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-apt".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-hold".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-shell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-unhold".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-update".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "scide".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "signal-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "qutebrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "sbuild-adduser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "slack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "steam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "surfshark".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "stress-ng".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "systemd-coredump".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "toybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "slirp4netns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "thunderbird".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "tup".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "userbindmount".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "unprivileged_userns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "lsb_release".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "trinity".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "uwsgi-core".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "vdens".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "virtiofsd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "kmod".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "vpnns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "wpcom".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "vivaldi-bin".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "unix-chkpwd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "rsyslogd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "/usr/bin/man".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s /sbin/apparmor_parser: Unable to replace "tcpdump".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
307s 
307s Error: At least one profile failed to load
307s Setting up libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ...
307s No schema files found: doing nothing.
307s Setting up libglib2.0-data (2.79.3-3ubuntu5) ...
307s Setting up vim-common (2:9.1.0016-1ubuntu6) ...
331s Setting up gcc-13-base:armhf (13.2.0-21ubuntu1) ...
331s Setting up libqrtr-glib0:armhf (1.2.2-1ubuntu3) ...
331s Setting up libslang2:armhf (2.3.3-3build1) ...
331s Setting up libnvme1t64 (1.8-3) ...
331s Setting up mtr-tiny (0.95-1.1build1) ...
331s Setting up gnupg-l10n (2.4.4-2ubuntu15) ...
331s Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) ...
331s Setting up libdbus-1-3:armhf (1.14.10-4ubuntu2) ...
331s Setting up xz-utils (5.6.0-0.2) ...
331s Setting up perl-modules-5.38 (5.38.2-3.2) ...
331s Setting up libproc2-0:armhf (2:4.0.4-4ubuntu2) ...
331s Setting up libpng16-16t64:armhf (1.6.43-3) ...
331s Setting up systemd-timesyncd (255.4-1ubuntu5) ...
332s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ...
332s Setting up libss2:armhf (1.47.0-2.4~exp1ubuntu2) ...
332s Setting up usb.ids (2024.03.18-1) ...
332s Setting up sudo (1.9.15p5-3ubuntu3) ...
332s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ...
332s Setting up gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) ...
332s Setting up libk5crypto3:armhf (1.20.1-6ubuntu1) ...
332s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ...
332s Setting up libfdisk1:armhf (2.39.3-9ubuntu2) ...
332s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-6) ...
332s Setting up libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) ...
332s Setting up python-apt-common (2.7.7) ...
332s Setting up mount (2.39.3-9ubuntu2) ...
332s Setting up dmsetup (2:1.02.185-3ubuntu2) ...
332s Setting up uuid-runtime (2.39.3-9ubuntu2) ...
334s uuidd.service is a disabled or a static unit not running, not starting it.
334s Setting up libmm-glib0:armhf (1.23.4-0ubuntu1) ...
334s Setting up groff-base (1.23.0-3build1) ...
334s Setting up libplymouth5:armhf (24.004.60-1ubuntu6) ...
334s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ...
334s Setting up jq (1.7.1-3) ...
334s Setting up procps (2:4.0.4-4ubuntu2) ...
334s Setting up gpgconf (2.4.4-2ubuntu15) ...
334s Setting up libpcap0.8t64:armhf (1.10.4-4.1ubuntu2) ...
334s Setting up libcryptsetup12:armhf (2:2.7.0-1ubuntu2) ...
334s Setting up libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) ...
334s Setting up libjson-glib-1.0-common (1.8.0-2build1) ...
334s Setting up libkrb5-3:armhf (1.20.1-6ubuntu1) ...
334s Setting up libpython3.11-minimal:armhf (3.11.8-1build4) ...
334s Setting up libusb-1.0-0:armhf (2:1.0.27-1) ...
334s Setting up libperl5.38t64:armhf (5.38.2-3.2) ...
334s Setting up tnftp (20230507-2build1) ...
334s Setting up libbinutils:armhf (2.42-4ubuntu1) ...
334s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ...
334s Setting up libfido2-1:armhf (1.14.0-1build1) ...
334s Setting up openssl (3.0.13-0ubuntu2) ...
334s Setting up libbsd0:armhf (0.12.1-1) ...
334s Setting up readline-common (8.2-4) ...
334s Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) ...
334s Setting up libxmuu1:armhf (2:1.1.3-3build1) ...
334s Setting up dbus-bin (1.14.10-4ubuntu2) ...
334s Setting up info (7.1-3build1) ...
334s Setting up liblocale-gettext-perl (1.07-6ubuntu4) ...
334s Setting up gpg (2.4.4-2ubuntu15) ...
334s Setting up libgudev-1.0-0:armhf (1:238-3ubuntu2) ...
334s Setting up libpolkit-gobject-1-0:armhf (124-1ubuntu1) ...
334s Setting up libbpf1:armhf (1:1.3.0-2build1) ...
334s Setting up libmbim-glib4:armhf (1.31.2-0ubuntu2) ...
334s Setting up rsync (3.2.7-1build1) ...
336s rsync.service is a disabled or a static unit not running, not starting it.
336s Setting up libudisks2-0:armhf (2.10.1-6) ...
336s Setting up libkmod2:armhf (31+20240202-2ubuntu4) ...
336s Setting up bolt (0.9.6-2build1) ...
337s bolt.service is a disabled or a static unit not running, not starting it.
337s Setting up gnupg-utils (2.4.4-2ubuntu15) ...
337s Setting up initramfs-tools-bin (0.142ubuntu23) ...
337s Setting up libctf0:armhf (2.42-4ubuntu1) ...
337s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ...
337s Setting up python3.11-minimal (3.11.8-1build4) ...
339s Setting up tcpdump (4.99.4-3ubuntu2) ...
339s apparmor_parser: Unable to replace "tcpdump".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
339s 
339s Setting up apt-utils (2.7.14) ...
339s Setting up gpg-agent (2.4.4-2ubuntu15) ...
340s Setting up libpython3.12-stdlib:armhf (3.12.2-4build3) ...
340s Setting up wget (1.21.4-1ubuntu2) ...
340s Setting up libxmlb2:armhf (0.3.15-1build1) ...
340s Setting up btrfs-progs (6.6.3-1.1build1) ...
340s Setting up libpython3.11-stdlib:armhf (3.11.8-1build4) ...
340s Setting up python3.12 (3.12.2-4build3) ...
343s Setting up gpgsm (2.4.4-2ubuntu15) ...
343s Setting up inetutils-telnet (2:2.5-3ubuntu3) ...
343s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ...
343s update-initramfs: deferring update (trigger activated)
344s e2scrub_all.service is a disabled or a static unit not running, not starting it.
344s Setting up libparted2t64:armhf (3.6-3.1build2) ...
344s Setting up linux-headers-generic (6.8.0-20.20+1) ...
344s Setting up dbus-daemon (1.14.10-4ubuntu2) ...
345s Setting up libmbim-proxy (1.31.2-0ubuntu2) ...
345s Setting up vim-tiny (2:9.1.0016-1ubuntu6) ...
345s Setting up kmod (31+20240202-2ubuntu4) ...
345s Setting up libnetplan1:armhf (1.0-1) ...
345s Setting up man-db (2.12.0-3build4) ...
345s Updating database of manual pages ...
348s apparmor_parser: Unable to replace "/usr/bin/man".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
348s 
348s man-db.service is a disabled or a static unit not running, not starting it.
349s Setting up fdisk (2.39.3-9ubuntu2) ...
349s Setting up libjson-glib-1.0-0:armhf (1.8.0-2build1) ...
349s Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) ...
349s Setting up libftdi1-2:armhf (1.5-6build4) ...
349s Setting up perl (5.38.2-3.2) ...
349s Setting up gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) ...
349s Setting up dbus (1.14.10-4ubuntu2) ...
349s A reboot is required to replace the running dbus-daemon.
349s Please reboot the system when convenient.
349s Setting up shared-mime-info (2.4-1build1) ...
350s Setting up libblockdev-utils3:armhf (3.1.0-1build1) ...
350s Setting up libgssapi-krb5-2:armhf (1.20.1-6ubuntu1) ...
350s Setting up udev (255.4-1ubuntu5) ...
352s Setting up ftp (20230507-2build1) ...
352s Setting up keyboxd (2.4.4-2ubuntu15) ...
352s Setting up libdpkg-perl (1.22.6ubuntu4) ...
352s Setting up libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) ...
352s Setting up libssh-4:armhf (0.10.6-2build1) ...
352s Setting up libblockdev-nvme3:armhf (3.1.0-1build1) ...
352s Setting up libblockdev-fs3:armhf (3.1.0-1build1) ...
352s Setting up kpartx (0.9.4-5ubuntu6) ...
352s Setting up libpam-systemd:armhf (255.4-1ubuntu5) ...
352s Setting up libpolkit-agent-1-0:armhf (124-1ubuntu1) ...
352s Setting up libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ...
352s Setting up netplan-generator (1.0-1) ...
352s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
352s Setting up initramfs-tools-core (0.142ubuntu23) ...
352s Setting up binutils-arm-linux-gnueabihf (2.42-4ubuntu1) ...
352s Setting up libarchive13t64:armhf (3.7.2-1.1ubuntu2) ...
352s Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) ...
352s Setting up libpython3-stdlib:armhf (3.12.2-0ubuntu1) ...
352s Setting up systemd-resolved (255.4-1ubuntu5) ...
354s Setting up python3.11 (3.11.8-1build4) ...
356s Setting up telnet (0.17+2.5-3ubuntu3) ...
356s Setting up initramfs-tools (0.142ubuntu23) ...
356s update-initramfs: deferring update (trigger activated)
356s Setting up libblockdev-mdraid3:armhf (3.1.0-1build1) ...
356s Setting up libcurl4t64:armhf (8.5.0-2ubuntu8) ...
356s Setting up bind9-libs:armhf (1:9.18.24-0ubuntu3) ...
356s Setting up libtirpc3t64:armhf (1.3.4+ds-1.1) ...
356s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ...
356s Setting up libblockdev-swap3:armhf (3.1.0-1build1) ...
356s Setting up plymouth (24.004.60-1ubuntu6) ...
356s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
356s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
357s Setting up iproute2 (6.1.0-1ubuntu5) ...
357s Setting up openssh-client (1:9.6p1-3ubuntu11) ...
357s Setting up libgusb2:armhf (0.4.8-1build1) ...
357s Setting up libblockdev-loop3:armhf (3.1.0-1build1) ...
357s Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu8) ...
357s Setting up parted (3.6-3.1build2) ...
357s Setting up libqmi-glib5:armhf (1.35.2-0ubuntu1) ...
357s Setting up python3 (3.12.2-0ubuntu1) ...
358s Setting up binutils (2.42-4ubuntu1) ...
358s Setting up python3-markupsafe (2.1.5-1build1) ...
358s Setting up libblockdev3:armhf (3.1.0-1build1) ...
358s Setting up libjcat1:armhf (0.2.0-2build2) ...
358s Setting up dpkg-dev (1.22.6ubuntu4) ...
358s Setting up libblockdev-part3:armhf (3.1.0-1build1) ...
358s Setting up dirmngr (2.4.4-2ubuntu15) ...
359s Setting up dbus-user-session (1.14.10-4ubuntu2) ...
359s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) ...
359s update-initramfs: deferring update (trigger activated)
359s Setting up python3-cryptography (41.0.7-4build2) ...
359s Setting up python3-gi (3.47.0-3build1) ...
360s Setting up python3-typing-extensions (4.10.0-1) ...
360s Setting up lsof (4.95.0-1build2) ...
360s Setting up python3-pyrsistent:armhf (0.20.0-1build1) ...
360s Setting up libnsl2:armhf (1.3.0-3build2) ...
360s Setting up gnupg (2.4.4-2ubuntu15) ...
360s Setting up python3-netplan (1.0-1) ...
360s Setting up curl (8.5.0-2ubuntu8) ...
360s Setting up libvolume-key1:armhf (0.3.12-7build1) ...
360s Setting up bind9-host (1:9.18.24-0ubuntu3) ...
360s Setting up python3-lib2to3 (3.12.2-3ubuntu1.1) ...
361s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ...
361s Setting up python3-distutils (3.12.2-3ubuntu1.1) ...
362s python3.12: can't get files for byte-compilation
362s Setting up openssh-sftp-server (1:9.6p1-3ubuntu11) ...
362s Setting up python3-dbus (1.3.2-5build2) ...
362s Setting up python3-setuptools (68.1.2-2ubuntu1) ...
364s Setting up gpg-wks-client (2.4.4-2ubuntu15) ...
364s Setting up openssh-server (1:9.6p1-3ubuntu11) ...
364s Replacing config file /etc/ssh/sshd_config with new version
366s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket.

369s Setting up libblockdev-crypto3:armhf (3.1.0-1build1) ...
369s Setting up python3-gdbm:armhf (3.12.2-3ubuntu1.1) ...
369s Setting up python3-apt (2.7.7) ...
369s Setting up libfwupd2:armhf (1.9.15-2) ...
369s Setting up python3-yaml (6.0.1-2build1) ...
370s Setting up libqmi-proxy (1.35.2-0ubuntu1) ...
370s Setting up netplan.io (1.0-1) ...
370s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ...
370s Setting up ubuntu-pro-client (31.2.2) ...
370s apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
370s 
373s Setting up fwupd (1.9.15-2) ...
374s fwupd-offline-update.service is a disabled or a static unit not running, not starting it.
374s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
374s fwupd.service is a disabled or a static unit not running, not starting it.
374s Setting up ubuntu-pro-client-l10n (31.2.2) ...
374s Setting up udisks2 (2.10.1-6) ...
374s sda: Failed to write 'change' to '/sys/devices/platform/LNRO0005:1f/virtio2/host0/target0:0:0/0:0:0:0/block/sda/uevent': Permission denied

374s sda1: Failed to write 'change' to '/sys/devices/platform/LNRO0005:1f/virtio2/host0/target0:0:0/0:0:0:0/block/sda/sda1/uevent': Permission denied

374s sda15: Failed to write 'change' to '/sys/devices/platform/LNRO0005:1f/virtio2/host0/target0:0:0/0:0:0:0/block/sda/sda15/uevent': Permission denied

374s sda2: Failed to write 'change' to '/sys/devices/platform/LNRO0005:1f/virtio2/host0/target0:0:0/0:0:0:0/block/sda/sda2/uevent': Permission denied

374s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied

374s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied

374s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied

374s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied

374s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied

374s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied

374s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied

374s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied

374s loop8: Failed to write 'change' to '/sys/devices/virtual/block/loop8/uevent': Permission denied

374s loop9: Failed to write 'change' to '/sys/devices/virtual/block/loop9/uevent': Permission denied

375s Setting up cloud-init (24.1.2-0ubuntu1) ...
378s Setting up ubuntu-minimal (1.536build1) ...
378s Setting up ubuntu-standard (1.536build1) ...
378s Processing triggers for libc-bin (2.39-0ubuntu6) ...
378s Processing triggers for ufw (0.36.2-5) ...
378s Processing triggers for install-info (7.1-3build1) ...
378s Processing triggers for initramfs-tools (0.142ubuntu23) ...
382s Reading package lists...
383s Building dependency tree...
383s Reading state information...
384s The following packages will be REMOVED:
384s   linux-headers-6.8.0-11* python3-distutils* python3-lib2to3*
385s 0 upgraded, 0 newly installed, 3 to remove and 1 not upgraded.
385s After this operation, 86.5 MB disk space will be freed.
385s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 78647 files and directories currently installed.)
385s Removing linux-headers-6.8.0-11 (6.8.0-11.11) ...
387s Removing python3-distutils (3.12.2-3ubuntu1.1) ...
387s Removing python3-lib2to3 (3.12.2-3ubuntu1.1) ...
390s autopkgtest [12:24:39]: rebooting testbed after setup commands that affected boot
444s autopkgtest [12:25:33]: testbed running kernel: Linux 5.4.0-170-generic #188-Ubuntu SMP Wed Jan 10 09:51:10 UTC 2024
470s autopkgtest [12:25:59]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-mcmc
481s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-mcmc 0.9-8-1 (dsc) [2083 B]
481s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-mcmc 0.9-8-1 (tar) [1542 kB]
481s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-mcmc 0.9-8-1 (diff) [3320 B]
481s gpgv: Signature made Tue Nov 21 10:57:44 2023 UTC
481s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
481s gpgv:                issuer "tille@debian.org"
481s gpgv: Can't check signature: No public key
481s dpkg-source: warning: cannot verify inline signature for ./r-cran-mcmc_0.9-8-1.dsc: no acceptable signature found
481s autopkgtest [12:26:10]: testing package r-cran-mcmc version 0.9-8-1
483s autopkgtest [12:26:12]: build not needed
487s autopkgtest [12:26:16]: test generic: preparing testbed
497s Reading package lists...
497s Building dependency tree...
497s Reading state information...
498s Starting pkgProblemResolver with broken count: 0
498s Starting 2 pkgProblemResolver with broken count: 0
498s Done
500s The following additional packages will be installed:
500s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3
500s   libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5
500s   libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8
500s   libjpeg8 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0
500s   libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6
500s   libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0
500s   libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-iso
500s   r-cran-mcmc r-cran-xtable unzip x11-common xdg-utils zip
500s Suggested packages:
500s   tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html
500s   r-cran-knitr r-cran-plm r-cran-zoo r-cran-survival
500s Recommended packages:
500s   r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl
500s   libx11-protocol-perl x11-utils x11-xserver-utils
500s The following NEW packages will be installed:
500s   autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core
500s   fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1
500s   libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6
500s   libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
500s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
500s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
500s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
500s   r-base-core r-cran-iso r-cran-mcmc r-cran-xtable unzip x11-common xdg-utils
500s   zip
500s 0 upgraded, 49 newly installed, 0 to remove and 1 not upgraded.
500s Need to get 38.0 MB/38.0 MB of archives.
500s After this operation, 68.1 MB of additional disk space will be used.
500s Get:1 /tmp/autopkgtest.K77nQb/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [716 B]
500s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfreetype6 armhf 2.13.2+dfsg-1build2 [331 kB]
500s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf fonts-dejavu-mono all 2.37-8 [502 kB]
500s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf fonts-dejavu-core all 2.37-8 [835 kB]
501s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu1 [37.4 kB]
501s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu1 [113 kB]
501s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fontconfig armhf 2.15.0-1.1ubuntu1 [189 kB]
501s Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libblas3 armhf 3.12.0-3 [123 kB]
501s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libpixman-1-0 armhf 0.42.2-1 [184 kB]
501s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-render0 armhf 1.15-1 [15.2 kB]
501s Get:11 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-shm0 armhf 1.15-1 [5852 B]
501s Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libxrender1 armhf 1:0.9.10-1.1 [16.5 kB]
501s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcairo2 armhf 1.18.0-1ubuntu1 [482 kB]
501s Get:14 http://ftpmaster.internal/ubuntu noble/main armhf libdatrie1 armhf 0.2.13-3 [16.9 kB]
501s Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB]
501s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgfortran5 armhf 14-20240315-1ubuntu1 [312 kB]
501s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgomp1 armhf 14-20240315-1ubuntu1 [125 kB]
501s Get:18 http://ftpmaster.internal/ubuntu noble/main armhf libgraphite2-3 armhf 1.3.14-2 [72.7 kB]
501s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libharfbuzz0b armhf 8.3.0-2build1 [446 kB]
501s Get:20 http://ftpmaster.internal/ubuntu noble/main armhf x11-common all 1:7.7+23ubuntu2 [23.4 kB]
501s Get:21 http://ftpmaster.internal/ubuntu noble/main armhf libice6 armhf 2:1.0.10-1build2 [36.4 kB]
501s Get:22 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu1 [123 kB]
501s Get:23 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B]
501s Get:24 http://ftpmaster.internal/ubuntu noble/main armhf liblapack3 armhf 3.12.0-3 [2085 kB]
501s Get:25 http://ftpmaster.internal/ubuntu noble/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu1 [152 kB]
501s Get:26 http://ftpmaster.internal/ubuntu noble/main armhf libthai-data all 0.1.29-2 [158 kB]
501s Get:27 http://ftpmaster.internal/ubuntu noble/main armhf libthai0 armhf 0.1.29-2 [15.1 kB]
501s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpango-1.0-0 armhf 1.52.1+ds-1 [206 kB]
501s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpangoft2-1.0-0 armhf 1.52.1+ds-1 [36.4 kB]
501s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpangocairo-1.0-0 armhf 1.52.1+ds-1 [24.9 kB]
501s Get:31 http://ftpmaster.internal/ubuntu noble/main armhf libpaper1 armhf 1.1.29 [12.5 kB]
501s Get:32 http://ftpmaster.internal/ubuntu noble/main armhf libpaper-utils armhf 1.1.29 [8170 B]
501s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsharpyuv0 armhf 1.3.2-0.4build2 [13.6 kB]
501s Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libsm6 armhf 2:1.2.3-1build2 [15.1 kB]
501s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtcl8.6 armhf 8.6.14+dfsg-1 [903 kB]
501s Get:36 http://ftpmaster.internal/ubuntu noble/main armhf libjbig0 armhf 2.1-6.1ubuntu1 [24.9 kB]
501s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libwebp7 armhf 1.3.2-0.4build2 [183 kB]
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501s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf r-base-core armhf 4.3.3-2build1 [26.6 MB]
502s Get:47 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-iso armhf 0.0-21-1 [164 kB]
502s Get:48 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-mcmc armhf 0.9-8-1 [1222 kB]
502s Get:49 http://ftpmaster.internal/ubuntu noble/universe armhf r-cran-xtable all 1:1.8-4-2 [689 kB]
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508s 
508s Creating config file /etc/papersize with new version
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509s Setting up libfreetype6:armhf (2.13.2+dfsg-1build2) ...
509s Setting up fonts-dejavu-mono (2.37-8) ...
509s Setting up libtcl8.6:armhf (8.6.14+dfsg-1) ...
509s Setting up fonts-dejavu-core (2.37-8) ...
509s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu1) ...
509s Setting up libgfortran5:armhf (14-20240315-1ubuntu1) ...
509s Setting up libwebp7:armhf (1.3.2-0.4build2) ...
509s Setting up libharfbuzz0b:armhf (8.3.0-2build1) ...
509s Setting up libthai-data (0.1.29-2) ...
509s Setting up libxss1:armhf (1:1.2.3-1build2) ...
509s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
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509s Setting up liblapack3:armhf (3.12.0-3) ...
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509s Setting up fontconfig-config (2.15.0-1.1ubuntu1) ...
509s Setting up libthai0:armhf (0.1.29-2) ...
509s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu1) ...
509s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu1) ...
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509s Setting up fontconfig (2.15.0-1.1ubuntu1) ...
511s Regenerating fonts cache... done.
511s Setting up libxft2:armhf (2.3.6-1) ...
511s Setting up libtk8.6:armhf (8.6.14-1) ...
511s Setting up libpango-1.0-0:armhf (1.52.1+ds-1) ...
511s Setting up libcairo2:armhf (1.18.0-1ubuntu1) ...
511s Setting up libxt6t64:armhf (1:1.2.1-1.2) ...
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511s Setting up r-base-core (4.3.3-2build1) ...
512s 
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512s Setting up r-cran-iso (0.0-21-1) ...
512s Setting up r-cran-xtable (1:1.8-4-2) ...
512s Setting up autopkgtest-satdep (0) ...
512s Processing triggers for man-db (2.12.0-3build4) ...
513s Processing triggers for install-info (7.1-3build1) ...
513s Processing triggers for libc-bin (2.39-0ubuntu6) ...
532s (Reading database ... 60588 files and directories currently installed.)
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538s autopkgtest [12:27:07]: test generic: [-----------------------
540s BEGIN TEST tests/accept-batch.R
540s 
540s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
540s Copyright (C) 2024 The R Foundation for Statistical Computing
540s Platform: arm-unknown-linux-gnueabihf (32-bit)
540s 
540s R is free software and comes with ABSOLUTELY NO WARRANTY.
540s You are welcome to redistribute it under certain conditions.
540s Type 'license()' or 'licence()' for distribution details.
540s 
540s R is a collaborative project with many contributors.
540s Type 'contributors()' for more information and
540s 'citation()' on how to cite R or R packages in publications.
540s 
540s Type 'demo()' for some demos, 'help()' for on-line help, or
540s 'help.start()' for an HTML browser interface to help.
540s Type 'q()' to quit R.
540s 
540s > 
540s > # new feature batching acceptance rates
540s > 
540s >  set.seed(42)
540s > 
540s >  library(mcmc)
540s > 
540s >  h <- function(x) if (all(x >= 0) && sum(x) <= 1) return(1) else return(-Inf)
540s >  out <- metrop(h, rep(0, 5), nbatch = 100, blen = 100, scale = 0.1,
540s +      debug = TRUE)
540s > 
540s >  all.equal(out$accept, mean(out$accept.batch))
540s [1] TRUE
540s > 
540s >  foo <- matrix(out$debug.accept, nrow = out$blen)
540s >  bar <- colMeans(foo)
540s >  all.equal(out$accept.batch, bar)
540s [1] TRUE
540s > 
540s >  options(digits = 4) # try to keep insanity of computer arithmetic under control
540s > 
540s >  out$accept
540s [1] 0.2257
540s >  t.test(out$accept.batch)$conf.int
540s [1] 0.2124 0.2390
540s attr(,"conf.level")
540s [1] 0.95
540s > 
540s > 
540s BEGIN TEST tests/circle.R
541s 
541s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
541s Copyright (C) 2024 The R Foundation for Statistical Computing
541s Platform: arm-unknown-linux-gnueabihf (32-bit)
541s 
541s R is free software and comes with ABSOLUTELY NO WARRANTY.
541s You are welcome to redistribute it under certain conditions.
541s Type 'license()' or 'licence()' for distribution details.
541s 
541s R is a collaborative project with many contributors.
541s Type 'contributors()' for more information and
541s 'citation()' on how to cite R or R packages in publications.
541s 
541s Type 'demo()' for some demos, 'help()' for on-line help, or
541s 'help.start()' for an HTML browser interface to help.
541s Type 'q()' to quit R.
541s 
541s > 
541s >  epsilon <- 1e-15
541s > 
541s >  library(mcmc)
541s > 
541s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
541s >  set.seed(42)
541s > 
541s >  d <- 5
541s > 
541s >  logh <- function(x) {
541s +      if (! is.numeric(x)) stop("x not numeric")
541s +      if (length(x) != d) stop("length(x) != d")
541s +      fred <- 1 - sum(x^2)
541s +      if (fred > 0) return(log(fred)) else return(-Inf)
541s +  }
541s > 
541s >  out.metro <- metrop(logh, rep(0, d), 1e3, scale = 0.01)
541s >  out.metro$accept
541s [1] 0.979
541s > 
541s >  out.metro <- metrop(out.metro, scale = 0.1)
541s >  out.metro$accept
541s [1] 0.72
541s > 
541s >  out.metro <- metrop(out.metro, scale = 0.5)
541s >  out.metro$accept
541s [1] 0.16
541s > 
541s >  out.metro <- metrop(out.metro, scale = 0.4)
541s >  out.metro$accept
541s [1] 0.228
541s > 
541s >  out.metro <- metrop(out.metro, nbatch = 1e2, debug = TRUE)
541s > 
541s >  all(out.metro$batch[- out.metro$nbatch, ] == out.metro$current[- 1, ])
541s [1] TRUE
541s >  all(out.metro$current[1, ] == out.metro$initial)
541s [1] TRUE
541s >  all(out.metro$batch[out.metro$nbatch, ] == out.metro$final)
541s [1] TRUE
541s > 
541s >  .Random.seed <- out.metro$initial.seed
541s >  d <- ncol(out.metro$proposal)
541s >  n <- nrow(out.metro$proposal)
541s >  my.proposal <- matrix(NA, n, d)
541s >  my.u <- double(n)
541s >  ska <- out.metro$scale
541s >  for (i in 1:n) {
541s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
541s +      if (is.na(out.metro$u[i])) {
541s +          my.u[i] <- NA
541s +      } else {
541s +          my.u[i] <- runif(1)
541s +      }
541s +  }
541s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
541s [1] TRUE
541s >  all(is.na(out.metro$u) == is.na(my.u))
541s [1] TRUE
541s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
541s [1] TRUE
541s > 
541s >  my.curr.log.green <- apply(out.metro$current, 1, logh)
541s >  my.prop.log.green <- apply(out.metro$proposal, 1, logh)
541s >  all(is.na(out.metro$u) == ((my.prop.log.green == -Inf) |
541s +      (my.prop.log.green > my.curr.log.green)))
541s [1] TRUE
541s >  foo <- my.prop.log.green - my.curr.log.green
541s >  blurfle <- foo - out.metro$log.green
541s >  blurfle[foo == -Inf & out.metro$log.green == -Inf] <- 0
541s >  max(blurfle) < epsilon
541s [1] TRUE
541s > 
541s >  my.accept <- (my.prop.log.green > -Inf) & (is.na(my.u) | my.u < exp(foo))
541s >  sum(my.accept) == round(n * out.metro$accept)
541s [1] TRUE
541s > 
541s >  my.path <- matrix(NA, n, d)
541s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
541s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
541s > 
541s >  all(my.path == out.metro$batch)
541s [1] TRUE
541s > 
541s > 
541s BEGIN TEST tests/initseq.R
541s 
541s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
541s Copyright (C) 2024 The R Foundation for Statistical Computing
541s Platform: arm-unknown-linux-gnueabihf (32-bit)
541s 
541s R is free software and comes with ABSOLUTELY NO WARRANTY.
541s You are welcome to redistribute it under certain conditions.
541s Type 'license()' or 'licence()' for distribution details.
541s 
541s R is a collaborative project with many contributors.
541s Type 'contributors()' for more information and
541s 'citation()' on how to cite R or R packages in publications.
541s 
541s Type 'demo()' for some demos, 'help()' for on-line help, or
541s 'help.start()' for an HTML browser interface to help.
541s Type 'q()' to quit R.
541s 
542s > 
542s >  library(mcmc)
542s > 
542s >  set.seed(42)
542s > 
542s >  n <- 1e5
542s >  rho <- 0.99
542s > 
542s >  x <- arima.sim(model = list(ar = rho), n = n)
542s >  gamma <- acf(x, lag.max = 1999, type = "covariance",
542s +      plot = FALSE)$acf
544s >  k <- seq(along = gamma)
544s >  Gamma <- gamma[k %% 2 == 1] + gamma[k %% 2 == 0]
544s >  k <- min(seq(along = Gamma)[Gamma < 0])
544s >  Gamma <- Gamma[1:k]
544s >  Gamma[k] < 0
544s [1] TRUE
544s >  Gamma[k] <- 0
544s > 
544s >  out <- .Call(mcmc:::C_initseq, x - mean(x))
544s >  names(out)
544s [1] "gamma0"    "Gamma.pos" "Gamma.dec" "Gamma.con" "var.pos"   "var.dec"  
544s [7] "var.con"  
544s > 
544s >  all.equal(gamma[1], out$gamma0)
544s [1] TRUE
544s > 
544s >  length(out$Gamma.pos) == length(Gamma)
544s [1] TRUE
544s >  all.equal(out$Gamma.pos, Gamma)
544s [1] TRUE
544s > 
544s >  Gamma.dec <- cummin(Gamma)
544s >  all.equal(out$Gamma.dec, Gamma.dec)
544s [1] TRUE
544s >  
544s > ## IGNORE_RDIFF_BEGIN
544s > library(Iso)
544s Iso 0.0-21
544s 
544s      An "infelicity" in the function ufit() (whereby 
544s      it was all too easy to conflate the location of 
544s      the mode with its index in the entries of the 
544s      "x" argument) has been corrected.  To this end, 
544s      ufit() now has arguments "lmode" (the location 
544s      of the mode), and "imode" (its index).  At most 
544s      one of these arguments should be specified.  See 
544s      the help for ufit().
544s > ## IGNORE_RDIFF_END
544s >  Gamma.con <- Gamma.dec[1] + cumsum(c(0, pava(diff(Gamma.dec))))
544s >  all.equal(out$Gamma.con, Gamma.con)
544s [1] TRUE
544s > 
544s >  all.equal(0, min(out$Gamma.pos - out$Gamma.dec))
544s [1] TRUE
544s >  max(diff(out$Gamma.dec)) < sqrt(.Machine$double.eps)
544s [1] TRUE
544s > 
544s >  all.equal(0, min(out$Gamma.dec - out$Gamma.con))
544s [1] TRUE
544s >  min(diff(diff(out$Gamma.con))) > (- sqrt(.Machine$double.eps))
544s [1] TRUE
544s > 
544s >  all.equal(2 * sum(out$Gamma.pos) - out$gamma0, out$var.pos)
544s [1] TRUE
544s >  all.equal(2 * sum(out$Gamma.dec) - out$gamma0, out$var.dec)
544s [1] TRUE
544s >  all.equal(2 * sum(out$Gamma.con) - out$gamma0, out$var.con)
544s [1] TRUE
544s > 
544s >  rev(out$Gamma.pos)[1] == 0
544s [1] TRUE
544s >  rev(out$Gamma.dec)[1] == 0
544s [1] TRUE
544s >  all.equal(rev(out$Gamma.con)[1], 0)
544s [1] TRUE
544s > 
544s > 
544s BEGIN TEST tests/isotropic.R
545s 
545s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
545s Copyright (C) 2024 The R Foundation for Statistical Computing
545s Platform: arm-unknown-linux-gnueabihf (32-bit)
545s 
545s R is free software and comes with ABSOLUTELY NO WARRANTY.
545s You are welcome to redistribute it under certain conditions.
545s Type 'license()' or 'licence()' for distribution details.
545s 
545s R is a collaborative project with many contributors.
545s Type 'contributors()' for more information and
545s 'citation()' on how to cite R or R packages in publications.
545s 
545s Type 'demo()' for some demos, 'help()' for on-line help, or
545s 'help.start()' for an HTML browser interface to help.
545s Type 'q()' to quit R.
545s 
545s > library(mcmc)
545s > isotropic <- mcmc:::isotropic
545s > isotropic.logjacobian <- mcmc:::isotropic.logjacobian
545s > 
545s > # create identity test function
545s > identity <- function(x) x
545s > d.identity <- function(x) 1
545s > 
545s > # check that isotropic is length preserving for vectors of lengths 1--1000
545s > all(sapply(1:1000, function(x) length(isotropic(identity)(rep(1, x))) == x))
545s [1] TRUE
545s >     
545s > # test that isotropic(identity) is an identity function
545s > all.equal(isotropic(identity)(1:10), 1:10)
545s [1] TRUE
545s > x <- seq(0, 1, length.out=200)
545s > all.equal(isotropic(identity)(x), x)
545s [1] TRUE
545s > 
545s > # make sure that isotropic.logjacobian(identity, d.identity) is a 0 function
545s > all.equal(isotropic.logjacobian(identity, d.identity)(1:10), 0)
545s [1] TRUE
545s > 
545s > # make sure that 0 as an input does not cause divide-by-zero errors
545s > all.equal(isotropic(identity)(0), 0)
545s [1] TRUE
545s > all.equal(isotropic(identity)(0 * 1:4), rep(0, 4))
545s [1] TRUE
545s > all.equal(isotropic.logjacobian(identity, d.identity)(0), 0)
545s [1] TRUE
545s > all.equal(isotropic.logjacobian(identity, d.identity)(0 * 1:4), 0)
545s [1] TRUE
545s > 
545s > # try isotropic with f(x) = x^2, then we should get 
545s > # istropic(f)(x) := |x| * x
545s > f <- function(x) x^2
545s > all.equal(isotropic(f)(1), 1)
545s [1] TRUE
545s > all.equal(isotropic(f)(c(1, 1)), sqrt(2) * c(1, 1))
545s [1] TRUE
545s > all.equal(isotropic(f)(c(1, 0, 1)), sqrt(2) * c(1, 0, 1))
545s [1] TRUE
545s > 
545s > # make sure lazy-loading works properly.
545s > g <- function(x) x^2
545s > g.iso <- isotropic(g)
545s > g <- function(x) x
545s > all.equal(g.iso(2), 2*2)
545s [1] TRUE
545s > 
545s BEGIN TEST tests/logit.R
545s 
545s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
545s Copyright (C) 2024 The R Foundation for Statistical Computing
545s Platform: arm-unknown-linux-gnueabihf (32-bit)
545s 
545s R is free software and comes with ABSOLUTELY NO WARRANTY.
545s You are welcome to redistribute it under certain conditions.
545s Type 'license()' or 'licence()' for distribution details.
545s 
545s R is a collaborative project with many contributors.
545s Type 'contributors()' for more information and
545s 'citation()' on how to cite R or R packages in publications.
545s 
545s Type 'demo()' for some demos, 'help()' for on-line help, or
545s 'help.start()' for an HTML browser interface to help.
545s Type 'q()' to quit R.
545s 
545s > 
545s >  epsilon <- 1e-15
545s > 
545s >  library(mcmc)
545s > 
545s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
545s >  set.seed(42)
545s > 
545s >  options(digits = 3)
545s > 
545s >  n <- 100
545s >  rho <- 0.5
545s >  beta0 <- 0.25
545s >  beta1 <- 1
545s >  beta2 <- 0.5
545s > 
545s >  x1 <- rnorm(n)
545s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
545s >  eta <- beta0 + beta1 * x1 + beta2 * x2
545s >  p <- 1 / (1 + exp(- eta))
545s >  y <- as.numeric(runif(n) < p)
545s > 
545s >  out <- glm(y ~ x1 + x2, family = binomial())
545s > ## IGNORE_RDIFF_BEGIN
545s >  summary(out)
545s 
545s Call:
545s glm(formula = y ~ x1 + x2, family = binomial())
545s 
545s Coefficients:
545s             Estimate Std. Error z value Pr(>|z|)    
545s (Intercept)   0.0599     0.2477    0.24  0.80905    
545s x1            1.3682     0.3844    3.56  0.00037 ***
545s x2            0.4760     0.3135    1.52  0.12886    
545s ---
545s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
545s 
545s (Dispersion parameter for binomial family taken to be 1)
545s 
545s     Null deviance: 138.469  on 99  degrees of freedom
545s Residual deviance:  99.293  on 97  degrees of freedom
545s AIC: 105.3
545s 
545s Number of Fisher Scoring iterations: 5
545s 
545s > ## IGNORE_RDIFF_END
545s > 
545s >  mlogl <- function(beta) {
545s +      if (length(beta) != 3) stop("length(beta) != 3")
545s +      beta0 <- beta[1]
545s +      beta1 <- beta[2]
545s +      beta2 <- beta[3]
545s +      eta <- beta0 + beta1 * x1 + beta2 * x2
545s +      p <- exp(eta) / (1 + exp(eta))
545s +      return(- sum(log(p[y == 1])) - sum(log(1 - p[y == 0])))
545s +  }
545s > 
545s > ## IGNORE_RDIFF_BEGIN
545s >  out.nlm <- nlm(mlogl, coefficients(out), print.level = 2)
545s iteration = 0
545s Parameter:
545s [1] 0.0599 1.3682 0.4760
545s Function Value
545s [1] 49.6
545s Gradient:
545s [1] 8.24e-06 5.50e-06 6.08e-06
545s 
545s Relative gradient close to zero.
545s Current iterate is probably solution.
545s 
545s > ## IGNORE_RDIFF_END
545s > 
545s >  logl <- function(beta) {
545s +      if (length(beta) != 3) stop("length(beta) != 3")
545s +      beta0 <- beta[1]
545s +      beta1 <- beta[2]
545s +      beta2 <- beta[3]
545s +      eta <- beta0 + beta1 * x1 + beta2 * x2
545s +      p <- exp(eta) / (1 + exp(eta))
545s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
546s +  }
546s > 
546s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
546s >  out.metro$accept
546s [1] 0.982
546s > 
546s >  out.metro <- metrop(out.metro, scale = 0.1)
546s >  out.metro$accept
546s [1] 0.795
546s > 
546s >  out.metro <- metrop(out.metro, scale = 0.5)
546s >  out.metro$accept
546s [1] 0.264
546s > 
546s >  apply(out.metro$batch, 2, mean)
546s [1] 0.0608 1.4230 0.5263
546s >  var(out.metro$batch)
546s          [,1]    [,2]     [,3]
546s [1,]  0.06755 -0.0108  0.00989
546s [2,] -0.01080  0.1758 -0.06155
546s [3,]  0.00989 -0.0615  0.10483
546s >  olbm(out.metro$batch, 25)
546s           [,1]      [,2]      [,3]
546s [1,]  4.54e-04  9.47e-05 -1.92e-05
546s [2,]  9.47e-05  1.84e-03 -6.45e-04
546s [3,] -1.92e-05 -6.45e-04  9.09e-04
546s > 
546s >  saveseed <- .Random.seed
546s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
546s +      scale = 0.5, debug = TRUE)
546s > 
546s >  all(out.metro$batch[- out.metro$nbatch, ] == out.metro$current[- 1, ])
546s [1] TRUE
546s >  all(out.metro$current[1, ] == out.metro$initial)
546s [1] TRUE
546s >  all(out.metro$batch[out.metro$nbatch, ] == out.metro$final)
546s [1] TRUE
546s > 
546s >  .Random.seed <- saveseed
546s >  d <- ncol(out.metro$proposal)
546s >  n <- nrow(out.metro$proposal)
546s >  my.proposal <- matrix(NA, n, d)
546s >  my.u <- double(n)
546s >  ska <- out.metro$scale
546s >  for (i in 1:n) {
546s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
546s +      if (is.na(out.metro$u[i])) {
546s +          my.u[i] <- NA
546s +      } else {
546s +          my.u[i] <- runif(1)
546s +      }
546s +  }
546s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
546s [1] TRUE
546s >  all(is.na(out.metro$u) == is.na(my.u))
546s [1] TRUE
546s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
546s [1] TRUE
546s > 
546s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
546s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
546s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
546s [1] TRUE
546s >  foo <- my.prop.log.green - my.curr.log.green
546s >  max(abs(foo - out.metro$log.green)) < epsilon
546s [1] TRUE
546s > 
546s >  my.accept <- is.na(my.u) | my.u < exp(foo)
546s >  sum(my.accept) == round(n * out.metro$accept)
546s [1] TRUE
546s > 
546s >  my.path <- matrix(NA, n, d)
546s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
546s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
546s > 
546s >  all(my.path == out.metro$batch)
546s [1] TRUE
546s > 
546s > 
546s BEGIN TEST tests/logitbat.R
546s 
546s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
546s Copyright (C) 2024 The R Foundation for Statistical Computing
546s Platform: arm-unknown-linux-gnueabihf (32-bit)
546s 
546s R is free software and comes with ABSOLUTELY NO WARRANTY.
546s You are welcome to redistribute it under certain conditions.
546s Type 'license()' or 'licence()' for distribution details.
546s 
546s R is a collaborative project with many contributors.
546s Type 'contributors()' for more information and
546s 'citation()' on how to cite R or R packages in publications.
546s 
546s Type 'demo()' for some demos, 'help()' for on-line help, or
546s 'help.start()' for an HTML browser interface to help.
546s Type 'q()' to quit R.
546s 
546s > 
546s >  # test batching (blen)
546s > 
546s >  epsilon <- 1e-15
546s > 
546s >  library(mcmc)
546s > 
546s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
546s >  set.seed(42)
546s > 
546s >  n <- 100
546s >  rho <- 0.5
546s >  beta0 <- 0.25
546s >  beta1 <- 1
546s >  beta2 <- 0.5
546s > 
546s >  x1 <- rnorm(n)
546s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
546s >  eta <- beta0 + beta1 * x1 + beta2 * x2
546s >  p <- 1 / (1 + exp(- eta))
546s >  y <- as.numeric(runif(n) < p)
546s > 
546s >  out <- glm(y ~ x1 + x2, family = binomial())
546s > 
546s >  logl <- function(beta) {
546s +      if (length(beta) != 3) stop("length(beta) != 3")
546s +      beta0 <- beta[1]
546s +      beta1 <- beta[2]
546s +      beta2 <- beta[3]
546s +      eta <- beta0 + beta1 * x1 + beta2 * x2
546s +      p <- exp(eta) / (1 + exp(eta))
546s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
546s +  }
546s > 
546s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
547s >  out.metro$accept
547s [1] 0.982
547s > 
547s >  out.metro <- metrop(out.metro, scale = 0.1)
547s >  out.metro$accept
547s [1] 0.795
547s > 
547s >  out.metro <- metrop(out.metro, scale = 0.5)
547s >  out.metro$accept
547s [1] 0.264
547s > 
547s >  apply(out.metro$batch, 2, mean)
547s [1] 0.06080257 1.42304941 0.52634149
547s > 
547s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
547s +      scale = 0.5, debug = TRUE, blen = 5)
547s > 
547s >  niter <- out.metro$nbatch * out.metro$blen * out.metro$nspac
547s >  niter == nrow(out.metro$current)
547s [1] TRUE
547s >  niter == nrow(out.metro$proposal)
547s [1] TRUE
547s >  all(out.metro$current[1, ] == out.metro$initial)
547s [1] TRUE
547s >  all(out.metro$current[niter, ] == out.metro$final) |
547s +      all(out.metro$proposal[niter, ] == out.metro$final)
547s [1] TRUE
547s > 
547s >  .Random.seed <- out.metro$initial.seed
547s >  d <- ncol(out.metro$proposal)
547s >  n <- nrow(out.metro$proposal)
547s >  my.proposal <- matrix(NA, n, d)
547s >  my.u <- double(n)
547s >  ska <- out.metro$scale
547s >  for (i in 1:n) {
547s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
547s +      if (is.na(out.metro$u[i])) {
547s +          my.u[i] <- NA
547s +      } else {
547s +          my.u[i] <- runif(1)
547s +      }
547s +  }
547s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
547s [1] TRUE
547s >  all(is.na(out.metro$u) == is.na(my.u))
547s [1] TRUE
547s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
547s [1] TRUE
547s > 
547s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
547s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
547s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
547s [1] TRUE
547s >  foo <- my.prop.log.green - my.curr.log.green
547s >  max(abs(foo - out.metro$log.green)) < epsilon
547s [1] TRUE
547s > 
547s >  my.accept <- is.na(my.u) | my.u < exp(foo)
547s >  sum(my.accept) == round(n * out.metro$accept)
547s [1] TRUE
547s >  if (my.accept[niter]) {
547s +      all(out.metro$proposal[niter, ] == out.metro$final)
547s +  } else {
547s +      all(out.metro$current[niter, ] == out.metro$final)
547s +  }
547s [1] TRUE
547s > 
547s >  my.current <- out.metro$current
547s >  my.current[my.accept, ] <- my.proposal[my.accept, ]
547s >  my.current <- rbind(out.metro$initial, my.current[- niter, ])
547s >  max(abs(out.metro$current - my.current)) < epsilon
547s [1] TRUE
547s > 
547s >  my.path <- matrix(NA, n, d)
547s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
547s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
547s >  nspac <- out.metro$nspac
547s > 
547s >  my.path <- my.path[seq(nspac, niter, by = nspac), ]
547s > 
547s >  foom <- array(as.vector(t(my.path)), c(d, out.metro$blen, out.metro$nbatch))
547s >  boom <- t(apply(foom, c(1, 3), mean))
547s > 
547s >  all(dim(boom) == dim(out.metro$batch))
547s [1] TRUE
547s >  max(abs(boom - out.metro$batch)) < epsilon
547s [1] TRUE
547s > 
547s > 
547s BEGIN TEST tests/logitfun.R
547s 
547s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
547s Copyright (C) 2024 The R Foundation for Statistical Computing
547s Platform: arm-unknown-linux-gnueabihf (32-bit)
547s 
547s R is free software and comes with ABSOLUTELY NO WARRANTY.
547s You are welcome to redistribute it under certain conditions.
547s Type 'license()' or 'licence()' for distribution details.
547s 
547s R is a collaborative project with many contributors.
547s Type 'contributors()' for more information and
547s 'citation()' on how to cite R or R packages in publications.
547s 
547s Type 'demo()' for some demos, 'help()' for on-line help, or
547s 'help.start()' for an HTML browser interface to help.
547s Type 'q()' to quit R.
547s 
547s > 
547s >  # test outfun (function)
547s > 
547s >  epsilon <- 1e-15
547s > 
547s >  library(mcmc)
547s > 
547s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
547s >  set.seed(42)
547s > 
547s >  n <- 100
547s >  rho <- 0.5
547s >  beta0 <- 0.25
547s >  beta1 <- 1
547s >  beta2 <- 0.5
547s > 
547s >  x1 <- rnorm(n)
547s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
547s >  eta <- beta0 + beta1 * x1 + beta2 * x2
547s >  p <- 1 / (1 + exp(- eta))
547s >  y <- as.numeric(runif(n) < p)
547s > 
547s >  out <- glm(y ~ x1 + x2, family = binomial())
547s > 
547s >  logl <- function(beta) {
547s +      if (length(beta) != 3) stop("length(beta) != 3")
547s +      beta0 <- beta[1]
547s +      beta1 <- beta[2]
547s +      beta2 <- beta[3]
547s +      eta <- beta0 + beta1 * x1 + beta2 * x2
547s +      p <- exp(eta) / (1 + exp(eta))
547s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
547s +  }
547s > 
547s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
547s >  out.metro$accept
547s [1] 0.982
547s > 
547s >  out.metro <- metrop(out.metro, scale = 0.1)
548s >  out.metro$accept
548s [1] 0.795
548s > 
548s >  out.metro <- metrop(out.metro, scale = 0.5)
548s >  out.metro$accept
548s [1] 0.264
548s > 
548s >  apply(out.metro$batch, 2, mean)
548s [1] 0.06080257 1.42304941 0.52634149
548s > 
548s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
548s +      scale = 0.5, debug = TRUE, outfun = function(x) c(x, x^2))
548s > 
548s >  niter <- out.metro$nbatch * out.metro$blen * out.metro$nspac
548s >  niter == nrow(out.metro$current)
548s [1] TRUE
548s >  niter == nrow(out.metro$proposal)
548s [1] TRUE
548s >  all(out.metro$current[1, ] == out.metro$initial)
548s [1] TRUE
548s >  all(out.metro$current[niter, ] == out.metro$final) |
548s +      all(out.metro$proposal[niter, ] == out.metro$final)
548s [1] TRUE
548s > 
548s >  .Random.seed <- out.metro$initial.seed
548s >  d <- ncol(out.metro$proposal)
548s >  n <- nrow(out.metro$proposal)
548s >  my.proposal <- matrix(NA, n, d)
548s >  my.u <- double(n)
548s >  ska <- out.metro$scale
548s >  for (i in 1:n) {
548s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
548s +      if (is.na(out.metro$u[i])) {
548s +          my.u[i] <- NA
548s +      } else {
548s +          my.u[i] <- runif(1)
548s +      }
548s +  }
548s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
548s [1] TRUE
548s >  all(is.na(out.metro$u) == is.na(my.u))
548s [1] TRUE
548s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
548s [1] TRUE
548s > 
548s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
548s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
548s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
548s [1] TRUE
548s >  foo <- my.prop.log.green - my.curr.log.green
548s >  max(abs(foo - out.metro$log.green)) < epsilon
548s [1] TRUE
548s > 
548s >  my.accept <- is.na(my.u) | my.u < exp(foo)
548s >  sum(my.accept) == round(n * out.metro$accept)
548s [1] TRUE
548s >  if (my.accept[niter]) {
548s +      all(out.metro$proposal[niter, ] == out.metro$final)
548s +  } else {
548s +      all(out.metro$current[niter, ] == out.metro$final)
548s +  }
548s [1] TRUE
548s > 
548s >  my.current <- out.metro$current
548s >  my.current[my.accept, ] <- my.proposal[my.accept, ]
548s >  my.current <- rbind(out.metro$initial, my.current[- niter, ])
548s >  max(abs(out.metro$current - my.current)) < epsilon
548s [1] TRUE
548s > 
548s >  my.path <- matrix(NA, n, d)
548s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
548s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
548s >  nspac <- out.metro$nspac
548s > 
548s >  my.path <- my.path[seq(nspac, niter, by = nspac), ]
548s > 
548s >  fred <- t(apply(my.path, 1, out.metro$outfun))
548s >  k <- ncol(fred)
548s > 
548s >  foom <- array(as.vector(t(fred)), c(k, out.metro$blen, out.metro$nbatch))
548s >  boom <- t(apply(foom, c(1, 3), mean))
548s > 
548s >  all(dim(boom) == dim(out.metro$batch))
548s [1] TRUE
548s >  max(abs(boom - out.metro$batch)) < epsilon
548s [1] TRUE
548s > 
548s >  goom <- cbind(my.path, my.path^2)
548s >  all(dim(goom) == dim(out.metro$batch))
548s [1] TRUE
548s >  max(abs(goom - out.metro$batch)) < epsilon
548s [1] TRUE
548s > 
548s BEGIN TEST tests/logitfunarg.R
548s 
548s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
548s Copyright (C) 2024 The R Foundation for Statistical Computing
548s Platform: arm-unknown-linux-gnueabihf (32-bit)
548s 
548s R is free software and comes with ABSOLUTELY NO WARRANTY.
548s You are welcome to redistribute it under certain conditions.
548s Type 'license()' or 'licence()' for distribution details.
548s 
548s R is a collaborative project with many contributors.
548s Type 'contributors()' for more information and
548s 'citation()' on how to cite R or R packages in publications.
548s 
548s Type 'demo()' for some demos, 'help()' for on-line help, or
548s 'help.start()' for an HTML browser interface to help.
548s Type 'q()' to quit R.
548s 
548s > 
548s >  # test outfun (function)
548s > 
548s >  epsilon <- 1e-15
548s > 
548s >  library(mcmc)
548s > 
548s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
548s >  set.seed(42)
548s > 
548s >  n <- 100
548s >  rho <- 0.5
548s >  beta0 <- 0.25
548s >  beta1 <- 1
548s >  beta2 <- 0.5
548s > 
548s >  x1 <- rnorm(n)
548s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
548s >  eta <- beta0 + beta1 * x1 + beta2 * x2
548s >  p <- 1 / (1 + exp(- eta))
548s >  y <- as.numeric(runif(n) < p)
548s > 
548s >  out <- glm(y ~ x1 + x2, family = binomial())
548s > 
548s >  logl <- function(beta) {
548s +      if (length(beta) != 3) stop("length(beta) != 3")
548s +      beta0 <- beta[1]
548s +      beta1 <- beta[2]
548s +      beta2 <- beta[3]
548s +      eta <- beta0 + beta1 * x1 + beta2 * x2
548s +      p <- exp(eta) / (1 + exp(eta))
548s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
548s +  }
548s > 
548s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
548s >  out.metro$accept
548s [1] 0.982
548s > 
548s >  out.metro <- metrop(out.metro, scale = 0.1)
548s >  out.metro$accept
548s [1] 0.795
548s > 
548s >  out.metro <- metrop(out.metro, scale = 0.5)
549s >  out.metro$accept
549s [1] 0.264
549s > 
549s >  apply(out.metro$batch, 2, mean)
549s [1] 0.06080257 1.42304941 0.52634149
549s > 
549s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
549s +      scale = 0.5, debug = TRUE, outfun = function(x) c(x, x^2))
549s > 
549s >  out.metro <- metrop(out.metro)
549s >  out.metro$outfun
549s function (x) 
549s c(x, x^2)
549s <bytecode: 0x384add8>
549s >  dim(out.metro$batch)
549s [1] 100   6
549s > 
549s >  logl <- function(beta, x1, x2, y) {
549s +      if (length(beta) != 3) stop("length(beta) != 3")
549s +      beta0 <- beta[1]
549s +      beta1 <- beta[2]
549s +      beta2 <- beta[3]
549s +      eta <- beta0 + beta1 * x1 + beta2 * x2
549s +      p <- exp(eta) / (1 + exp(eta))
549s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
549s +  }
549s > 
549s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
549s +      scale = 0.5, debug = TRUE, x1 = x1, x2 = x2, y = y)
549s >  out.metro$lud
549s function (beta, x1, x2, y) 
549s {
549s     if (length(beta) != 3) 
549s         stop("length(beta) != 3")
549s     beta0 <- beta[1]
549s     beta1 <- beta[2]
549s     beta2 <- beta[3]
549s     eta <- beta0 + beta1 * x1 + beta2 * x2
549s     p <- exp(eta)/(1 + exp(eta))
549s     return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
549s }
549s >  out.metro <- metrop(out.metro, x1 = x1, x2 = x2, y = y)
549s >  out.metro$lud
549s function (beta, x1, x2, y) 
549s {
549s     if (length(beta) != 3) 
549s         stop("length(beta) != 3")
549s     beta0 <- beta[1]
549s     beta1 <- beta[2]
549s     beta2 <- beta[3]
549s     eta <- beta0 + beta1 * x1 + beta2 * x2
549s     p <- exp(eta)/(1 + exp(eta))
549s     return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
549s }
549s > 
549s > 
549s BEGIN TEST tests/logitidx.R
549s 
549s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
549s Copyright (C) 2024 The R Foundation for Statistical Computing
549s Platform: arm-unknown-linux-gnueabihf (32-bit)
549s 
549s R is free software and comes with ABSOLUTELY NO WARRANTY.
549s You are welcome to redistribute it under certain conditions.
549s Type 'license()' or 'licence()' for distribution details.
549s 
549s R is a collaborative project with many contributors.
549s Type 'contributors()' for more information and
549s 'citation()' on how to cite R or R packages in publications.
549s 
549s Type 'demo()' for some demos, 'help()' for on-line help, or
549s 'help.start()' for an HTML browser interface to help.
549s Type 'q()' to quit R.
549s 
549s > 
549s >  # test outfun (positive index vector)
549s > 
549s >  epsilon <- 1e-15
549s > 
549s >  library(mcmc)
549s > 
549s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
549s >  set.seed(42)
549s > 
549s >  n <- 100
549s >  rho <- 0.5
549s >  beta0 <- 0.25
549s >  beta1 <- 1
549s >  beta2 <- 0.5
549s > 
549s >  x1 <- rnorm(n)
549s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
549s >  eta <- beta0 + beta1 * x1 + beta2 * x2
549s >  p <- 1 / (1 + exp(- eta))
549s >  y <- as.numeric(runif(n) < p)
549s > 
549s >  out <- glm(y ~ x1 + x2, family = binomial())
549s > 
549s >  logl <- function(beta) {
549s +      if (length(beta) != 3) stop("length(beta) != 3")
549s +      beta0 <- beta[1]
549s +      beta1 <- beta[2]
549s +      beta2 <- beta[3]
549s +      eta <- beta0 + beta1 * x1 + beta2 * x2
549s +      p <- exp(eta) / (1 + exp(eta))
549s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
549s +  }
549s > 
549s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
549s >  out.metro$accept
549s [1] 0.982
549s > 
549s >  out.metro <- metrop(out.metro, scale = 0.1)
549s >  out.metro$accept
549s [1] 0.795
549s > 
549s >  out.metro <- metrop(out.metro, scale = 0.5)
549s >  out.metro$accept
549s [1] 0.264
549s > 
549s >  apply(out.metro$batch, 2, mean)
549s [1] 0.06080257 1.42304941 0.52634149
549s > 
549s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
549s +      scale = 0.5, debug = TRUE, outfun = c(2, 3))
550s > 
550s >  niter <- out.metro$nbatch * out.metro$blen * out.metro$nspac
550s >  niter == nrow(out.metro$current)
550s [1] TRUE
550s >  niter == nrow(out.metro$proposal)
550s [1] TRUE
550s >  all(out.metro$current[1, ] == out.metro$initial)
550s [1] TRUE
550s >  all(out.metro$current[niter, ] == out.metro$final) |
550s +      all(out.metro$proposal[niter, ] == out.metro$final)
550s [1] TRUE
550s > 
550s >  .Random.seed <- out.metro$initial.seed
550s >  d <- ncol(out.metro$proposal)
550s >  n <- nrow(out.metro$proposal)
550s >  my.proposal <- matrix(NA, n, d)
550s >  my.u <- double(n)
550s >  ska <- out.metro$scale
550s >  for (i in 1:n) {
550s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
550s +      if (is.na(out.metro$u[i])) {
550s +          my.u[i] <- NA
550s +      } else {
550s +          my.u[i] <- runif(1)
550s +      }
550s +  }
550s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
550s [1] TRUE
550s >  all(is.na(out.metro$u) == is.na(my.u))
550s [1] TRUE
550s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
550s [1] TRUE
550s > 
550s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
550s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
550s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
550s [1] TRUE
550s >  foo <- my.prop.log.green - my.curr.log.green
550s >  max(abs(foo - out.metro$log.green)) < epsilon
550s [1] TRUE
550s > 
550s >  my.accept <- is.na(my.u) | my.u < exp(foo)
550s >  sum(my.accept) == round(n * out.metro$accept)
550s [1] TRUE
550s >  if (my.accept[niter]) {
550s +      all(out.metro$proposal[niter, ] == out.metro$final)
550s +  } else {
550s +      all(out.metro$current[niter, ] == out.metro$final)
550s +  }
550s [1] TRUE
550s > 
550s >  my.current <- out.metro$current
550s >  my.current[my.accept, ] <- my.proposal[my.accept, ]
550s >  my.current <- rbind(out.metro$initial, my.current[- niter, ])
550s >  max(abs(out.metro$current - my.current)) < epsilon
550s [1] TRUE
550s > 
550s >  my.path <- matrix(NA, n, d)
550s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
550s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
550s >  nspac <- out.metro$nspac
550s > 
550s >  my.path <- my.path[seq(nspac, niter, by = nspac), ]
550s > 
550s >  fred <- my.path[ , out.metro$outfun]
550s >  k <- ncol(fred)
550s > 
550s >  foom <- array(as.vector(t(fred)), c(k, out.metro$blen, out.metro$nbatch))
550s >  boom <- t(apply(foom, c(1, 3), mean))
550s > 
550s >  all(dim(boom) == dim(out.metro$batch))
550s [1] TRUE
550s >  max(abs(boom - out.metro$batch)) < epsilon
550s [1] TRUE
550s > 
550s > 
550s BEGIN TEST tests/logitlogidx.R
550s 
550s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
550s Copyright (C) 2024 The R Foundation for Statistical Computing
550s Platform: arm-unknown-linux-gnueabihf (32-bit)
550s 
550s R is free software and comes with ABSOLUTELY NO WARRANTY.
550s You are welcome to redistribute it under certain conditions.
550s Type 'license()' or 'licence()' for distribution details.
550s 
550s R is a collaborative project with many contributors.
550s Type 'contributors()' for more information and
550s 'citation()' on how to cite R or R packages in publications.
550s 
550s Type 'demo()' for some demos, 'help()' for on-line help, or
550s 'help.start()' for an HTML browser interface to help.
550s Type 'q()' to quit R.
550s 
550s > 
550s >  # test outfun (logical index vector)
550s > 
550s >  epsilon <- 1e-15
550s > 
550s >  library(mcmc)
550s > 
550s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
550s >  set.seed(42)
550s > 
550s >  n <- 100
550s >  rho <- 0.5
550s >  beta0 <- 0.25
550s >  beta1 <- 1
550s >  beta2 <- 0.5
550s > 
550s >  x1 <- rnorm(n)
550s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
550s >  eta <- beta0 + beta1 * x1 + beta2 * x2
550s >  p <- 1 / (1 + exp(- eta))
550s >  y <- as.numeric(runif(n) < p)
550s > 
550s >  out <- glm(y ~ x1 + x2, family = binomial())
550s > 
550s >  logl <- function(beta) {
550s +      if (length(beta) != 3) stop("length(beta) != 3")
550s +      beta0 <- beta[1]
550s +      beta1 <- beta[2]
550s +      beta2 <- beta[3]
550s +      eta <- beta0 + beta1 * x1 + beta2 * x2
550s +      p <- exp(eta) / (1 + exp(eta))
550s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
550s +  }
550s > 
550s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
550s >  out.metro$accept
550s [1] 0.982
550s > 
550s >  out.metro <- metrop(out.metro, scale = 0.1)
550s >  out.metro$accept
550s [1] 0.795
550s > 
550s >  out.metro <- metrop(out.metro, scale = 0.5)
550s >  out.metro$accept
550s [1] 0.264
550s > 
550s >  apply(out.metro$batch, 2, mean)
550s [1] 0.06080257 1.42304941 0.52634149
550s > 
550s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
550s +      scale = 0.5, debug = TRUE, outfun = seq(1:3) > 1)
550s > 
550s >  niter <- out.metro$nbatch * out.metro$blen * out.metro$nspac
550s >  niter == nrow(out.metro$current)
550s [1] TRUE
550s >  niter == nrow(out.metro$proposal)
550s [1] TRUE
550s >  all(out.metro$current[1, ] == out.metro$initial)
550s [1] TRUE
550s >  all(out.metro$current[niter, ] == out.metro$final) |
550s +      all(out.metro$proposal[niter, ] == out.metro$final)
550s [1] TRUE
550s > 
550s >  .Random.seed <- out.metro$initial.seed
550s >  d <- ncol(out.metro$proposal)
550s >  n <- nrow(out.metro$proposal)
550s >  my.proposal <- matrix(NA, n, d)
550s >  my.u <- double(n)
550s >  ska <- out.metro$scale
550s >  for (i in 1:n) {
550s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
550s +      if (is.na(out.metro$u[i])) {
550s +          my.u[i] <- NA
550s +      } else {
550s +          my.u[i] <- runif(1)
550s +      }
550s +  }
550s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
550s [1] TRUE
550s >  all(is.na(out.metro$u) == is.na(my.u))
550s [1] TRUE
550s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
550s [1] TRUE
550s > 
550s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
550s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
550s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
550s [1] TRUE
550s >  foo <- my.prop.log.green - my.curr.log.green
550s >  max(abs(foo - out.metro$log.green)) < epsilon
550s [1] TRUE
550s > 
550s >  my.accept <- is.na(my.u) | my.u < exp(foo)
550s >  sum(my.accept) == round(n * out.metro$accept)
550s [1] TRUE
550s >  if (my.accept[niter]) {
550s +      all(out.metro$proposal[niter, ] == out.metro$final)
550s +  } else {
550s +      all(out.metro$current[niter, ] == out.metro$final)
550s +  }
550s [1] TRUE
550s > 
550s >  my.current <- out.metro$current
550s >  my.current[my.accept, ] <- my.proposal[my.accept, ]
550s >  my.current <- rbind(out.metro$initial, my.current[- niter, ])
550s >  max(abs(out.metro$current - my.current)) < epsilon
550s [1] TRUE
550s > 
550s >  my.path <- matrix(NA, n, d)
550s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
550s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
550s >  nspac <- out.metro$nspac
550s > 
550s >  my.path <- my.path[seq(nspac, niter, by = nspac), ]
550s > 
550s >  fred <- my.path[ , out.metro$outfun]
550s >  k <- ncol(fred)
550s > 
550s >  foom <- array(as.vector(t(fred)), c(k, out.metro$blen, out.metro$nbatch))
550s >  boom <- t(apply(foom, c(1, 3), mean))
550s > 
550s >  all(dim(boom) == dim(out.metro$batch))
550s [1] TRUE
550s >  max(abs(boom - out.metro$batch)) < epsilon
550s [1] TRUE
550s > 
550s > 
550s BEGIN TEST tests/logitmat.R
550s 
550s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
550s Copyright (C) 2024 The R Foundation for Statistical Computing
550s Platform: arm-unknown-linux-gnueabihf (32-bit)
550s 
550s R is free software and comes with ABSOLUTELY NO WARRANTY.
550s You are welcome to redistribute it under certain conditions.
550s Type 'license()' or 'licence()' for distribution details.
550s 
550s R is a collaborative project with many contributors.
550s Type 'contributors()' for more information and
550s 'citation()' on how to cite R or R packages in publications.
550s 
550s Type 'demo()' for some demos, 'help()' for on-line help, or
550s 'help.start()' for an HTML browser interface to help.
550s Type 'q()' to quit R.
550s 
551s > 
551s >  # test matrix scaling
551s > 
551s >  epsilon <- 1e-15
551s > 
551s >  library(mcmc)
551s > 
551s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
551s >  set.seed(42)
551s > 
551s >  n <- 100
551s >  rho <- 0.5
551s >  beta0 <- 0.25
551s >  beta1 <- 1
551s >  beta2 <- 0.5
551s > 
551s >  x1 <- rnorm(n)
551s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
551s >  eta <- beta0 + beta1 * x1 + beta2 * x2
551s >  p <- 1 / (1 + exp(- eta))
551s >  y <- as.numeric(runif(n) < p)
551s > 
551s >  out <- glm(y ~ x1 + x2, family = binomial())
551s > 
551s >  logl <- function(beta) {
551s +      if (length(beta) != 3) stop("length(beta) != 3")
551s +      beta0 <- beta[1]
551s +      beta1 <- beta[2]
551s +      beta2 <- beta[3]
551s +      eta <- beta0 + beta1 * x1 + beta2 * x2
551s +      p <- exp(eta) / (1 + exp(eta))
551s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
551s +  }
551s > 
551s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
551s >  out.metro$accept
551s [1] 0.982
551s > 
551s >  out.metro <- metrop(out.metro, scale = 0.1)
551s >  out.metro$accept
551s [1] 0.795
551s > 
551s >  out.metro <- metrop(out.metro, scale = 0.5)
551s >  out.metro$accept
551s [1] 0.264
551s > 
551s >  apply(out.metro$batch, 2, mean)
551s [1] 0.06080257 1.42304941 0.52634149
551s >  fred <- var(out.metro$batch)
551s >  sally <- t(chol(fred))
551s >  max(abs(fred - sally %*% t(sally))) < epsilon
551s [1] TRUE
551s > 
551s >  out.metro <- metrop(out.metro, scale = sally)
551s >  out.metro$accept
551s [1] 0.451
551s > 
551s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
551s +      scale = sally, debug = TRUE)
551s >  names(out.metro)
551s  [1] "accept"       "batch"        "initial"      "final"        "accept.batch"
551s  [6] "current"      "proposal"     "log.green"    "u"            "z"           
551s [11] "debug.accept" "initial.seed" "final.seed"   "time"         "lud"         
551s [16] "nbatch"       "blen"         "nspac"        "scale"        "debug"       
551s > 
551s >  niter <- out.metro$nbatch * out.metro$blen * out.metro$nspac
551s >  niter == nrow(out.metro$current)
551s [1] TRUE
551s >  niter == nrow(out.metro$proposal)
551s [1] TRUE
551s >  all(out.metro$current[1, ] == out.metro$initial)
551s [1] TRUE
551s >  all(out.metro$current[niter, ] == out.metro$final) |
551s +      all(out.metro$proposal[niter, ] == out.metro$final)
551s [1] TRUE
551s > 
551s >  .Random.seed <- out.metro$initial.seed
551s >  d <- ncol(out.metro$proposal)
551s >  n <- nrow(out.metro$proposal)
551s >  my.proposal <- matrix(NA, n, d)
551s >  my.u <- double(n)
551s >  my.z <- matrix(NA, n, d)
551s >  ska <- out.metro$scale
551s >  for (i in 1:n) {
551s +      zed <- rnorm(d)
551s +      my.proposal[i, ] <- out.metro$current[i, ] + ska %*% zed
551s +      if (is.na(out.metro$u[i])) {
551s +          my.u[i] <- NA
551s +      } else {
551s +          my.u[i] <- runif(1)
551s +      }
551s +      my.z[i, ] <- zed
551s +  }
551s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
551s [1] TRUE
551s > 
551s >  all(is.na(out.metro$u) == is.na(my.u))
551s [1] TRUE
551s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
551s [1] TRUE
551s >  identical(out.metro$z, my.z)
551s [1] TRUE
551s > 
551s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
551s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
551s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
551s [1] TRUE
551s >  foo <- my.prop.log.green - my.curr.log.green
551s >  max(abs(foo - out.metro$log.green)) < epsilon
551s [1] TRUE
551s > 
551s >  my.accept <- is.na(my.u) | my.u < exp(foo)
551s >  sum(my.accept) == round(n * out.metro$accept)
551s [1] TRUE
551s >  if (my.accept[niter]) {
551s +      all(out.metro$proposal[niter, ] == out.metro$final)
551s +  } else {
551s +      all(out.metro$current[niter, ] == out.metro$final)
551s +  }
551s [1] TRUE
551s >  identical(my.accept, out.metro$debug.accept)
551s [1] TRUE
551s > 
551s >  my.current <- out.metro$current
551s >  my.current[my.accept, ] <- my.proposal[my.accept, ]
551s >  my.current <- rbind(out.metro$initial, my.current[- niter, ])
551s >  max(abs(out.metro$current - my.current)) < epsilon
551s [1] TRUE
551s > 
551s >  my.path <- matrix(NA, n, d)
551s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
551s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
551s >  nspac <- out.metro$nspac
551s > 
551s >  my.path <- my.path[seq(nspac, niter, by = nspac), ]
551s > 
551s >  fred <- my.path
551s >  k <- ncol(fred)
551s > 
551s >  foom <- array(as.vector(t(fred)), c(k, out.metro$blen, out.metro$nbatch))
551s >  boom <- t(apply(foom, c(1, 3), mean))
551s > 
551s >  all(dim(boom) == dim(out.metro$batch))
551s [1] TRUE
551s >  max(abs(boom - out.metro$batch)) < epsilon
551s [1] TRUE
551s > 
551s > 
551s BEGIN TEST tests/logitnegidx.R
551s 
551s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
551s Copyright (C) 2024 The R Foundation for Statistical Computing
551s Platform: arm-unknown-linux-gnueabihf (32-bit)
551s 
551s R is free software and comes with ABSOLUTELY NO WARRANTY.
551s You are welcome to redistribute it under certain conditions.
551s Type 'license()' or 'licence()' for distribution details.
551s 
551s R is a collaborative project with many contributors.
551s Type 'contributors()' for more information and
551s 'citation()' on how to cite R or R packages in publications.
551s 
551s Type 'demo()' for some demos, 'help()' for on-line help, or
551s 'help.start()' for an HTML browser interface to help.
551s Type 'q()' to quit R.
551s 
552s > 
552s >  # test outfun (negative index vector)
552s > 
552s >  epsilon <- 1e-15
552s > 
552s >  library(mcmc)
552s > 
552s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
552s >  set.seed(42)
552s > 
552s >  n <- 100
552s >  rho <- 0.5
552s >  beta0 <- 0.25
552s >  beta1 <- 1
552s >  beta2 <- 0.5
552s > 
552s >  x1 <- rnorm(n)
552s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
552s >  eta <- beta0 + beta1 * x1 + beta2 * x2
552s >  p <- 1 / (1 + exp(- eta))
552s >  y <- as.numeric(runif(n) < p)
552s > 
552s >  out <- glm(y ~ x1 + x2, family = binomial())
552s > 
552s >  logl <- function(beta) {
552s +      if (length(beta) != 3) stop("length(beta) != 3")
552s +      beta0 <- beta[1]
552s +      beta1 <- beta[2]
552s +      beta2 <- beta[3]
552s +      eta <- beta0 + beta1 * x1 + beta2 * x2
552s +      p <- exp(eta) / (1 + exp(eta))
552s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
552s +  }
552s > 
552s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
552s >  out.metro$accept
552s [1] 0.982
552s > 
552s >  out.metro <- metrop(out.metro, scale = 0.1)
552s >  out.metro$accept
552s [1] 0.795
552s > 
552s >  out.metro <- metrop(out.metro, scale = 0.5)
552s >  out.metro$accept
552s [1] 0.264
552s > 
552s >  apply(out.metro$batch, 2, mean)
552s [1] 0.06080257 1.42304941 0.52634149
552s > 
552s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
552s +      scale = 0.5, debug = TRUE, outfun = - 2)
552s > 
552s >  niter <- out.metro$nbatch * out.metro$blen * out.metro$nspac
552s >  niter == nrow(out.metro$current)
552s [1] TRUE
552s >  niter == nrow(out.metro$proposal)
552s [1] TRUE
552s >  all(out.metro$current[1, ] == out.metro$initial)
552s [1] TRUE
552s >  all(out.metro$current[niter, ] == out.metro$final) |
552s +      all(out.metro$proposal[niter, ] == out.metro$final)
552s [1] TRUE
552s > 
552s >  .Random.seed <- out.metro$initial.seed
552s >  d <- ncol(out.metro$proposal)
552s >  n <- nrow(out.metro$proposal)
552s >  my.proposal <- matrix(NA, n, d)
552s >  my.u <- double(n)
552s >  ska <- out.metro$scale
552s >  for (i in 1:n) {
552s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
552s +      if (is.na(out.metro$u[i])) {
552s +          my.u[i] <- NA
552s +      } else {
552s +          my.u[i] <- runif(1)
552s +      }
552s +  }
552s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
552s [1] TRUE
552s >  all(is.na(out.metro$u) == is.na(my.u))
552s [1] TRUE
552s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
552s [1] TRUE
552s > 
552s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
552s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
552s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
552s [1] TRUE
552s >  foo <- my.prop.log.green - my.curr.log.green
552s >  max(abs(foo - out.metro$log.green)) < epsilon
552s [1] TRUE
552s > 
552s >  my.accept <- is.na(my.u) | my.u < exp(foo)
552s >  sum(my.accept) == round(n * out.metro$accept)
552s [1] TRUE
552s >  if (my.accept[niter]) {
552s +      all(out.metro$proposal[niter, ] == out.metro$final)
552s +  } else {
552s +      all(out.metro$current[niter, ] == out.metro$final)
552s +  }
552s [1] TRUE
552s > 
552s >  my.current <- out.metro$current
552s >  my.current[my.accept, ] <- my.proposal[my.accept, ]
552s >  my.current <- rbind(out.metro$initial, my.current[- niter, ])
552s >  max(abs(out.metro$current - my.current)) < epsilon
552s [1] TRUE
552s > 
552s >  my.path <- matrix(NA, n, d)
552s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
552s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
552s >  nspac <- out.metro$nspac
552s > 
552s >  my.path <- my.path[seq(nspac, niter, by = nspac), ]
552s > 
552s >  fred <- my.path[ , out.metro$outfun]
552s >  k <- ncol(fred)
552s > 
552s >  foom <- array(as.vector(t(fred)), c(k, out.metro$blen, out.metro$nbatch))
552s >  boom <- t(apply(foom, c(1, 3), mean))
552s > 
552s >  all(dim(boom) == dim(out.metro$batch))
552s [1] TRUE
552s >  max(abs(boom - out.metro$batch)) < epsilon
552s [1] TRUE
552s > 
552s > 
552s BEGIN TEST tests/logitsub.R
552s 
552s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
552s Copyright (C) 2024 The R Foundation for Statistical Computing
552s Platform: arm-unknown-linux-gnueabihf (32-bit)
552s 
552s R is free software and comes with ABSOLUTELY NO WARRANTY.
552s You are welcome to redistribute it under certain conditions.
552s Type 'license()' or 'licence()' for distribution details.
552s 
552s R is a collaborative project with many contributors.
552s Type 'contributors()' for more information and
552s 'citation()' on how to cite R or R packages in publications.
552s 
552s Type 'demo()' for some demos, 'help()' for on-line help, or
552s 'help.start()' for an HTML browser interface to help.
552s Type 'q()' to quit R.
552s 
552s > 
552s >  # test spacing (nspac)
552s > 
552s >  epsilon <- 1e-15
552s > 
552s >  library(mcmc)
552s > 
552s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
552s >  set.seed(42)
552s > 
552s >  n <- 100
552s >  rho <- 0.5
552s >  beta0 <- 0.25
552s >  beta1 <- 1
552s >  beta2 <- 0.5
552s > 
552s >  x1 <- rnorm(n)
552s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
552s >  eta <- beta0 + beta1 * x1 + beta2 * x2
552s >  p <- 1 / (1 + exp(- eta))
552s >  y <- as.numeric(runif(n) < p)
552s > 
552s >  out <- glm(y ~ x1 + x2, family = binomial())
552s > 
552s >  logl <- function(beta) {
552s +      if (length(beta) != 3) stop("length(beta) != 3")
552s +      beta0 <- beta[1]
552s +      beta1 <- beta[2]
552s +      beta2 <- beta[3]
552s +      eta <- beta0 + beta1 * x1 + beta2 * x2
552s +      p <- exp(eta) / (1 + exp(eta))
552s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
552s +  }
552s > 
552s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
552s >  out.metro$accept
552s [1] 0.982
552s > 
552s >  out.metro <- metrop(out.metro, scale = 0.1)
553s >  out.metro$accept
553s [1] 0.795
553s > 
553s >  out.metro <- metrop(out.metro, scale = 0.5)
553s >  out.metro$accept
553s [1] 0.264
553s > 
553s >  apply(out.metro$batch, 2, mean)
553s [1] 0.06080257 1.42304941 0.52634149
553s > 
553s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
553s +      scale = 0.5, debug = TRUE, nspac = 3)
553s > 
553s >  niter <- out.metro$nbatch * out.metro$blen * out.metro$nspac
553s >  niter == nrow(out.metro$current)
553s [1] TRUE
553s >  niter == nrow(out.metro$proposal)
553s [1] TRUE
553s >  all(out.metro$current[1, ] == out.metro$initial)
553s [1] TRUE
553s >  all(out.metro$current[niter, ] == out.metro$final) |
553s +      all(out.metro$proposal[niter, ] == out.metro$final)
553s [1] TRUE
553s > 
553s >  .Random.seed <- out.metro$initial.seed
553s >  d <- ncol(out.metro$proposal)
553s >  n <- nrow(out.metro$proposal)
553s >  my.proposal <- matrix(NA, n, d)
553s >  my.u <- double(n)
553s >  ska <- out.metro$scale
553s >  for (i in 1:n) {
553s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
553s +      if (is.na(out.metro$u[i])) {
553s +          my.u[i] <- NA
553s +      } else {
553s +          my.u[i] <- runif(1)
553s +      }
553s +  }
553s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
553s [1] TRUE
553s >  all(is.na(out.metro$u) == is.na(my.u))
553s [1] TRUE
553s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
553s [1] TRUE
553s > 
553s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
553s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
553s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
553s [1] TRUE
553s >  foo <- my.prop.log.green - my.curr.log.green
553s >  max(abs(foo - out.metro$log.green)) < epsilon
553s [1] TRUE
553s > 
553s >  my.accept <- is.na(my.u) | my.u < exp(foo)
553s >  sum(my.accept) == round(n * out.metro$accept)
553s [1] TRUE
553s >  if (my.accept[niter]) {
553s +      all(out.metro$proposal[niter, ] == out.metro$final)
553s +  } else {
553s +      all(out.metro$current[niter, ] == out.metro$final)
553s +  }
553s [1] TRUE
553s > 
553s >  my.current <- out.metro$current
553s >  my.current[my.accept, ] <- my.proposal[my.accept, ]
553s >  my.current <- rbind(out.metro$initial, my.current[- niter, ])
553s >  max(abs(out.metro$current - my.current)) < epsilon
553s [1] TRUE
553s > 
553s >  my.path <- matrix(NA, n, d)
553s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
553s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
553s >  nspac <- out.metro$nspac
553s >  my.path <- my.path[seq(nspac, niter, by = nspac), ]
553s >  all(dim(my.path) == dim(out.metro$batch))
553s [1] TRUE
553s > 
553s >  all(my.path == out.metro$batch)
553s [1] TRUE
553s > 
553s > 
553s BEGIN TEST tests/logitsubbat.R
553s 
553s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
553s Copyright (C) 2024 The R Foundation for Statistical Computing
553s Platform: arm-unknown-linux-gnueabihf (32-bit)
553s 
553s R is free software and comes with ABSOLUTELY NO WARRANTY.
553s You are welcome to redistribute it under certain conditions.
553s Type 'license()' or 'licence()' for distribution details.
553s 
553s R is a collaborative project with many contributors.
553s Type 'contributors()' for more information and
553s 'citation()' on how to cite R or R packages in publications.
553s 
553s Type 'demo()' for some demos, 'help()' for on-line help, or
553s 'help.start()' for an HTML browser interface to help.
553s Type 'q()' to quit R.
553s 
553s > 
553s >  # test batching (blen) and spacing (nspac) together
553s > 
553s >  epsilon <- 1e-15
553s > 
553s >  library(mcmc)
553s > 
553s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
553s >  set.seed(42)
553s > 
553s >  n <- 100
553s >  rho <- 0.5
553s >  beta0 <- 0.25
553s >  beta1 <- 1
553s >  beta2 <- 0.5
553s > 
553s >  x1 <- rnorm(n)
553s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
553s >  eta <- beta0 + beta1 * x1 + beta2 * x2
553s >  p <- 1 / (1 + exp(- eta))
553s >  y <- as.numeric(runif(n) < p)
553s > 
553s >  out <- glm(y ~ x1 + x2, family = binomial())
553s > 
553s >  logl <- function(beta) {
553s +      if (length(beta) != 3) stop("length(beta) != 3")
553s +      beta0 <- beta[1]
553s +      beta1 <- beta[2]
553s +      beta2 <- beta[3]
553s +      eta <- beta0 + beta1 * x1 + beta2 * x2
553s +      p <- exp(eta) / (1 + exp(eta))
553s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
553s +  }
553s > 
553s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
553s >  out.metro$accept
553s [1] 0.982
553s > 
553s >  out.metro <- metrop(out.metro, scale = 0.1)
553s >  out.metro$accept
553s [1] 0.795
553s > 
553s >  out.metro <- metrop(out.metro, scale = 0.5)
553s >  out.metro$accept
553s [1] 0.264
553s > 
553s >  apply(out.metro$batch, 2, mean)
553s [1] 0.06080257 1.42304941 0.52634149
553s > 
553s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
553s +      scale = 0.5, debug = TRUE, blen = 5, nspac = 3)
554s > 
554s >  niter <- out.metro$nbatch * out.metro$blen * out.metro$nspac
554s >  niter == nrow(out.metro$current)
554s [1] TRUE
554s >  niter == nrow(out.metro$proposal)
554s [1] TRUE
554s >  all(out.metro$current[1, ] == out.metro$initial)
554s [1] TRUE
554s >  all(out.metro$current[niter, ] == out.metro$final) |
554s +      all(out.metro$proposal[niter, ] == out.metro$final)
554s [1] TRUE
554s > 
554s >  .Random.seed <- out.metro$initial.seed
554s >  d <- ncol(out.metro$proposal)
554s >  n <- nrow(out.metro$proposal)
554s >  my.proposal <- matrix(NA, n, d)
554s >  my.u <- double(n)
554s >  ska <- out.metro$scale
554s >  for (i in 1:n) {
554s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
554s +      if (is.na(out.metro$u[i])) {
554s +          my.u[i] <- NA
554s +      } else {
554s +          my.u[i] <- runif(1)
554s +      }
554s +  }
554s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
554s [1] TRUE
554s >  all(is.na(out.metro$u) == is.na(my.u))
554s [1] TRUE
554s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
554s [1] TRUE
554s > 
554s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
554s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
554s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
554s [1] TRUE
554s >  foo <- my.prop.log.green - my.curr.log.green
554s >  max(abs(foo - out.metro$log.green)) < epsilon
554s [1] TRUE
554s > 
554s >  my.accept <- is.na(my.u) | my.u < exp(foo)
554s >  sum(my.accept) == round(n * out.metro$accept)
554s [1] TRUE
554s >  if (my.accept[niter]) {
554s +      all(out.metro$proposal[niter, ] == out.metro$final)
554s +  } else {
554s +      all(out.metro$current[niter, ] == out.metro$final)
554s +  }
554s [1] TRUE
554s > 
554s >  my.current <- out.metro$current
554s >  my.current[my.accept, ] <- my.proposal[my.accept, ]
554s >  my.current <- rbind(out.metro$initial, my.current[- niter, ])
554s >  max(abs(out.metro$current - my.current)) < epsilon
554s [1] TRUE
554s > 
554s >  my.path <- matrix(NA, n, d)
554s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
554s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
554s >  nspac <- out.metro$nspac
554s > 
554s >  my.path <- my.path[seq(nspac, niter, by = nspac), ]
554s > 
554s >  foom <- array(as.vector(t(my.path)), c(d, out.metro$blen, out.metro$nbatch))
554s >  boom <- t(apply(foom, c(1, 3), mean))
554s > 
554s >  all(dim(boom) == dim(out.metro$batch))
554s [1] TRUE
554s >  max(abs(boom - out.metro$batch)) < epsilon
554s [1] TRUE
554s > 
554s > 
554s BEGIN TEST tests/logitvec.R
554s 
554s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
554s Copyright (C) 2024 The R Foundation for Statistical Computing
554s Platform: arm-unknown-linux-gnueabihf (32-bit)
554s 
554s R is free software and comes with ABSOLUTELY NO WARRANTY.
554s You are welcome to redistribute it under certain conditions.
554s Type 'license()' or 'licence()' for distribution details.
554s 
554s R is a collaborative project with many contributors.
554s Type 'contributors()' for more information and
554s 'citation()' on how to cite R or R packages in publications.
554s 
554s Type 'demo()' for some demos, 'help()' for on-line help, or
554s 'help.start()' for an HTML browser interface to help.
554s Type 'q()' to quit R.
554s 
554s > 
554s >  # test vector (diag(foo)) scaling
554s > 
554s >  epsilon <- 1e-15
554s > 
554s >  library(mcmc)
554s > 
554s >  suppressWarnings(RNGkind("Marsaglia-Multicarry"))
554s >  set.seed(42)
554s > 
554s >  n <- 100
554s >  rho <- 0.5
554s >  beta0 <- 0.25
554s >  beta1 <- 1
554s >  beta2 <- 0.5
554s > 
554s >  x1 <- rnorm(n)
554s >  x2 <- rho * x1 + sqrt(1 - rho^2) * rnorm(n)
554s >  eta <- beta0 + beta1 * x1 + beta2 * x2
554s >  p <- 1 / (1 + exp(- eta))
554s >  y <- as.numeric(runif(n) < p)
554s > 
554s >  out <- glm(y ~ x1 + x2, family = binomial())
554s > 
554s >  logl <- function(beta) {
554s +      if (length(beta) != 3) stop("length(beta) != 3")
554s +      beta0 <- beta[1]
554s +      beta1 <- beta[2]
554s +      beta2 <- beta[3]
554s +      eta <- beta0 + beta1 * x1 + beta2 * x2
554s +      p <- exp(eta) / (1 + exp(eta))
554s +      return(sum(log(p[y == 1])) + sum(log(1 - p[y == 0])))
554s +  }
554s > 
554s >  out.metro <- metrop(logl, coefficients(out), 1e3, scale = 0.01)
554s >  out.metro$accept
554s [1] 0.982
554s > 
554s >  out.metro <- metrop(out.metro, scale = 0.1)
554s >  out.metro$accept
554s [1] 0.795
554s > 
554s >  out.metro <- metrop(out.metro, scale = 0.5)
554s >  out.metro$accept
554s [1] 0.264
554s > 
554s >  apply(out.metro$batch, 2, mean)
554s [1] 0.06080257 1.42304941 0.52634149
554s >  sally <- apply(out.metro$batch, 2, sd)
554s > 
554s >  out.metro <- metrop(out.metro, scale = sally)
554s >  out.metro$accept
554s [1] 0.398
554s > 
554s >  out.metro <- metrop(logl, as.numeric(coefficients(out)), 1e2,
554s +      scale = sally, debug = TRUE)
554s > 
554s >  niter <- out.metro$nbatch * out.metro$blen * out.metro$nspac
554s >  niter == nrow(out.metro$current)
554s [1] TRUE
554s >  niter == nrow(out.metro$proposal)
554s [1] TRUE
554s >  all(out.metro$current[1, ] == out.metro$initial)
554s [1] TRUE
554s >  all(out.metro$current[niter, ] == out.metro$final) |
554s +      all(out.metro$proposal[niter, ] == out.metro$final)
554s [1] TRUE
554s > 
554s >  .Random.seed <- out.metro$initial.seed
554s >  d <- ncol(out.metro$proposal)
554s >  n <- nrow(out.metro$proposal)
554s >  my.proposal <- matrix(NA, n, d)
554s >  my.u <- double(n)
554s >  ska <- out.metro$scale
554s >  for (i in 1:n) {
554s +      my.proposal[i, ] <- out.metro$current[i, ] + ska * rnorm(d)
554s +      if (is.na(out.metro$u[i])) {
554s +          my.u[i] <- NA
554s +      } else {
554s +          my.u[i] <- runif(1)
554s +      }
554s +  }
554s >  max(abs(out.metro$proposal - my.proposal)) < epsilon
554s [1] TRUE
554s > 
554s >  all(is.na(out.metro$u) == is.na(my.u))
554s [1] TRUE
554s >  all(out.metro$u[!is.na(out.metro$u)] == my.u[!is.na(my.u)])
554s [1] TRUE
554s > 
554s >  my.curr.log.green <- apply(out.metro$current, 1, logl)
554s >  my.prop.log.green <- apply(out.metro$proposal, 1, logl)
554s >  all(is.na(out.metro$u) == (my.prop.log.green > my.curr.log.green))
554s [1] TRUE
554s >  foo <- my.prop.log.green - my.curr.log.green
554s >  max(abs(foo - out.metro$log.green)) < epsilon
554s [1] TRUE
554s > 
554s >  my.accept <- is.na(my.u) | my.u < exp(foo)
554s >  sum(my.accept) == round(n * out.metro$accept)
554s [1] TRUE
554s >  if (my.accept[niter]) {
554s +      all(out.metro$proposal[niter, ] == out.metro$final)
554s +  } else {
554s +      all(out.metro$current[niter, ] == out.metro$final)
554s +  }
554s [1] TRUE
554s > 
554s >  my.current <- out.metro$current
554s >  my.current[my.accept, ] <- my.proposal[my.accept, ]
554s >  my.current <- rbind(out.metro$initial, my.current[- niter, ])
554s >  max(abs(out.metro$current - my.current)) < epsilon
554s [1] TRUE
554s > 
554s >  my.path <- matrix(NA, n, d)
554s >  my.path[my.accept, ] <- out.metro$proposal[my.accept, ]
554s >  my.path[! my.accept, ] <- out.metro$current[! my.accept, ]
554s >  nspac <- out.metro$nspac
554s > 
554s >  my.path <- my.path[seq(nspac, niter, by = nspac), ]
554s > 
554s >  fred <- my.path
554s >  k <- ncol(fred)
554s > 
554s >  foom <- array(as.vector(t(fred)), c(k, out.metro$blen, out.metro$nbatch))
554s >  boom <- t(apply(foom, c(1, 3), mean))
554s > 
554s >  all(dim(boom) == dim(out.metro$batch))
554s [1] TRUE
554s >  max(abs(boom - out.metro$batch)) < epsilon
554s [1] TRUE
554s > 
554s > 
554s BEGIN TEST tests/morph.R
555s 
555s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
555s Copyright (C) 2024 The R Foundation for Statistical Computing
555s Platform: arm-unknown-linux-gnueabihf (32-bit)
555s 
555s R is free software and comes with ABSOLUTELY NO WARRANTY.
555s You are welcome to redistribute it under certain conditions.
555s Type 'license()' or 'licence()' for distribution details.
555s 
555s R is a collaborative project with many contributors.
555s Type 'contributors()' for more information and
555s 'citation()' on how to cite R or R packages in publications.
555s 
555s Type 'demo()' for some demos, 'help()' for on-line help, or
555s 'help.start()' for an HTML browser interface to help.
555s Type 'q()' to quit R.
555s 
555s > library(mcmc)
555s > isotropic <- mcmc:::isotropic
555s > isotropic.logjacobian <- mcmc:::isotropic.logjacobian
555s > 
555s > # make sure morph identity works properly
555s > TestMorphIdentity <- function(m.id) {
555s +   ident.func <- function(x) x
555s +   if (!all.equal(m.id$transform(1:10), 1:10))
555s +     return(FALSE)
555s +   if (!all.equal(m.id$inverse(1:10), 1:10))
555s +     return(FALSE)
555s +   x <- seq(-1,1, length.out=15)
555s +   if (!all.equal(sapply(x, m.id$lud(function(x) dnorm(x, log=TRUE))),
555s +                  dnorm(x, log=TRUE)))
555s +     return(FALSE)
555s +   if (!all.equal(m.id$outfun(ident.func)(x), x))
555s +     return(FALSE)
555s +   return(TRUE)
555s + }
555s > 
555s > TestMorphIdentity(morph())
555s [1] TRUE
555s > TestMorphIdentity(morph.identity())
555s [1] TRUE
555s > 
555s > TestMorphIdentityOutfun <- function(m) {
555s +   f <- m$outfun(NULL)
555s +   x <- 1:20
555s +   if (!identical(x, f(x)))
555s +     return(FALSE)
555s +   f <- m$outfun(c(6, 8))
555s +   if (!identical(x[c(6, 8)], f(x)))
555s +     return(FALSE)
555s +   i <- rep(FALSE, 20)
555s +   i[c(1, 3, 5)] <- TRUE
555s +   f <- m$outfun(i)
555s +   if (!identical(x[i], f(x)))
555s +     return(FALSE)
555s +   return(TRUE)
555s + }
555s > 
555s > TestMorphIdentityOutfun(morph())
555s [1] TRUE
555s > TestMorphIdentityOutfun(morph.identity())
555s [1] TRUE
555s > 
555s > # make sure that morph and morph.identity give back the same things
555s > all.equal(sort(names(morph.identity())), sort(names(morph(b=1))))
555s [1] TRUE
555s > 
555s > # test center parameter, univariate version
555s > zero.func <- function(x) 0
555s > center <- 2
555s > x <- seq(-1,1, length.out=15)
555s > morph.center <- morph(center=center)
555s > all.equal(sapply(x, morph.center$transform), x-center)
555s [1] TRUE
555s > all.equal(sapply(x, morph.center$inverse), x+center)
555s [1] TRUE
555s > all.equal(sapply(x, morph.center$lud(function(y) dnorm(y, log=TRUE))),
555s +           dnorm(x, log=TRUE, mean=-2))
555s [1] TRUE
555s > 
555s > # test center parameter, multivariate version
555s > center <- 1:4
555s > x <- rep(0, 4)
555s > morph.center <- morph(center=center)
555s > lud.mult.dnorm <- function(x) prod(dnorm(x, log=TRUE))
555s > all.equal(morph.center$transform(x), x-center)
555s [1] TRUE
555s > all.equal(morph.center$inverse(x), x+center)
555s [1] TRUE
555s > all.equal(morph.center$lud(lud.mult.dnorm)(x),
555s +           lud.mult.dnorm(x - center))
555s [1] TRUE
555s > # test 'r'.
555s > r <- 1
555s > morph.r <- morph(r=r)
555s > x <- seq(-1, 1, length.out=20)
555s > all.equal(sapply(x, morph.r$lud(function(x) dnorm(x, log=TRUE))),
555s +           dnorm(x, log=TRUE))
555s [1] TRUE
555s > x <- seq(1.1, 2, length.out=10)
555s > all(sapply(x, morph.r$lud(function(x) dnorm(x, log=TRUE)))
555s +     !=
555s +     dnorm(x, log=TRUE))
555s [1] TRUE
555s > 
555s > TestExponentialEvenPWithRInverse <- function() {
555s +   r <- 0.3
555s +   p <- 2.2
555s +   morph.r <- morph(r=r, p=p)
555s +   x <- seq(0, r, length.out=20)
555s +   all.equal(x, sapply(x, morph.r$inverse))
555s + }
555s > 
555s > TestExponentialEvenPWithRInverse()
555s [1] TRUE
555s > 
555s > # make sure morph$lud passes '...' arguments.
555s > mean <- 2
555s > ident.morph <- morph()
555s > dnorm.morph <- ident.morph$lud(function(x, mean=0)
555s +                                  dnorm(x, mean=mean, log=TRUE))
555s > all.equal(dnorm.morph(2, mean), dnorm(2, mean=mean, log=TRUE))
555s [1] TRUE
555s > x <- seq(-3, 3, length.out=20)
555s > m2 <- morph(r=10)
555s > dnorm.morph <- m2$lud(function(x, mean)
555s +                         dnorm(x, mean=mean, log=TRUE))
555s > all.equal(sapply(x, function(y) dnorm.morph(y, 2)),
555s +           dnorm(x, mean=2, log=TRUE))
555s [1] TRUE
555s > 
555s > # make sure morph$outfun passes '...' arguments.
555s > outfun.orig <- function(x, mean) x + mean
555s > ident.morph <- morph()
555s > mean <- 1
555s > outfun.morph <- ident.morph$outfun(outfun.orig)
555s > all.equal(outfun.morph(1:10, mean), 1:10+mean)
555s [1] TRUE
555s > 
555s > m2 <- morph(r=10)
555s > outfun.morph <- m2$outfun(outfun.orig)
555s > all.equal(sapply(1:10, function(x) outfun.morph(x, mean)), 1:10+mean)
555s [1] TRUE
555s > 
555s > ###########################################################################
555s > # test built-in exponential and polynomial transformations.
555s > f <- morph(b=3)
555s > x <- seq(0, 10, length.out=100)
555s > all.equal(x, sapply(sapply(x, f$transform), f$inverse))
555s [1] TRUE
555s > 
555s > f <- morph(p=3)
555s > all.equal(x, sapply(sapply(x, f$transform), f$inverse))
555s [1] TRUE
555s > 
555s > f <- morph(p=3, r=10)
555s > all.equal(-10:10, Vectorize(f$transform)(-10:10))
555s [1] TRUE
555s > 
555s > f <- morph(p=3, b=1)
555s > all.equal(x, sapply(sapply(x, f$transform), f$inverse))
555s [1] TRUE
555s > 
555s BEGIN TEST tests/morph.metrop.R
555s 
555s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
555s Copyright (C) 2024 The R Foundation for Statistical Computing
555s Platform: arm-unknown-linux-gnueabihf (32-bit)
555s 
555s R is free software and comes with ABSOLUTELY NO WARRANTY.
555s You are welcome to redistribute it under certain conditions.
555s Type 'license()' or 'licence()' for distribution details.
555s 
555s R is a collaborative project with many contributors.
555s Type 'contributors()' for more information and
555s 'citation()' on how to cite R or R packages in publications.
555s 
555s Type 'demo()' for some demos, 'help()' for on-line help, or
555s 'help.start()' for an HTML browser interface to help.
555s Type 'q()' to quit R.
555s 
555s > library(mcmc)
555s > 
555s > .morph.unmorph <- mcmc:::.morph.unmorph
555s > 
555s > ###########################################################################
555s > # basic functionality check, can morph.metro run?  Can we change the
555s > # transformation?
555s > set.seed(42)
555s > obj <- morph.metrop(function(x) dt(x, df=3, log=TRUE),
555s +                     100, 100, morph=morph(b=3))
555s > obj <- morph.metrop(obj, morph=morph(b=1))
555s > 
555s > obj <- morph.metrop(function(x) prod(dt(x, df=3, log=TRUE)),
555s +                     rep(100, 3), 100, morph=morph(p=3, b=1))
555s > obj <- morph.metrop(obj, morph=morph(r=1, p=3, b=1))
556s > 
556s > all.equal(class(obj), c("mcmc", "morph.metropolis"))
556s [1] TRUE
556s > 
556s > ###########################################################################
556s > # check .morph.unmorph
556s > obj <- list(final=10)
556s > outfun <- function(x) x
556s > m <- morph(p=3)
556s > obj <- .morph.unmorph(obj, m, outfun)
556s > all.equal(class(obj), c("mcmc", "morph.metropolis"))
556s [1] TRUE
556s > all.equal(sort(names(obj)),
556s +           sort(c("final", "morph", "morph.final", "outfun")))
556s [1] TRUE
556s > all.equal(c(obj$final, obj$morph.final), c(m$inverse(10), 10))
556s [1] TRUE
556s > all.equal(obj$outfun, outfun)
556s [1] TRUE
556s > all.equal(obj$morph, m)
556s [1] TRUE
556s > 
556s BEGIN TEST tests/morphtoo.R
556s 
556s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
556s Copyright (C) 2024 The R Foundation for Statistical Computing
556s Platform: arm-unknown-linux-gnueabihf (32-bit)
556s 
556s R is free software and comes with ABSOLUTELY NO WARRANTY.
556s You are welcome to redistribute it under certain conditions.
556s Type 'license()' or 'licence()' for distribution details.
556s 
556s R is a collaborative project with many contributors.
556s Type 'contributors()' for more information and
556s 'citation()' on how to cite R or R packages in publications.
556s 
556s Type 'demo()' for some demos, 'help()' for on-line help, or
556s 'help.start()' for an HTML browser interface to help.
556s Type 'q()' to quit R.
556s 
556s > 
556s >  library(mcmc)
556s > 
556s >  x <- seq(0, 10, length = 10001)
556s > 
556s >  ### sub-exponentially light transformation
556s > 
556s >  b <- 0.5
556s >  fsub <- morph(b = b)
556s > 
556s >  y <- unlist(Map(fsub$inverse, x))
556s > 
556s >  myfsub <- function(x) ifelse(x > 1 / b, exp(b * x) - exp(1) / 3,
556s +      (x * b)^3 * exp(1) / 6 + x * b * exp(1) / 2)
556s >  y2 <- myfsub(x)
556s >  all.equal(y, y2, tolerance = 1e-14)
556s [1] TRUE
556s > 
556s >  z <- unlist(Map(fsub$transform, y))
556s >  all.equal(z, x, tolerance = 1e-14)
556s [1] TRUE
556s > 
556s >  ### exponentially light transformation
556s > 
556s >  r <- 5 
556s >  p <- 3
556s >  fp3 <- morph(r = r)
556s > 
556s >  y <- unlist(Map(fp3$inverse, x))
556s > 
556s >  myfp3 <- function(x) ifelse(x < r, x, x + (x - r)^p)
556s >  y2 <- myfp3(x)
556s >  all.equal(y, y2, tolerance = 1e-14)
556s [1] TRUE
556s > 
556s >  z <- unlist(Map(fp3$transform, y))
556s >  all.equal(z, x, tolerance = 1e-12)
556s [1] TRUE
556s > 
556s >  ### both together
556s > 
556s >  fboth <- morph(b = b, r = r)
556s > 
556s >  y <- unlist(Map(fboth$inverse, x))
557s >  y2 <- myfsub(myfp3(x))
557s >  all.equal(y, y2, tolerance = 1e-14)
557s [1] TRUE
557s > 
557s >  z <- unlist(Map(fboth$transform, y))
557s >  all.equal(z, x, tolerance = 1e-12)
557s [1] TRUE
557s > 
557s >  ### exponentially light transformation with p != 3
557s > 
557s >  r <- 5 
557s >  p <- 2.2
557s >  fpo <- morph(r = r, p = p)
557s > 
557s >  y <- unlist(Map(fpo$inverse, x))
557s > 
557s >  myfpo <- function(x) ifelse(x < r, x, x + (x - r)^p)
557s >  y2 <- myfpo(x)
557s >  all.equal(y, y2, tolerance = 1e-14)
557s [1] TRUE
557s > 
557s >  z <- unlist(Map(fpo$transform, y))
558s >  all.equal(z, x, tolerance = 1e-14)
558s [1] TRUE
558s > 
558s > 
558s BEGIN TEST tests/saveseed.R
558s 
558s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
558s Copyright (C) 2024 The R Foundation for Statistical Computing
558s Platform: arm-unknown-linux-gnueabihf (32-bit)
558s 
558s R is free software and comes with ABSOLUTELY NO WARRANTY.
558s You are welcome to redistribute it under certain conditions.
558s Type 'license()' or 'licence()' for distribution details.
558s 
558s R is a collaborative project with many contributors.
558s Type 'contributors()' for more information and
558s 'citation()' on how to cite R or R packages in publications.
558s 
558s Type 'demo()' for some demos, 'help()' for on-line help, or
558s 'help.start()' for an HTML browser interface to help.
558s Type 'q()' to quit R.
558s 
558s > 
558s >  library(mcmc)
558s > 
558s >  set.seed(42)
558s > 
558s >  h <- function(x) if (all(x >= 0) && sum(x) <= 1) return(1) else return(-Inf)
558s >  out <- metrop(h, initial = rep(0, 5), nbatch = 100, blen = 17, nspac = 3,
558s +      scale = 0.1)
559s > 
559s >  save.seed <- .Random.seed
559s > 
559s >  out1 <- metrop(out)
559s >  out2 <- metrop(out1)
559s >  out3 <- metrop(out, nbatch = 2 * out$nbatch)
559s > 
559s >  fred <- rbind(out1$batch, out2$batch)
559s >  identical(fred, out3$batch)
559s [1] TRUE
559s > 
559s > 
559s BEGIN TEST tests/saveseedmorph.R
559s 
559s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
559s Copyright (C) 2024 The R Foundation for Statistical Computing
559s Platform: arm-unknown-linux-gnueabihf (32-bit)
559s 
559s R is free software and comes with ABSOLUTELY NO WARRANTY.
559s You are welcome to redistribute it under certain conditions.
559s Type 'license()' or 'licence()' for distribution details.
559s 
559s R is a collaborative project with many contributors.
559s Type 'contributors()' for more information and
559s 'citation()' on how to cite R or R packages in publications.
559s 
559s Type 'demo()' for some demos, 'help()' for on-line help, or
559s 'help.start()' for an HTML browser interface to help.
559s Type 'q()' to quit R.
559s 
559s > 
559s >  library(mcmc)
559s > 
559s >  set.seed(42)
559s > 
559s >  h <- function(x) if (all(x >= 0) && sum(x) <= 1) return(1) else return(-Inf)
559s >  out <- morph.metrop(obj = h, initial = rep(0, 5), nbatch = 100, blen = 17,
559s +      nspac = 3, scale = 0.1)
559s > 
559s >  out1 <- morph.metrop(out)
559s >  out2 <- morph.metrop(out1)
559s >  out3 <- morph.metrop(out, nbatch = 2 * out$nbatch)
559s > 
559s >  fred <- rbind(out1$batch, out2$batch)
559s >  identical(fred, out3$batch)
559s [1] TRUE
559s > 
559s >  out <- morph.metrop(out, morph = morph(p = 2.2, r = 0.3))
559s > 
559s >  out1 <- morph.metrop(out)
559s >  out2 <- morph.metrop(out1)
560s >  out3 <- morph.metrop(out, nbatch = 2 * out$nbatch)
560s > 
560s >  fred <- rbind(out1$batch, out2$batch)
560s >  identical(fred, out3$batch)
560s [1] TRUE
560s > 
560s > 
560s BEGIN TEST tests/temp-par-witch.R
560s 
560s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
560s Copyright (C) 2024 The R Foundation for Statistical Computing
560s Platform: arm-unknown-linux-gnueabihf (32-bit)
560s 
560s R is free software and comes with ABSOLUTELY NO WARRANTY.
560s You are welcome to redistribute it under certain conditions.
560s Type 'license()' or 'licence()' for distribution details.
560s 
560s R is a collaborative project with many contributors.
560s Type 'contributors()' for more information and
560s 'citation()' on how to cite R or R packages in publications.
560s 
560s Type 'demo()' for some demos, 'help()' for on-line help, or
560s 'help.start()' for an HTML browser interface to help.
560s Type 'q()' to quit R.
560s 
560s > 
560s >  if ((! exists("DEBUG")) || (! identical(DEBUG, TRUE))) DEBUG <- FALSE
560s > 
560s >  library(mcmc)
560s > 
560s >  options(digits=4) # avoid rounding differences
560s > 
560s >  set.seed(42)
560s > 
560s >  save.initial.seed <- .Random.seed
560s > 
560s >  d <- 3
560s >  witch.which <- 1 - (1 / 2)^(1 / d) * (1 / 4)^(seq(0, 5) / d)
560s >  witch.which
560s [1] 0.2063 0.5000 0.6850 0.8016 0.8750 0.9213
560s > 
560s >  ncomp <- length(witch.which)
560s > 
560s >  neighbors <- matrix(FALSE, ncomp, ncomp)
560s >  neighbors[row(neighbors) == col(neighbors) + 1] <- TRUE
560s >  neighbors[row(neighbors) == col(neighbors) - 1] <- TRUE
560s >  neighbors[row(neighbors) == col(neighbors) + 2] <- TRUE
560s >  neighbors[row(neighbors) == col(neighbors) - 2] <- TRUE
560s > 
560s >  ludfun <- function(state) {
560s +      stopifnot(is.numeric(state))
560s +      stopifnot(length(state) == d + 1)
560s +      icomp <- state[1]
560s +      stopifnot(icomp == as.integer(icomp))
560s +      stopifnot(1 <= icomp && icomp <= ncomp)
560s +      theta <- state[-1]
560s +      if (any(abs(theta) > 1.0)) return(-Inf)
560s +      bnd <- witch.which[icomp]
560s +      if(bnd >= 1.0)
560s +          stop(sprintf("witch.which[%d] >= 1.0", icomp))
560s +      if(bnd <= 0.0)
560s +          stop(sprintf("witch.which[%d] <= 0.0", icomp))
560s +      if (all(abs(theta) > bnd))
560s +          return(- (d + 1) * log(2) - d * log(1 - bnd))
560s +      return(- (d + 1) * log(2) - log1p(- (1 - bnd)^d))
560s +  }
560s > 
560s >  thetas <- matrix(0, ncomp, d)
560s >  out <- temper(ludfun, initial = thetas, neighbors = neighbors, nbatch = 50,
560s +      blen = 13, nspac = 7, scale = 0.3456789, parallel = TRUE, debug = DEBUG)
560s > 
560s >  names(out)
560s  [1] "lud"          "neighbors"    "nbatch"       "blen"         "nspac"       
560s  [6] "scale"        "outfun"       "debug"        "parallel"     "initial.seed"
560s [11] "final.seed"   "time"         "batch"        "acceptx"      "accepti"     
560s [16] "initial"      "final"       
560s > 
560s >  out$acceptx
560s [1] 0.6336 0.4974 0.3245 0.6022 0.6130 0.5914
560s > 
560s >  out$accepti
560s        [,1]   [,2]   [,3]   [,4]   [,5]   [,6]
560s [1,]     NA 0.7051 0.5497     NA     NA     NA
560s [2,] 0.7523     NA 0.5547 0.6288     NA     NA
560s [3,] 0.5794 0.5865     NA 0.5309 0.5476     NA
560s [4,]     NA 0.6667 0.5506     NA 0.8272 0.6837
560s [5,]     NA     NA 0.5439 0.8926     NA 0.8374
560s [6,]     NA     NA     NA 0.8391 0.9023     NA
560s > 
560s >  ### check that have prob 1 / 2 for corners
560s > 
560s >  outfun <- function(state) {
560s +      stopifnot(is.matrix(state))
560s +      ncomp <- nrow(state)
560s +      d <- ncol(state)
560s +      foo <- sweep(abs(state), 1, witch.which)
560s +      bar <- apply(foo > 0, 1, all) 
560s +      return(as.numeric(bar))
560s +  }
560s > 
560s >  out2 <- temper(out, outfun = outfun)
561s > 
561s >  colMeans(out2$batch)
561s [1] 0.54923 0.40923 0.39538 0.09692 0.12923 0.60000
561s >  apply(out2$batch, 2, sd) / sqrt(out$nbatch)
561s [1] 0.03482 0.04817 0.05464 0.02856 0.02113 0.05131
561s > 
561s >  ### try again
561s > 
561s >  out3 <- temper(out2, blen = 103)
565s > 
565s >  foo <- cbind(colMeans(out3$batch),
565s +      apply(out3$batch, 2, sd) / sqrt(out$nbatch))
565s >  colnames(foo) <- c("means", "MCSE")
565s >  foo
565s       means    MCSE
565s [1,] 0.5231 0.01390
565s [2,] 0.5361 0.02213
565s [3,] 0.4905 0.03961
565s [4,] 0.5652 0.04909
565s [5,] 0.4056 0.05107
565s [6,] 0.2450 0.05108
565s > 
565s > 
565s BEGIN TEST tests/temp-par.R
565s 
565s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
565s Copyright (C) 2024 The R Foundation for Statistical Computing
565s Platform: arm-unknown-linux-gnueabihf (32-bit)
565s 
565s R is free software and comes with ABSOLUTELY NO WARRANTY.
565s You are welcome to redistribute it under certain conditions.
565s Type 'license()' or 'licence()' for distribution details.
565s 
565s R is a collaborative project with many contributors.
565s Type 'contributors()' for more information and
565s 'citation()' on how to cite R or R packages in publications.
565s 
565s Type 'demo()' for some demos, 'help()' for on-line help, or
565s 'help.start()' for an HTML browser interface to help.
565s Type 'q()' to quit R.
565s 
565s > 
565s >  library(mcmc)
565s > 
565s >  set.seed(42)
565s > 
565s >  data(foo)
565s >  attach(foo)
565s > 
565s >  out <- glm(y ~ x1 + x2 + x3, family = binomial, x = TRUE)
565s > ## IGNORE_RDIFF_BEGIN
565s >  summary(out)
565s 
565s Call:
565s glm(formula = y ~ x1 + x2 + x3, family = binomial, x = TRUE)
565s 
565s Coefficients:
565s             Estimate Std. Error z value Pr(>|z|)    
565s (Intercept)   0.5772     0.2766   2.087 0.036930 *  
565s x1            0.3362     0.4256   0.790 0.429672    
565s x2            0.8475     0.4701   1.803 0.071394 .  
565s x3            1.5143     0.4426   3.422 0.000622 ***
565s ---
565s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
565s 
565s (Dispersion parameter for binomial family taken to be 1)
565s 
565s     Null deviance: 134.602  on 99  degrees of freedom
565s Residual deviance:  86.439  on 96  degrees of freedom
565s AIC: 94.439
565s 
565s Number of Fisher Scoring iterations: 5
565s 
565s > ## IGNORE_RDIFF_END
565s > 
565s >  modmat <- out$x
565s > 
565s >  models <- cbind(rep(0:1, each = 4), rep(rep(0:1, times = 2), each = 2),
565s +                rep(0:1, times = 4))
565s > 
565s >  exes <- paste("x", 1:3, sep = "")
565s >  betas <- NULL
565s >  for (i in 1:nrow(models)) {
565s +      inies <- as.logical(models[i, ])
565s +      foo <- exes[inies]
565s +      bar <- paste("y ~", paste(foo, collapse = " + "))
565s +      if (! any(inies)) bar <- paste(bar, "1")
565s +      baz <- glm(as.formula(bar), family = binomial)
565s +      beta <- rep(0, 4)
565s +      beta[c(TRUE, inies)] <- baz$coef
565s +      betas <- rbind(betas, beta)
565s +  }
565s > 
565s >  neighbors <- matrix(FALSE, nrow(models), nrow(models))
565s >  for (i in 1:nrow(neighbors)) {
565s +      for (j in 1:ncol(neighbors)) {
565s +          foo <- models[i, ]
565s +          bar <- models[j, ]
565s +          if (sum(foo != bar) == 1) neighbors[i, j] <- TRUE
565s +      }
565s +  }
565s > 
565s >  ludfun <- function(state, ...) {
565s +      stopifnot(is.numeric(state))
565s +      stopifnot(length(state) == ncol(models) + 2)
565s +      stopifnot(length(state) == ncol(models) + 2)
565s +      icomp <- state[1]
565s +      stopifnot(icomp == as.integer(icomp))
565s +      stopifnot(1 <= icomp && icomp <= nrow(models))
565s +      beta <- state[-1]
565s +      inies <- c(TRUE, as.logical(models[icomp, ]))
565s +      beta.logl <- beta
565s +      beta.logl[! inies] <- 0
565s +      eta <- as.numeric(modmat %*% beta.logl)
565s +      logp <- ifelse(eta < 0, eta - log1p(exp(eta)), - log1p(exp(- eta)))
565s +      logq <- ifelse(eta < 0, - log1p(exp(eta)), - eta - log1p(exp(- eta)))
565s +      logl <- sum(logp[y == 1]) + sum(logq[y == 0])
565s +      val <- logl - sum(beta^2) / 2
565s +      return(val)
565s +  }
565s > 
565s >  ludval <- NULL
565s >  for (i in 1:nrow(models)) ludval <- c(ludval, ludfun(c(i, betas[i, ])))
565s >  all(is.finite(ludval))
565s [1] TRUE
565s > 
565s > 
565s >  out <- temper(ludfun, initial = betas, neighbors = neighbors, nbatch = 20,
565s +      blen = 10, nspac = 5, scale = 0.56789, parallel = TRUE, debug = TRUE)
566s > 
566s >  names(out)
566s  [1] "lud"           "neighbors"     "nbatch"        "blen"         
566s  [5] "nspac"         "scale"         "outfun"        "debug"        
566s  [9] "parallel"      "initial.seed"  "final.seed"    "time"         
566s [13] "batch"         "acceptx"       "accepti"       "initial"      
566s [17] "final"         "which"         "unif.which"    "state"        
566s [21] "log.hastings"  "unif.hastings" "proposal"      "acceptd"      
566s [25] "norm"          "unif.choose"   "coproposal"   
566s > 
566s >  ### check decision about within-component or jump/swap
566s > 
566s >  identical(out$unif.which < 0.5, out$which)
566s [1] TRUE
566s > 
566s >  identical(out$which, out$proposal[ , 1] == out$coproposal[ , 1])
566s [1] TRUE
566s > 
566s >  ### check proposal and coproposal are actually current state or part thereof
566s > 
566s >  prop <- out$proposal
566s >  coprop <- out$coproposal
566s >  prop.i <- prop[ , 1]
566s >  coprop.i <- coprop[ , 1]
566s >  alt.prop <- prop
566s >  alt.coprop <- coprop
566s >  for (i in 1:nrow(prop)) {
566s +      alt.prop[i, ] <- c(prop.i[i], out$state[i, prop.i[i], ])
566s +      alt.coprop[i, ] <- c(coprop.i[i], out$state[i, coprop.i[i], ])
566s +  }
566s >  identical(coprop, alt.coprop)
566s [1] TRUE
566s >  identical(prop[! out$which, ], alt.prop[! out$which, ])
566s [1] TRUE
566s >  identical(prop[out$which, 1], alt.prop[out$which, 1])
566s [1] TRUE
566s > 
566s >  ### check hastings ratio calculated correctly
566s > 
566s >  foo <- apply(prop, 1, ludfun)
566s >  fooco <- apply(coprop, 1, ludfun)
566s >  prop[ , 1] <- out$coproposal[ , 1]
566s >  coprop[ , 1] <- out$proposal[ , 1]
566s >  foo.swap <- apply(prop, 1, ludfun)
566s >  fooco.swap <- apply(coprop, 1, ludfun)
566s >  log.haste <- ifelse(out$which, foo - fooco,
566s +      foo.swap + fooco.swap - foo - fooco)
566s >  all.equal(log.haste, out$log.hastings)
566s [1] TRUE
566s > 
566s >  ### check hastings rejection decided correctly
566s > 
566s >  identical(out$log.hastings >= 0, is.na(out$unif.hastings))
566s [1] TRUE
566s >  all(out$log.hastings < 0 | out$acceptd)
566s [1] TRUE
566s >  identical(out$acceptd,
566s +      out$log.hastings >= 0 | out$unif.hastings < exp(out$log.hastings))
566s [1] TRUE
566s > 
566s >  ### check acceptance carried out or not (according to decision) correctly
566s > 
566s >  before <- out$state
566s >  after <- before
566s >  after[- dim(after)[1], , ] <- before[-1, , ]
566s >  after[dim(after)[1], , ] <- out$final
566s >  my.after <- before
566s >  for (i in 1:length(out$acceptd)) {
566s +      if (out$acceptd[i]) {
566s +          if (out$which[i]) {
566s +              j <- out$proposal[i, 1]
566s +              my.after[i, j, ] <- out$proposal[i, -1]
566s +          } else {
566s +              j <- out$proposal[i, 1]
566s +              k <- out$coproposal[i, 1]
566s +              my.after[i, j, ] <- out$coproposal[i, -1]
566s +              my.after[i, k, ] <- out$proposal[i, -1]
566s +          }
566s +      }
566s +  }
566s >  identical(after, my.after)
566s [1] TRUE
566s > 
566s >  ### check within-component proposal
566s > 
566s >  my.coproposal.within <- out$coproposal[out$which, ]
566s >  proposal.within <- out$proposal[out$which, ]
566s >  my.z <- out$norm[out$which, ]
566s >  my.proposal.within <- my.coproposal.within
566s >  my.proposal.within[ , -1] <- my.coproposal.within[ , -1] + out$scale * my.z
566s >  all.equal(proposal.within, my.proposal.within)
566s [1] TRUE
566s > 
566s >  my.unif.choose <- out$unif.choose[out$which, 1]
566s >  my.i <- floor(nrow(models) * my.unif.choose) + 1
566s >  all(1 <= my.i & my.i <= nrow(models))
566s [1] TRUE
566s >  identical(my.i, my.coproposal.within[ , 1])
566s [1] TRUE
566s > 
566s >  ### check swap proposal
566s > 
566s >  coproposal.swap <- out$coproposal[! out$which, ]
566s >  proposal.swap <- out$proposal[! out$which, ]
566s >  unif.choose.swap <- out$unif.choose[! out$which, ]
566s >  my.i <- floor(nrow(models) * unif.choose.swap[ , 1]) + 1
566s >  nneighbors <- apply(out$neighbors, 1, sum)
566s >  my.nneighbors <- nneighbors[my.i]
566s >  my.k <- floor(my.nneighbors * unif.choose.swap[ , 2]) + 1
566s >  my.j <- my.k
566s >  foo <- seq(1, ncol(out$neighbors))
566s >  for (i in seq(along = my.j)) {
566s +      my.j[i] <- (foo[out$neighbors[my.i[i], ]])[my.k[i]]
566s +  }
566s >  identical(coproposal.swap[ , 1], my.i)
566s [1] TRUE
566s >  identical(proposal.swap[ , 1], my.j)
566s [1] TRUE
566s > 
566s >  ### check standard normal and uniform random numbers are as purported
566s > 
566s >  save.Random.seed <- .Random.seed
566s >  .Random.seed <- out$initial.seed
566s > 
566s >  nx <- ncol(out$initial)
566s >  niter <- out$nbatch * out$blen * out$nspac
566s >  my.norm <- matrix(NA, nrow = nrow(out$norm), ncol = ncol(out$norm))
566s >  my.unif.which <- rep(NA, niter)
566s >  my.unif.hastings <- rep(NA, niter)
566s >  my.unif.choose <- matrix(NA, niter, 2)
566s >  for (iiter in 1:niter) {
566s +      my.unif.which[iiter] <- runif(1)
566s +      if (out$which[iiter]) {
566s +          my.unif.choose[iiter, 1] <- runif(1)
566s +          my.norm[iiter, ] <- rnorm(nx)
566s +          if (out$log.hastings[iiter] < 0) my.unif.hastings[iiter] <- runif(1) 
566s +      } else {
566s +          my.unif.choose[iiter, ] <- runif(2)
566s +          if (out$log.hastings[iiter] < 0) my.unif.hastings[iiter] <- runif(1) 
566s +      }
566s +  }
567s >  identical(my.norm, out$norm)
567s [1] TRUE
567s >  identical(my.unif.which, out$unif.which)
567s [1] TRUE
567s >  identical(my.unif.hastings, out$unif.hastings)
567s [1] TRUE
567s >  identical(my.unif.choose, out$unif.choose)
567s [1] TRUE
567s > 
567s >  .Random.seed <- save.Random.seed
567s > 
567s >  ### check batch means
567s > 
567s >  foo <- after[seq(1, niter) %% out$nspac == 0, , ]
567s >  foo <- array(as.vector(foo), dim = c(out$blen, out$nbatch, dim(foo)[2:3]))
567s >  foo <- apply(foo, c(2, 3, 4), mean)
567s >  all.equal(foo, out$batch)
567s [1] TRUE
567s > 
567s >  ### check acceptance rates
567s > 
567s >  accept.within <- out$acceptd[out$which]
567s >  my.i.within <- out$coproposal[out$which, 1]
567s >  my.acceptx <- as.vector(sapply(split(accept.within, my.i.within), mean))
567s >  identical(my.acceptx, out$acceptx)
567s [1] TRUE
567s > 
567s >  accept.swap <- out$acceptd[! out$which]
567s >  my.i.swap <- out$coproposal[! out$which, 1]
567s >  my.j.swap <- out$proposal[! out$which, 1]
567s >  nmodel <- nrow(out$neighbors)
567s >  my.accepti <- matrix(NA, nmodel, nmodel)
567s >  for (i in 1:nmodel) {
567s +      for (j in 1:nmodel) {
567s +          if (out$neighbors[i, j]) {
567s +              my.accepti[i, j] <-
567s +                  mean(accept.swap[my.i.swap == i & my.j.swap == j])
567s +          }
567s +      }
567s +  }
567s >  identical(my.accepti, out$accepti)
567s [1] TRUE
567s > 
567s >  ### check scale vector
567s > 
567s >  nx <- ncol(models) + 1
567s >  newscale <- rnorm(nx, 0.5, 0.1)
567s > 
567s >  out <- temper(out, scale = newscale)
567s > 
567s >  my.coproposal.within <- out$coproposal[out$which, ]
567s >  proposal.within <- out$proposal[out$which, ]
567s >  my.z <- out$norm[out$which, ]
567s >  my.proposal.within <- my.coproposal.within
567s >  my.proposal.within[ , -1] <- my.coproposal.within[ , -1] +
567s +      sweep(my.z, 2, out$scale, "*")
567s >  all.equal(proposal.within, my.proposal.within)
567s [1] TRUE
567s > 
567s >  ### check scale matrix
567s > 
567s >  matscale <- matrix(rnorm(nx * nx, 0.0, 0.1), nx, nx)
567s >  diag(matscale) <- 0.56789
567s > 
567s >  out <- temper(out, scale = matscale)
567s > 
567s >  my.coproposal.within <- out$coproposal[out$which, ]
567s >  proposal.within <- out$proposal[out$which, ]
567s >  my.z <- out$norm[out$which, ]
567s >  my.proposal.within <- my.coproposal.within
567s >  my.proposal.within[ , -1] <- my.coproposal.within[ , -1] +
567s +      my.z %*% t(out$scale)
567s >  all.equal(proposal.within, my.proposal.within)
567s [1] TRUE
567s > 
567s >  ### check scale list
567s > 
567s >  lisztscale <- list(0.56789, newscale, matscale, matscale, newscale,
567s +      0.98765, 0.98765, newscale)
567s > 
567s >  out <- temper(out, scale = lisztscale)
568s > 
568s >  my.coproposal.within <- out$coproposal[out$which, ]
568s >  proposal.within <- out$proposal[out$which, ]
568s >  my.z <- out$norm[out$which, ]
568s >  my.proposal.within <- my.coproposal.within
568s >  for (iiter in 1:nrow(my.z)) {
568s +      my.i <- my.coproposal.within[iiter, 1]
568s +      my.scale <- out$scale[[my.i]]
568s +      if (is.matrix(my.scale)) {
568s +          my.proposal.within[iiter, -1] <- my.coproposal.within[iiter, -1] +
568s +              my.z[iiter, , drop = FALSE] %*% t(my.scale)
568s +      } else {
568s +          my.proposal.within[iiter, -1] <- my.coproposal.within[iiter, -1] +
568s +              my.z[iiter, ] * my.scale
568s +      }
568s +  }
568s >  all.equal(proposal.within, my.proposal.within)
568s [1] TRUE
568s > 
568s >  ### check outfun
568s > 
568s >  outfun <- function(state, icomp, ...) {
568s +      stopifnot(is.matrix(state))
568s +      stopifnot(is.numeric(state))
568s +      nx <- ncol(betas)
568s +      ncomp <- nrow(betas)
568s +      stopifnot(ncol(state) == nx)
568s +      stopifnot(nrow(state) == ncomp)
568s +      stopifnot(1 <= icomp && icomp <= ncomp)
568s +      foo <- state[icomp, ]
568s +      bar <- foo^2
568s +      return(c(foo, bar))
568s +  }
568s > 
568s >  out <- temper(out, outfun = outfun, icomp = 4)
568s > 
568s >  before <- out$state
568s >  after <- before
568s >  after[- dim(after)[1], , ] <- before[-1, , ]
568s >  after[dim(after)[1], , ] <- out$final
568s >  outies <- apply(after, 1, outfun, icomp = 4)
568s >  outies <- t(outies)
568s > 
568s >  foo <- outies[seq(1, niter) %% out$nspac == 0, ]
568s >  foo <- array(as.vector(foo), dim = c(out$blen, out$nbatch, dim(foo)[2]))
568s >  foo <- apply(foo, c(2, 3), mean)
568s >  all.equal(foo, out$batch)
568s [1] TRUE
568s > 
568s > 
568s BEGIN TEST tests/temp-ser-witch.R
568s 
568s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
568s Copyright (C) 2024 The R Foundation for Statistical Computing
568s Platform: arm-unknown-linux-gnueabihf (32-bit)
568s 
568s R is free software and comes with ABSOLUTELY NO WARRANTY.
568s You are welcome to redistribute it under certain conditions.
568s Type 'license()' or 'licence()' for distribution details.
568s 
568s R is a collaborative project with many contributors.
568s Type 'contributors()' for more information and
568s 'citation()' on how to cite R or R packages in publications.
568s 
568s Type 'demo()' for some demos, 'help()' for on-line help, or
568s 'help.start()' for an HTML browser interface to help.
568s Type 'q()' to quit R.
568s 
569s > 
569s >  library(mcmc)
569s > 
569s >  set.seed(42)
569s > 
569s >  d <- 3
569s >  witch.which <- 1 - (1 / 2)^(1 / d) * (1 / 4)^(seq(0, 5) / d)
569s >  witch.which
569s [1] 0.2062995 0.5000000 0.6850197 0.8015749 0.8750000 0.9212549
569s > 
569s >  ncomp <- length(witch.which)
569s > 
569s >  neighbors <- matrix(FALSE, ncomp, ncomp)
569s >  neighbors[row(neighbors) == col(neighbors) + 1] <- TRUE
569s >  neighbors[row(neighbors) == col(neighbors) - 1] <- TRUE
569s >  neighbors[row(neighbors) == col(neighbors) + 2] <- TRUE
569s >  neighbors[row(neighbors) == col(neighbors) - 2] <- TRUE
569s > 
569s >  ludfun <- function(state) {
569s +      stopifnot(is.numeric(state))
569s +      stopifnot(length(state) == d + 1)
569s +      icomp <- state[1]
569s +      stopifnot(icomp == as.integer(icomp))
569s +      stopifnot(1 <= icomp && icomp <= ncomp)
569s +      theta <- state[-1]
569s +      if (any(abs(theta) > 1.0)) return(-Inf)
569s +      bnd <- witch.which[icomp]
569s +      if(bnd >= 1.0)
569s +          stop(sprintf("witch.which[%d] >= 1.0", icomp))
569s +      if(bnd <= 0.0)
569s +          stop(sprintf("witch.which[%d] <= 0.0", icomp))
569s +      if (all(abs(theta) > bnd))
569s +          return(- (d + 1) * log(2) - d * log(1 - bnd))
569s +      return(- (d + 1) * log(2) - log1p(- (1 - bnd)^d))
569s +  }
569s > 
569s >  initial <- c(1, rep(0, d))
569s > 
569s >  out <- temper(ludfun, initial = initial, neighbors = neighbors,
569s +      nbatch = 50, blen = 13, nspac = 7, scale = 0.3456789)
569s > 
569s >  names(out)
569s  [1] "lud"          "neighbors"    "nbatch"       "blen"         "nspac"       
569s  [6] "scale"        "outfun"       "debug"        "parallel"     "initial.seed"
569s [11] "final.seed"   "time"         "batch"        "acceptx"      "accepti"     
569s [16] "initial"      "final"        "ibatch"      
569s > 
569s >  out$acceptx
569s [1] 0.6388889 0.4385246 0.3631714 0.4885246 0.4709677 0.4735516
569s > 
569s >  out$accepti
569s           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
569s [1,]        NA 0.5071770 0.2727273        NA        NA        NA
569s [2,] 0.7070064        NA 0.4355828 0.4186047        NA        NA
569s [3,] 0.5816327 0.8039216        NA 0.5888889 0.5662651        NA
569s [4,]        NA 0.7415730 0.8571429        NA 0.7857143 0.6626506
569s [5,]        NA        NA 0.5204082 0.6516854        NA 0.8378378
569s [6,]        NA        NA        NA 0.3515152 0.5056818        NA
569s > 
569s >  colMeans(out$ibatch)
569s [1] 0.1830769 0.2153846 0.1630769 0.1369231 0.1353846 0.1661538
569s > 
569s >  ### check that have prob 1 / 2 for corners
569s > 
569s >  outfun <- function(state) {
569s +      stopifnot(is.numeric(state))
569s +      icomp <- state[1]
569s +      stopifnot(icomp == as.integer(icomp))
569s +      stopifnot(1 <= icomp && icomp <= length(witch.which))
569s +      theta <- state[-1]
569s +      foo <- all(abs(theta) > witch.which[icomp])
569s +      bar <- rep(0, length(witch.which))
569s +      baz <- rep(0, length(witch.which))
569s +      bar[icomp] <- as.numeric(foo)
569s +      baz[icomp] <- 1
569s +      return(c(bar, baz))
569s +  }
569s > 
569s >  out <- temper(out, blen = 103, outfun = outfun, debug = TRUE)
571s > 
571s >  eta.batch <- out$batch[ , seq(1, ncomp)]
571s >  noo.batch <- out$batch[ , seq(ncomp + 1, ncomp + ncomp)]
571s >  eta <- colMeans(eta.batch)
571s >  noo <- colMeans(noo.batch)
571s >  mu <- eta / noo
571s >  eta
571s [1] 0.06660194 0.06388350 0.05766990 0.06563107 0.10368932 0.22912621
571s >  noo
571s [1] 0.1365049 0.1258252 0.1293204 0.1370874 0.1716505 0.2996117
571s >  mu
571s [1] 0.4879090 0.5077160 0.4459459 0.4787535 0.6040724 0.7647440
571s > 
571s >  eta.batch.rel <- sweep(eta.batch, 2, eta, "/")
571s >  noo.batch.rel <- sweep(noo.batch, 2, noo, "/")
571s >  mu.batch.rel <- eta.batch.rel - noo.batch.rel
571s > 
571s >  mu.mcse.rel <- apply(mu.batch.rel, 2, sd) / sqrt(out$nbatch)
571s >  mu.mcse.rel
571s [1] 0.05010927 0.07897321 0.09678339 0.12636113 0.11261781 0.07082685
571s > 
571s >  foo <- cbind(mu, mu * mu.mcse.rel)
571s >  colnames(foo) <- c("means", "MCSE")
571s >  foo
571s          means       MCSE
571s [1,] 0.4879090 0.02444876
571s [2,] 0.5077160 0.04009596
571s [3,] 0.4459459 0.04316016
571s [4,] 0.4787535 0.06049584
571s [5,] 0.6040724 0.06802931
571s [6,] 0.7647440 0.05416441
571s > 
571s >  ### check decision about within-component or jump/swap
571s > 
571s >  identical(out$unif.which < 0.5, out$which)
571s [1] TRUE
571s > 
571s >  identical(out$which, out$proposal[ , 1] == out$state[ , 1])
571s [1] TRUE
571s > 
571s >  ### check hastings ratio calculated correctly
571s > 
571s >  n <- apply(neighbors, 1, sum)
571s >  i <- out$state[ , 1]
571s >  istar <- out$proposal[ , 1]
571s >  foo <- apply(out$state, 1, ludfun)
573s >  bar <- apply(out$proposal, 1, ludfun)
575s >  my.log.hastings <- bar - foo - log(n[istar]) + log(n[i])
575s >  all.equal(my.log.hastings, out$log.hastings)
575s [1] TRUE
575s > 
575s > 
575s BEGIN TEST tests/temp-ser.R
575s 
575s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
575s Copyright (C) 2024 The R Foundation for Statistical Computing
575s Platform: arm-unknown-linux-gnueabihf (32-bit)
575s 
575s R is free software and comes with ABSOLUTELY NO WARRANTY.
575s You are welcome to redistribute it under certain conditions.
575s Type 'license()' or 'licence()' for distribution details.
575s 
575s R is a collaborative project with many contributors.
575s Type 'contributors()' for more information and
575s 'citation()' on how to cite R or R packages in publications.
575s 
575s Type 'demo()' for some demos, 'help()' for on-line help, or
575s 'help.start()' for an HTML browser interface to help.
575s Type 'q()' to quit R.
575s 
575s > 
575s >  library(mcmc)
575s > 
575s >  set.seed(42)
575s > 
575s >  data(foo)
575s >  attach(foo)
575s > 
575s >  out <- glm(y ~ x1 + x2 + x3, family = binomial, x = TRUE)
575s > ## IGNORE_RDIFF_BEGIN
575s >  summary(out)
575s 
575s Call:
575s glm(formula = y ~ x1 + x2 + x3, family = binomial, x = TRUE)
575s 
575s Coefficients:
575s             Estimate Std. Error z value Pr(>|z|)    
575s (Intercept)   0.5772     0.2766   2.087 0.036930 *  
575s x1            0.3362     0.4256   0.790 0.429672    
575s x2            0.8475     0.4701   1.803 0.071394 .  
575s x3            1.5143     0.4426   3.422 0.000622 ***
575s ---
575s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
575s 
575s (Dispersion parameter for binomial family taken to be 1)
575s 
575s     Null deviance: 134.602  on 99  degrees of freedom
575s Residual deviance:  86.439  on 96  degrees of freedom
575s AIC: 94.439
575s 
575s Number of Fisher Scoring iterations: 5
575s 
575s > ## IGNORE_RDIFF_END
575s > 
575s >  modmat <- out$x
575s > 
575s >  models <- cbind(rep(0:1, each = 4), rep(rep(0:1, times = 2), each = 2),
575s +                rep(0:1, times = 4))
575s > 
575s >  exes <- paste("x", 1:3, sep = "")
575s >  models[nrow(models), ]
575s [1] 1 1 1
575s >  beta.initial <- c(nrow(models), out$coefficients)
575s > 
575s >  neighbors <- matrix(FALSE, nrow(models), nrow(models))
575s >  for (i in 1:nrow(neighbors)) {
575s +      for (j in 1:ncol(neighbors)) {
575s +          foo <- models[i, ]
575s +          bar <- models[j, ]
575s +          if (sum(foo != bar) == 1) neighbors[i, j] <- TRUE
575s +      }
575s +  }
575s >  neighbors
575s       [,1]  [,2]  [,3]  [,4]  [,5]  [,6]  [,7]  [,8]
575s [1,] FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE
575s [2,]  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE
575s [3,]  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE
575s [4,] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE
575s [5,]  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
575s [6,] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE
575s [7,] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE
575s [8,] FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE
575s > 
575s >  ludfun <- function(state, log.pseudo.prior, ...) {
575s +      stopifnot(is.numeric(state))
575s +      stopifnot(length(state) == ncol(models) + 2)
575s +      icomp <- state[1]
575s +      stopifnot(icomp == as.integer(icomp))
575s +      stopifnot(1 <= icomp && icomp <= nrow(models))
575s +      stopifnot(is.numeric(log.pseudo.prior))
575s +      stopifnot(length(log.pseudo.prior) == nrow(models))
575s +      beta <- state[-1]
575s +      inies <- c(TRUE, as.logical(models[icomp, ]))
575s +      beta.logl <- beta
575s +      beta.logl[! inies] <- 0
575s +      eta <- as.numeric(modmat %*% beta.logl)
575s +      logp <- ifelse(eta < 0, eta - log1p(exp(eta)), - log1p(exp(- eta)))
575s +      logq <- ifelse(eta < 0, - log1p(exp(eta)), - eta - log1p(exp(- eta)))
575s +      logl <- sum(logp[y == 1]) + sum(logq[y == 0])
575s +      val <- logl - sum(beta^2) / 2 + log.pseudo.prior[icomp]
575s +      return(val)
575s +  }
575s > 
575s >  qux <- c(25.01, 5.875, 9.028, 0.6959, 11.73,  2.367, 5.864, 0.0)
575s > 
575s >  out <- temper(ludfun, initial = beta.initial, neighbors = neighbors,
575s +      nbatch = 25, blen = 20, nspac = 5, scale = 0.56789, debug = TRUE,
575s +      log.pseudo.prior = qux)
576s > 
576s >  names(out)
576s  [1] "lud"           "neighbors"     "nbatch"        "blen"         
576s  [5] "nspac"         "scale"         "outfun"        "debug"        
576s  [9] "parallel"      "initial.seed"  "final.seed"    "time"         
576s [13] "batch"         "acceptx"       "accepti"       "initial"      
576s [17] "final"         "ibatch"        "which"         "unif.which"   
576s [21] "state"         "log.hastings"  "unif.hastings" "proposal"     
576s [25] "acceptd"       "norm"          "unif.choose"  
576s > 
576s >  apply(out$ibatch, 2, mean)
576s [1] 0.776 0.170 0.000 0.006 0.024 0.010 0.004 0.010
576s > 
576s >  ### check decision about within-component or jump/swap
576s > 
576s >  identical(out$unif.which < 0.5, out$which)
576s [1] TRUE
576s > 
576s >  identical(out$which, out$proposal[ , 1] == out$state[ , 1])
576s [1] TRUE
576s > 
576s >  ### check hastings ratio calculated correctly
576s > 
576s >  foo <- apply(out$state, 1, ludfun, log.pseudo.prior = qux)
576s >  bar <- apply(out$proposal, 1, ludfun, log.pseudo.prior = qux)
577s >  all.equal(bar - foo, out$log.hastings)
577s [1] TRUE
577s > 
577s >  ### check hastings rejection decided correctly
577s > 
577s >  identical(out$log.hastings >= 0, is.na(out$unif.hastings))
577s [1] TRUE
577s >  all(out$log.hastings < 0 | out$acceptd)
577s [1] TRUE
577s >  identical(out$acceptd,
577s +      out$log.hastings >= 0 | out$unif.hastings < exp(out$log.hastings))
577s [1] TRUE
577s > 
577s >  ### check acceptance carried out or not (according to decision) correctly
577s > 
577s >  before <- out$state
577s >  after <- before
577s >  after[- dim(after)[1], ] <- before[-1, ]
577s >  after[dim(after)[1], ] <- out$final
577s >  my.after <- before
577s >  my.after[out$acceptd, ] <- out$proposal[out$acceptd, ]
577s >  identical(after, my.after)
577s [1] TRUE
577s > 
577s >  ### check within-component proposal
577s > 
577s >  my.coproposal.within <- out$state[out$which, ]
577s >  proposal.within <- out$proposal[out$which, ]
577s >  my.z <- out$norm[out$which, ]
577s >  my.proposal.within <- my.coproposal.within
577s >  my.proposal.within[ , -1] <- my.coproposal.within[ , -1] + out$scale * my.z
577s >  all.equal(proposal.within, my.proposal.within)
577s [1] TRUE
577s > 
577s >  ### check swap proposal
577s > 
577s >  coproposal.swap <- out$state[! out$which, ]
577s >  proposal.swap <- out$proposal[! out$which, ]
577s >  unif.choose.swap <- out$unif.choose[! out$which]
577s >  my.i <- coproposal.swap[ , 1]
577s >  nneighbors <- apply(out$neighbors, 1, sum)
577s >  my.nneighbors <- nneighbors[my.i]
577s >  my.k <- floor(my.nneighbors * unif.choose.swap) + 1
577s >  my.j <- my.k
577s >  foo <- seq(1, ncol(out$neighbors))
577s >  for (i in seq(along = my.j)) {
577s +      my.j[i] <- (foo[out$neighbors[my.i[i], ]])[my.k[i]]
577s +  }
577s >  identical(coproposal.swap[ , 1], my.i)
577s [1] TRUE
577s >  identical(proposal.swap[ , 1], my.j)
577s [1] TRUE
577s > 
577s >  ### check standard normal and uniform random numbers are as purported
577s > 
577s >  save.Random.seed <- .Random.seed
577s >  .Random.seed <- out$initial.seed
577s > 
577s >  nx <- length(out$initial) - 1
577s >  niter <- out$nbatch * out$blen * out$nspac
577s >  my.norm <- matrix(NA, nrow = nrow(out$norm), ncol = ncol(out$norm))
577s >  my.unif.which <- rep(NA, niter)
577s >  my.unif.hastings <- rep(NA, niter)
577s >  my.unif.choose <- rep(NA, niter)
577s >  for (iiter in 1:niter) {
577s +      my.unif.which[iiter] <- runif(1)
577s +      if (out$which[iiter]) {
577s +          my.norm[iiter, ] <- rnorm(nx)
577s +          if (out$log.hastings[iiter] < 0) my.unif.hastings[iiter] <- runif(1) 
577s +      } else {
577s +          my.unif.choose[iiter] <- runif(1)
577s +          if (out$log.hastings[iiter] < 0) my.unif.hastings[iiter] <- runif(1) 
577s +      }
577s +  }
577s >  identical(my.norm, out$norm)
577s [1] TRUE
577s >  identical(my.unif.which, out$unif.which)
577s [1] TRUE
577s >  identical(my.unif.hastings, out$unif.hastings)
577s [1] TRUE
577s >  identical(my.unif.choose, out$unif.choose)
577s [1] TRUE
577s > 
577s >  .Random.seed <- save.Random.seed
577s > 
577s >  ### check batch means
577s > 
577s >  my.xstate <- after[ , -1]
577s >  foo <- my.xstate[seq(1, niter) %% out$nspac == 0, ]
577s >  foo <- array(as.vector(foo), dim = c(out$blen, out$nbatch, dim(foo)[2]))
577s >  foo <- apply(foo, c(2, 3), mean)
577s >  all.equal(foo, out$batch)
577s [1] TRUE
577s > 
577s >  ### check ibatch means
577s > 
577s >  my.istate <- after[ , 1]
577s >  my.istate.matrix <- matrix(0, length(my.istate), nrow(models))
577s >  for (i in 1:nrow(my.istate.matrix))
577s +      my.istate.matrix[i, my.istate[i]] <- 1
577s >  foo <- my.istate.matrix[seq(1, niter) %% out$nspac == 0, ]
577s >  foo <- array(as.vector(foo), dim = c(out$blen, out$nbatch, dim(foo)[2]))
577s >  foo <- apply(foo, c(2, 3), mean)
577s >  all.equal(foo, out$ibatch)
577s [1] TRUE
577s > 
577s >  ### check acceptance rates
577s > 
577s >  nmodel <- nrow(out$neighbors)
577s > 
577s >  accept.within <- out$acceptd[out$which]
577s >  my.i.within <- out$state[out$which, 1]
577s >  my.i.within.accept <- my.i.within[accept.within]
577s >  my.acceptx.numer <- tabulate(my.i.within.accept, nbins = nmodel)
577s >  my.acceptx.denom <- tabulate(my.i.within, nbins = nmodel)
577s >  my.acceptx <- my.acceptx.numer / my.acceptx.denom
577s >  identical(my.acceptx, out$acceptx)
577s [1] TRUE
577s > 
577s >  accept.swap <- out$acceptd[! out$which]
577s >  my.i.swap <- out$state[! out$which, 1]
577s >  my.j.swap <- out$proposal[! out$which, 1]
577s >  my.accepti <- matrix(NA, nmodel, nmodel)
577s >  for (i in 1:nmodel) {
577s +      for (j in 1:nmodel) {
577s +          if (out$neighbors[i, j]) {
577s +              my.accepti[i, j] <-
577s +                  mean(accept.swap[my.i.swap == i & my.j.swap == j])
577s +          }
577s +      }
577s +  }
577s >  identical(my.accepti, out$accepti)
577s [1] TRUE
577s > 
577s >  ### check scale vector
577s > 
577s >  nx <- ncol(models) + 1
577s >  newscale <- rnorm(nx, 0.5, 0.1)
577s > 
577s >  out <- temper(out, scale = newscale, log.pseudo.prior = qux)
578s > 
578s >  my.coproposal.within <- out$state[out$which, ]
578s >  proposal.within <- out$proposal[out$which, ]
578s >  my.z <- out$norm[out$which, ]
578s >  my.proposal.within <- my.coproposal.within
578s >  my.proposal.within[ , -1] <- my.coproposal.within[ , -1] +
578s +      sweep(my.z, 2, out$scale, "*")
578s >  all.equal(proposal.within, my.proposal.within)
578s [1] TRUE
578s > 
578s >  ### check scale matrix
578s > 
578s >  matscale <- matrix(rnorm(nx * nx, 0.0, 0.1), nx, nx)
578s >  diag(matscale) <- 0.56789
578s > 
578s >  out <- temper(out, scale = matscale, log.pseudo.prior = qux)
579s > 
579s >  my.coproposal.within <- out$state[out$which, ]
579s >  proposal.within <- out$proposal[out$which, ]
579s >  my.z <- out$norm[out$which, ]
579s >  my.proposal.within <- my.coproposal.within
579s >  my.proposal.within[ , -1] <- my.coproposal.within[ , -1] +
579s +      my.z %*% t(out$scale)
579s >  all.equal(proposal.within, my.proposal.within)
579s [1] TRUE
579s > 
579s >  ### check scale list
579s > 
579s >  lisztscale <- list(0.56789, newscale, matscale, matscale, newscale,
579s +      0.98765, 0.98765, newscale)
579s > 
579s >  out <- temper(out, scale = lisztscale, log.pseudo.prior = qux)
579s > 
579s >  my.coproposal.within <- out$state[out$which, ]
579s >  proposal.within <- out$proposal[out$which, ]
579s >  my.z <- out$norm[out$which, ]
579s >  my.proposal.within <- my.coproposal.within
579s >  for (iiter in 1:nrow(my.z)) {
579s +      my.i <- my.coproposal.within[iiter, 1]
579s +      my.scale <- out$scale[[my.i]]
579s +      if (is.matrix(my.scale)) {
579s +          my.proposal.within[iiter, -1] <- my.coproposal.within[iiter, -1] +
579s +              my.z[iiter, , drop = FALSE] %*% t(my.scale)
579s +      } else {
579s +          my.proposal.within[iiter, -1] <- my.coproposal.within[iiter, -1] +
579s +              my.z[iiter, ] * my.scale
579s +      }
579s +  }
579s >  all.equal(proposal.within, my.proposal.within)
579s [1] TRUE
579s > 
579s >  ### check outfun
579s > 
579s >  outfun <- function(state, icomp) {
579s +      stopifnot(is.matrix(state))
579s +      stopifnot(is.numeric(state))
579s +      nx <- ncol(initial)
579s +      ncomp <- nrow(initial)
579s +      stopifnot(ncol(state) == nx)
579s +      stopifnot(nrow(state) == ncomp)
579s +      stopifnot(1 <= icomp & icomp <= ncomp)
579s +      foo <- state[icomp, ]
579s +      bar <- foo^2
579s +      return(c(foo, bar))
579s +  }
579s > 
579s >  ncomp <- nrow(models)
579s >  nx <- length(beta.initial) - 1
579s > 
579s >  outfun <- function(state, icomp, ...) {
579s +      stopifnot(is.numeric(state))
579s +      stopifnot(length(state) == nx + 1)
579s +      istate <- state[1]
579s +      stopifnot(istate == as.integer(istate))
579s +      stopifnot(1 <= istate && istate <= ncomp)
579s +      stopifnot(1 <= icomp && icomp <= ncomp)
579s +      if (istate == icomp) {
579s +          foo <- state[-1]
579s +      } else {
579s +          foo <- rep(0, nx)
579s +      }
579s +      bar <- foo^2
579s +      return(c(foo, bar))
579s +  }
579s > 
579s >  out <- temper(ludfun, initial = out$final, neighbors = neighbors,
579s +      nbatch = 25, blen = 20, nspac = 5, scale = 0.56789, debug = TRUE,
579s +      outfun = outfun, log.pseudo.prior = qux, icomp = 4)
580s > 
580s >  before <- out$state
580s >  after <- before
580s >  after[- dim(after)[1], ] <- before[-1, ]
580s >  after[dim(after)[1], ] <- out$final
580s >  outies <- apply(after, 1, outfun, icomp = 4)
580s >  outies <- t(outies)
580s > 
580s >  foo <- outies[seq(1, niter) %% out$nspac == 0, ]
580s >  foo <- array(as.vector(foo), dim = c(out$blen, out$nbatch, dim(foo)[2]))
580s >  foo <- apply(foo, c(2, 3), mean)
580s >  all.equal(foo, out$batch)
580s [1] TRUE
580s > 
580s > 
580s BEGIN TEST tests/zero-error.R
580s 
580s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
580s Copyright (C) 2024 The R Foundation for Statistical Computing
580s Platform: arm-unknown-linux-gnueabihf (32-bit)
580s 
580s R is free software and comes with ABSOLUTELY NO WARRANTY.
580s You are welcome to redistribute it under certain conditions.
580s Type 'license()' or 'licence()' for distribution details.
580s 
580s R is a collaborative project with many contributors.
580s Type 'contributors()' for more information and
580s 'citation()' on how to cite R or R packages in publications.
580s 
580s Type 'demo()' for some demos, 'help()' for on-line help, or
580s 'help.start()' for an HTML browser interface to help.
580s Type 'q()' to quit R.
580s 
580s > 
580s >  library(mcmc)
580s > 
580s > # should give intelligible error (unlike before ver 0.9-8)
580s > 
580s >  suppressMessages(try(metrop(function(x) x, double(0), nbatch = 10)))
581s Error in system.time(out <- .Call(C_metrop, func1, initial, nbatch, blen,  : 
581s   argument "initial" must have nonzero length
581s > 
581s autopkgtest [12:27:50]: test generic: -----------------------]
605s generic              PASS
605s autopkgtest [12:28:14]: test generic:  - - - - - - - - - - results - - - - - - - - - -
608s autopkgtest [12:28:17]: test pkg-r-autopkgtest: preparing testbed
618s Reading package lists...
618s Building dependency tree...
618s Reading state information...
619s Starting pkgProblemResolver with broken count: 0
619s Starting 2 pkgProblemResolver with broken count: 0
619s Done
621s The following additional packages will be installed:
621s   build-essential cpp cpp-13 cpp-13-arm-linux-gnueabihf
621s   cpp-arm-linux-gnueabihf dctrl-tools g++ g++-13 g++-13-arm-linux-gnueabihf
621s   g++-arm-linux-gnueabihf gcc gcc-13 gcc-13-arm-linux-gnueabihf
621s   gcc-arm-linux-gnueabihf gfortran gfortran-13 gfortran-13-arm-linux-gnueabihf
621s   gfortran-arm-linux-gnueabihf icu-devtools libasan8 libatomic1 libblas-dev
621s   libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev
621s   libgfortran-13-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev
621s   libjpeg8-dev liblapack-dev liblzma-dev libmpc3 libncurses-dev libpcre2-16-0
621s   libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev
621s   libreadline-dev libstdc++-13-dev libubsan1 linux-libc-dev pkg-config
621s   pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev
621s Suggested packages:
621s   cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib
621s   manpages-dev autoconf automake libtool flex bison gdb gcc-doc
621s   gdb-arm-linux-gnueabihf gfortran-doc gfortran-13-doc libcoarrays-dev
621s   liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc
621s   libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic
621s   texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
621s   texlive-latex-recommended texlive-latex-extra texinfo
621s Recommended packages:
621s   bzip2-doc manpages manpages-dev libc-devtools libpng-tools
621s The following NEW packages will be installed:
621s   autopkgtest-satdep build-essential cpp cpp-13 cpp-13-arm-linux-gnueabihf
621s   cpp-arm-linux-gnueabihf dctrl-tools g++ g++-13 g++-13-arm-linux-gnueabihf
621s   g++-arm-linux-gnueabihf gcc gcc-13 gcc-13-arm-linux-gnueabihf
621s   gcc-arm-linux-gnueabihf gfortran gfortran-13 gfortran-13-arm-linux-gnueabihf
621s   gfortran-arm-linux-gnueabihf icu-devtools libasan8 libatomic1 libblas-dev
621s   libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev
621s   libgfortran-13-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev
621s   libjpeg8-dev liblapack-dev liblzma-dev libmpc3 libncurses-dev libpcre2-16-0
621s   libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev
621s   libreadline-dev libstdc++-13-dev libubsan1 linux-libc-dev pkg-config
621s   pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev
621s 0 upgraded, 56 newly installed, 0 to remove and 1 not upgraded.
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624s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf r-base-dev all 4.3.3-2build1 [4334 B]
624s Get:56 http://ftpmaster.internal/ubuntu noble/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
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629s Preparing to unpack .../31-gfortran_4%3a13.2.0-7ubuntu1_armhf.deb ...
629s Unpacking gfortran (4:13.2.0-7ubuntu1) ...
629s Selecting previously unselected package icu-devtools.
629s Preparing to unpack .../32-icu-devtools_74.2-1ubuntu1_armhf.deb ...
629s Unpacking icu-devtools (74.2-1ubuntu1) ...
630s Selecting previously unselected package libblas-dev:armhf.
630s Preparing to unpack .../33-libblas-dev_3.12.0-3_armhf.deb ...
630s Unpacking libblas-dev:armhf (3.12.0-3) ...
630s Selecting previously unselected package libbz2-dev:armhf.
630s Preparing to unpack .../34-libbz2-dev_1.0.8-5ubuntu1_armhf.deb ...
630s Unpacking libbz2-dev:armhf (1.0.8-5ubuntu1) ...
630s Selecting previously unselected package libicu-dev:armhf.
630s Preparing to unpack .../35-libicu-dev_74.2-1ubuntu1_armhf.deb ...
630s Unpacking libicu-dev:armhf (74.2-1ubuntu1) ...
630s Selecting previously unselected package libjpeg-turbo8-dev:armhf.
630s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-2ubuntu1_armhf.deb ...
630s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-2ubuntu1) ...
630s Selecting previously unselected package libjpeg8-dev:armhf.
630s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ...
630s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ...
630s Selecting previously unselected package libjpeg-dev:armhf.
630s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_armhf.deb ...
630s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ...
630s Selecting previously unselected package liblapack-dev:armhf.
630s Preparing to unpack .../39-liblapack-dev_3.12.0-3_armhf.deb ...
630s Unpacking liblapack-dev:armhf (3.12.0-3) ...
631s Selecting previously unselected package libncurses-dev:armhf.
631s Preparing to unpack .../40-libncurses-dev_6.4+20240113-1ubuntu1_armhf.deb ...
631s Unpacking libncurses-dev:armhf (6.4+20240113-1ubuntu1) ...
631s Selecting previously unselected package libpcre2-16-0:armhf.
631s Preparing to unpack .../41-libpcre2-16-0_10.42-4ubuntu1_armhf.deb ...
631s Unpacking libpcre2-16-0:armhf (10.42-4ubuntu1) ...
631s Selecting previously unselected package libpcre2-32-0:armhf.
631s Preparing to unpack .../42-libpcre2-32-0_10.42-4ubuntu1_armhf.deb ...
631s Unpacking libpcre2-32-0:armhf (10.42-4ubuntu1) ...
631s Selecting previously unselected package libpcre2-posix3:armhf.
631s Preparing to unpack .../43-libpcre2-posix3_10.42-4ubuntu1_armhf.deb ...
631s Unpacking libpcre2-posix3:armhf (10.42-4ubuntu1) ...
631s Selecting previously unselected package libpcre2-dev:armhf.
631s Preparing to unpack .../44-libpcre2-dev_10.42-4ubuntu1_armhf.deb ...
631s Unpacking libpcre2-dev:armhf (10.42-4ubuntu1) ...
631s Selecting previously unselected package libpkgconf3:armhf.
631s Preparing to unpack .../45-libpkgconf3_1.8.1-2_armhf.deb ...
631s Unpacking libpkgconf3:armhf (1.8.1-2) ...
631s Selecting previously unselected package zlib1g-dev:armhf.
631s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg-3.1ubuntu1_armhf.deb ...
631s Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu1) ...
631s Selecting previously unselected package libpng-dev:armhf.
631s Preparing to unpack .../47-libpng-dev_1.6.43-3_armhf.deb ...
631s Unpacking libpng-dev:armhf (1.6.43-3) ...
631s Selecting previously unselected package libreadline-dev:armhf.
631s Preparing to unpack .../48-libreadline-dev_8.2-4_armhf.deb ...
631s Unpacking libreadline-dev:armhf (8.2-4) ...
631s Selecting previously unselected package pkgconf-bin.
631s Preparing to unpack .../49-pkgconf-bin_1.8.1-2_armhf.deb ...
631s Unpacking pkgconf-bin (1.8.1-2) ...
631s Selecting previously unselected package pkgconf:armhf.
631s Preparing to unpack .../50-pkgconf_1.8.1-2_armhf.deb ...
631s Unpacking pkgconf:armhf (1.8.1-2) ...
631s Selecting previously unselected package pkg-config:armhf.
631s Preparing to unpack .../51-pkg-config_1.8.1-2_armhf.deb ...
631s Unpacking pkg-config:armhf (1.8.1-2) ...
631s Selecting previously unselected package liblzma-dev:armhf.
631s Preparing to unpack .../52-liblzma-dev_5.6.0-0.2_armhf.deb ...
631s Unpacking liblzma-dev:armhf (5.6.0-0.2) ...
631s Selecting previously unselected package r-base-dev.
631s Preparing to unpack .../53-r-base-dev_4.3.3-2build1_all.deb ...
631s Unpacking r-base-dev (4.3.3-2build1) ...
632s Selecting previously unselected package pkg-r-autopkgtest.
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632s Unpacking autopkgtest-satdep (0) ...
632s Setting up linux-libc-dev:armhf (6.8.0-20.20) ...
632s Setting up libpcre2-16-0:armhf (10.42-4ubuntu1) ...
632s Setting up libpcre2-32-0:armhf (10.42-4ubuntu1) ...
632s Setting up libpkgconf3:armhf (1.8.1-2) ...
632s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
632s Setting up libmpc3:armhf (1.3.1-1) ...
632s Setting up libatomic1:armhf (14-20240315-1ubuntu1) ...
632s Setting up icu-devtools (74.2-1ubuntu1) ...
632s Setting up pkgconf-bin (1.8.1-2) ...
632s Setting up liblzma-dev:armhf (5.6.0-0.2) ...
632s Setting up libubsan1:armhf (14-20240315-1ubuntu1) ...
632s Setting up libpcre2-posix3:armhf (10.42-4ubuntu1) ...
632s Setting up libcrypt-dev:armhf (1:4.4.36-4) ...
632s Setting up libasan8:armhf (14-20240315-1ubuntu1) ...
632s Setting up libisl23:armhf (0.26-3) ...
632s Setting up libc-dev-bin (2.39-0ubuntu6) ...
632s Setting up libcc1-0:armhf (14-20240315-1ubuntu1) ...
632s Setting up libblas-dev:armhf (3.12.0-3) ...
632s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
632s Setting up dctrl-tools (2.24-3build2) ...
632s Setting up cpp-13-arm-linux-gnueabihf (13.2.0-21ubuntu1) ...
632s Setting up pkgconf:armhf (1.8.1-2) ...
632s Setting up liblapack-dev:armhf (3.12.0-3) ...
632s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
632s Setting up pkg-config:armhf (1.8.1-2) ...
632s Setting up libgcc-13-dev:armhf (13.2.0-21ubuntu1) ...
632s Setting up libc6-dev:armhf (2.39-0ubuntu6) ...
632s Setting up libgfortran-13-dev:armhf (13.2.0-21ubuntu1) ...
632s Setting up libicu-dev:armhf (74.2-1ubuntu1) ...
632s Setting up cpp-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
632s Setting up libstdc++-13-dev:armhf (13.2.0-21ubuntu1) ...
632s Setting up libbz2-dev:armhf (1.0.8-5ubuntu1) ...
632s Setting up libjpeg-turbo8-dev:armhf (2.1.5-2ubuntu1) ...
632s Setting up libncurses-dev:armhf (6.4+20240113-1ubuntu1) ...
632s Setting up libpcre2-dev:armhf (10.42-4ubuntu1) ...
632s Setting up cpp-13 (13.2.0-21ubuntu1) ...
632s Setting up libreadline-dev:armhf (8.2-4) ...
632s Setting up gcc-13-arm-linux-gnueabihf (13.2.0-21ubuntu1) ...
632s Setting up gcc-13 (13.2.0-21ubuntu1) ...
632s Setting up zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu1) ...
632s Setting up cpp (4:13.2.0-7ubuntu1) ...
632s Setting up libjpeg8-dev:armhf (8c-2ubuntu11) ...
632s Setting up gcc-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
632s Setting up g++-13-arm-linux-gnueabihf (13.2.0-21ubuntu1) ...
632s Setting up gfortran-13-arm-linux-gnueabihf (13.2.0-21ubuntu1) ...
632s Setting up g++-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
632s Setting up g++-13 (13.2.0-21ubuntu1) ...
632s Setting up libpng-dev:armhf (1.6.43-3) ...
632s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ...
632s Setting up gcc (4:13.2.0-7ubuntu1) ...
632s Setting up gfortran-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
632s Setting up gfortran-13 (13.2.0-21ubuntu1) ...
632s Setting up g++ (4:13.2.0-7ubuntu1) ...
632s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
632s Setting up build-essential (12.10ubuntu1) ...
632s Setting up gfortran (4:13.2.0-7ubuntu1) ...
632s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
632s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
632s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
632s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
632s Setting up r-base-dev (4.3.3-2build1) ...
632s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
632s Setting up autopkgtest-satdep (0) ...
632s Processing triggers for man-db (2.12.0-3build4) ...
633s Processing triggers for install-info (7.1-3build1) ...
633s Processing triggers for libc-bin (2.39-0ubuntu6) ...
647s (Reading database ... 64009 files and directories currently installed.)
647s Removing autopkgtest-satdep (0) ...
653s autopkgtest [12:29:02]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
653s autopkgtest [12:29:02]: test pkg-r-autopkgtest: [-----------------------
655s Test: Try to load the R library mcmc
655s 
655s R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
655s Copyright (C) 2024 The R Foundation for Statistical Computing
655s Platform: arm-unknown-linux-gnueabihf (32-bit)
655s 
655s R is free software and comes with ABSOLUTELY NO WARRANTY.
655s You are welcome to redistribute it under certain conditions.
655s Type 'license()' or 'licence()' for distribution details.
655s 
655s R is a collaborative project with many contributors.
655s Type 'contributors()' for more information and
655s 'citation()' on how to cite R or R packages in publications.
655s 
655s Type 'demo()' for some demos, 'help()' for on-line help, or
655s 'help.start()' for an HTML browser interface to help.
655s Type 'q()' to quit R.
655s 
655s > library('mcmc')
655s > 
655s > 
655s Other tests are currently unsupported!
655s They will be progressively added.
656s autopkgtest [12:29:05]: test pkg-r-autopkgtest: -----------------------]
659s autopkgtest [12:29:08]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
659s pkg-r-autopkgtest    PASS
663s autopkgtest [12:29:12]: @@@@@@@@@@@@@@@@@@@@ summary
663s generic              PASS
663s pkg-r-autopkgtest    PASS