0s autopkgtest [23:41:23]: starting date and time: 2024-03-22 23:41:23+0000 0s autopkgtest [23:41:23]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [23:41:23]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9titci21/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed --apt-upgrade htslib --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build2 curl/8.5.0-2ubuntu7' -- lxd -r lxd-armhf-10.145.243.79 lxd-armhf-10.145.243.79:autopkgtest/ubuntu/noble/armhf 24s autopkgtest [23:41:47]: testbed dpkg architecture: armhf 26s autopkgtest [23:41:49]: testbed apt version: 2.7.12 26s autopkgtest [23:41:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 34s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 34s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 34s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3979 kB] 34s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 34s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [641 kB] 34s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 34s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 34s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 34s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [4064 kB] 34s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 34s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [49.1 kB] 34s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 37s Fetched 9425 kB in 2s (5364 kB/s) 37s Reading package lists... 46s tee: /proc/self/fd/2: Permission denied 67s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 67s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 69s Reading package lists... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 70s Calculating upgrade... 70s The following packages were automatically installed and are no longer required: 70s linux-headers-6.8.0-11 python3-lib2to3 70s Use 'apt autoremove' to remove them. 70s The following packages will be REMOVED: 70s libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1 70s libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11 70s libhogweed6 libmagic1 libnetplan0 libnettle8 libnpth0 libnvme1 libparted2 70s libpcap0.8 libperl5.38 libpng16-16 libpsl5 libreadline8 libreiserfscore0 70s libssl3 libtirpc3 libuv1 linux-headers-6.8.0-11-generic python3-distutils 70s The following NEW packages will be installed: 70s libapt-pkg6.0t64 libarchive13t64 libatm1t64 libcurl3t64-gnutls libcurl4t64 70s libdb5.3t64 libelf1t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 70s libglib2.0-0t64 libgnutls30t64 libgpgme11t64 libhogweed6t64 libmagic1t64 70s libnetplan1 libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64 70s libpcap0.8t64 libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64 70s libreiserfscore0t64 libssl3t64 libtirpc3t64 libuv1t64 linux-headers-6.8.0-20 70s linux-headers-6.8.0-20-generic xdg-user-dirs 70s The following packages have been kept back: 70s multipath-tools 70s The following packages will be upgraded: 70s apparmor apt apt-utils bind9-dnsutils bind9-host bind9-libs binutils 70s binutils-arm-linux-gnueabihf binutils-common bolt bsdextrautils bsdutils 70s btrfs-progs coreutils cryptsetup-bin curl dbus dbus-bin dbus-daemon 70s dbus-session-bus-common dbus-system-bus-common dbus-user-session dhcpcd-base 70s dirmngr dmsetup dpkg dpkg-dev e2fsprogs e2fsprogs-l10n eject fdisk file ftp 70s fwupd gawk gcc-13-base gcc-14-base gir1.2-girepository-2.0 gir1.2-glib-2.0 70s gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv 70s groff-base ibverbs-providers inetutils-telnet info initramfs-tools 70s initramfs-tools-bin initramfs-tools-core install-info iproute2 jq keyboxd 70s kmod kpartx krb5-locales libapparmor1 libaudit-common libaudit1 libbinutils 70s libblkid1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 70s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 70s libblockdev-utils3 libblockdev3 libbpf1 libbrotli1 libbsd0 libc-bin libc6 70s libcap-ng0 libcom-err2 libcryptsetup12 libctf-nobfd0 libctf0 libdbus-1-3 70s libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libevent-core-2.1-7 70s libexpat1 libfdisk1 libfido2-1 libftdi1-2 libfwupd2 libgcc-s1 70s libgirepository-1.0-1 libglib2.0-data libgssapi-krb5-2 libgudev-1.0-0 70s libgusb2 libibverbs1 libjcat1 libjq1 libjson-glib-1.0-0 70s libjson-glib-1.0-common libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 70s libldap-common libldap2 liblocale-gettext-perl liblzma5 libmagic-mgc 70s libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 libnghttp2-14 libnsl2 70s libnss-systemd libpam-modules libpam-modules-bin libpam-runtime 70s libpam-systemd libpam0g libplymouth5 libpolkit-agent-1-0 70s libpolkit-gobject-1-0 libprotobuf-c1 libpython3-stdlib libpython3.11-minimal 70s libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libqmi-glib5 70s libqmi-proxy libqrtr-glib0 librtmp1 libsasl2-2 libsasl2-modules 70s libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 70s libsframe1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssh-4 libstdc++6 70s libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl 70s libtirpc-common libudev1 libudisks2-0 libusb-1.0-0 libuuid1 libvolume-key1 70s libxml2 libxmlb2 libxmuu1 linux-headers-generic locales logsave lshw lsof 70s man-db mount mtr-tiny netplan-generator netplan.io openssh-client 70s openssh-server openssh-sftp-server openssl parted perl perl-base 70s perl-modules-5.38 pinentry-curses plymouth plymouth-theme-ubuntu-text psmisc 70s python-apt-common python3 python3-apt python3-cryptography python3-dbus 70s python3-gdbm python3-gi python3-lib2to3 python3-minimal python3-netplan 70s python3-pkg-resources python3-pyrsistent python3-setuptools 70s python3-typing-extensions python3-yaml python3.11 python3.11-minimal 70s python3.12 python3.12-minimal readline-common rsync shared-mime-info sudo 70s systemd systemd-dev systemd-resolved systemd-sysv systemd-timesyncd tcpdump 70s telnet tnftp ubuntu-pro-client ubuntu-pro-client-l10n udev udisks2 usb.ids 70s util-linux uuid-runtime vim-common vim-tiny wget xxd xz-utils zlib1g 70s 234 upgraded, 32 newly installed, 31 to remove and 1 not upgraded. 70s Need to get 106 MB of archives. 70s After this operation, 84.4 MB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu2 [102 kB] 71s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240315-1ubuntu1 [47.0 kB] 71s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240315-1ubuntu1 [41.5 kB] 71s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240315-1ubuntu1 [714 kB] 71s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.39-0ubuntu6 [2827 kB] 71s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbrotli1 armhf 1.1.0-2build1 [319 kB] 71s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-5.1ubuntu1 [119 kB] 71s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5-3 armhf 1.20.1-5.1ubuntu1 [321 kB] 71s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5support0 armhf 1.20.1-5.1ubuntu1 [31.4 kB] 71s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libk5crypto3 armhf 1.20.1-5.1ubuntu1 [78.6 kB] 71s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB] 71s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu1 [49.2 kB] 71s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build6 [51.3 kB] 71s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udisks2 armhf 2.10.1-6 [276 kB] 71s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudisks2-0 armhf 2.10.1-6 [143 kB] 71s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu2 [160 kB] 71s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma5 armhf 5.6.0-0.2 [117 kB] 71s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kmod armhf 31+20240202-2ubuntu4 [91.8 kB] 71s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu4 [44.9 kB] 71s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.4-1ubuntu5 [103 kB] 71s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-timesyncd armhf 255.4-1ubuntu5 [36.0 kB] 71s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB] 71s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit-common all 1:3.1.2-2.1 [5674 B] 71s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.4-2build1 [13.5 kB] 71s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit1 armhf 1:3.1.2-2.1 [44.3 kB] 71s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.3-5ubuntu3 [62.0 kB] 71s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2ubuntu1 [70.9 kB] 71s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl4t64 armhf 8.5.0-2ubuntu7 [296 kB] 71s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf curl armhf 8.5.0-2ubuntu7 [219 kB] 71s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.7 kB] 71s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf wget armhf 1.21.4-1ubuntu2 [317 kB] 71s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tnftp armhf 20230507-2build1 [98.6 kB] 71s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpcap0.8t64 armhf 1.10.4-4.1ubuntu1 [137 kB] 71s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tcpdump armhf 4.99.4-3ubuntu2 [425 kB] 71s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.4-1ubuntu5 [2009 kB] 71s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-resolved armhf 255.4-1ubuntu5 [289 kB] 71s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sudo armhf 1.9.15p5-3ubuntu3 [936 kB] 71s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf rsync armhf 3.2.7-1build1 [413 kB] 71s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-cryptography armhf 41.0.7-4build2 [788 kB] 71s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.13-0ubuntu2 [975 kB] 72s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu11 [35.5 kB] 72s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-client armhf 1:9.6p1-3ubuntu11 [890 kB] 72s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-server armhf 1:9.6p1-3ubuntu11 [503 kB] 72s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20 all 6.8.0-20.20 [13.6 MB] 72s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20-generic armhf 6.8.0-20.20 [1287 kB] 72s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-generic armhf 6.8.0-20.20+1 [9610 B] 72s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3t64 armhf 3.0.13-0ubuntu2 [1558 kB] 72s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnss-systemd armhf 255.4-1ubuntu5 [148 kB] 72s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.4-1ubuntu5 [166 kB] 72s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.4-1ubuntu5 [3502 kB] 72s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udev armhf 255.4-1ubuntu5 [1852 kB] 72s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.4-1ubuntu5 [11.9 kB] 72s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-systemd armhf 255.4-1ubuntu5 [216 kB] 72s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.4-1ubuntu5 [410 kB] 72s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu3 [47.0 kB] 72s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.3-5ubuntu3 [261 kB] 72s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] 72s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-user-session armhf 1.14.10-4ubuntu2 [9962 B] 72s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapparmor1 armhf 4.0.0-beta3-0ubuntu2 [45.0 kB] 72s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libexpat1 armhf 2.6.1-2 [65.9 kB] 72s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB] 72s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-bin armhf 1.14.10-4ubuntu2 [37.1 kB] 72s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus armhf 1.14.10-4ubuntu2 [28.1 kB] 72s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-daemon armhf 1.14.10-4ubuntu2 [109 kB] 72s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdbus-1-3 armhf 1.14.10-4ubuntu2 [190 kB] 72s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu2 [171 kB] 72s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.5-1ubuntu2 [49.5 kB] 72s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu2 [135 kB] 72s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu2 [34.4 kB] 72s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu2 [238 kB] 72s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu2 [196 kB] 72s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu2 [134 kB] 72s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-utils3 armhf 3.1.0-1build1 [16.9 kB] 72s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libvolume-key1 armhf 0.3.12-7build1 [38.4 kB] 72s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjcat1 armhf 0.2.0-2build2 [30.4 kB] 72s Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf parted armhf 3.6-3.1build2 [39.4 kB] 72s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libparted2t64 armhf 3.6-3.1build2 [143 kB] 72s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12 armhf 3.12.2-4build3 [645 kB] 72s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12-minimal armhf 3.12.2-4build3 [1942 kB] 72s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-stdlib armhf 3.12.2-4build3 [1906 kB] 72s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-minimal armhf 3.12.2-4build3 [816 kB] 72s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-5ubuntu1 [19.0 kB] 72s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11 armhf 3.11.8-1build4 [589 kB] 72s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11-minimal armhf 3.11.8-1build4 [1795 kB] 73s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-stdlib armhf 3.11.8-1build4 [1810 kB] 73s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-minimal armhf 3.11.8-1build4 [826 kB] 73s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu1 [599 kB] 73s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build2 [12.7 kB] 73s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build2 [8962 B] 73s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 73s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-6 [661 kB] 73s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gdbm armhf 3.12.2-3ubuntu2 [17.1 kB] 73s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main armhf man-db armhf 2.12.0-3build4 [1196 kB] 73s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm6t64 armhf 1.23-5.1 [30.3 kB] 73s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm-compat4t64 armhf 1.23-5.1 [6208 B] 73s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38t64 armhf 5.38.2-3.2 [4101 kB] 73s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3.2 [231 kB] 73s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3.2 [1671 kB] 73s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu4 [15.0 kB] 73s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnettle8t64 armhf 3.9.1-2.2 [187 kB] 73s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libhogweed6t64 armhf 3.9.1-2.2 [187 kB] 73s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu2 [1046 kB] 73s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap2 armhf 2.6.7+dfsg-1~exp1ubuntu6 [172 kB] 73s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu7 [290 kB] 73s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main armhf shared-mime-info armhf 2.4-1build1 [470 kB] 73s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-girepository-2.0 armhf 1.79.1-1ubuntu6 [24.8 kB] 73s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-glib-2.0 armhf 2.79.3-3ubuntu5 [182 kB] 74s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgirepository-1.0-1 armhf 1.79.1-1ubuntu6 [106 kB] 74s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gi armhf 3.47.0-3build1 [219 kB] 74s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dbus armhf 1.3.2-5build2 [94.7 kB] 74s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnetplan1 armhf 1.0-1 [113 kB] 74s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-netplan armhf 1.0-1 [22.5 kB] 74s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan-generator armhf 1.0-1 [58.7 kB] 74s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-bin armhf 0.142ubuntu23 [20.3 kB] 74s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-core all 0.142ubuntu23 [50.1 kB] 74s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools all 0.142ubuntu23 [9058 B] 74s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan.io armhf 1.0-1 [64.3 kB] 74s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmlb2 armhf 0.3.15-1build1 [57.0 kB] 74s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqrtr-glib0 armhf 1.2.2-1ubuntu3 [15.4 kB] 74s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-glib5 armhf 1.35.2-0ubuntu1 [908 kB] 74s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-proxy armhf 1.35.2-0ubuntu1 [5732 B] 74s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-agent-1-0 armhf 124-1ubuntu1 [15.3 kB] 74s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-gobject-1-0 armhf 124-1ubuntu1 [44.1 kB] 74s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-0t64 armhf 2.79.3-3ubuntu5 [1414 kB] 74s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfwupd2 armhf 1.9.15-1 [123 kB] 74s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libarchive13t64 armhf 3.7.2-1.1ubuntu2 [330 kB] 74s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fwupd armhf 1.9.15-1 [4349 kB] 74s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.14 [210 kB] 74s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0t64 armhf 2.7.14 [986 kB] 74s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.14 [1368 kB] 74s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client-l10n armhf 31.2.1 [19.4 kB] 74s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client armhf 31.2.1 [216 kB] 74s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main armhf keyboxd armhf 2.4.4-2ubuntu15 [111 kB] 74s Get:134 http://ftpmaster.internal/ubuntu noble/main armhf libnpth0t64 armhf 1.6-3.1 [6940 B] 74s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu15 [224 kB] 74s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu15 [524 kB] 74s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-wks-client armhf 2.4.4-2ubuntu15 [87.4 kB] 74s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-utils armhf 2.4.4-2ubuntu15 [158 kB] 74s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu15 [235 kB] 74s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgsm armhf 2.4.4-2ubuntu15 [241 kB] 74s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreadline8t64 armhf 8.2-3.1build1 [129 kB] 74s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gawk armhf 1:5.2.1-2build2 [415 kB] 74s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fdisk armhf 2.39.3-9ubuntu2 [135 kB] 74s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu15 [115 kB] 74s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dirmngr armhf 2.4.4-2ubuntu15 [346 kB] 74s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg all 2.4.4-2ubuntu15 [359 kB] 74s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-apt armhf 2.7.6build1 [162 kB] 74s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main armhf pinentry-curses armhf 1.2.1-3ubuntu4 [36.7 kB] 74s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-yaml armhf 6.0.1-2build1 [117 kB] 74s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python-apt-common all 2.7.6build1 [19.8 kB] 74s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-setuptools all 68.1.2-2ubuntu1 [396 kB] 74s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB] 74s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.6ubuntu4 [1229 kB] 74s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-minimal armhf 3.12.2-0ubuntu1 [27.1 kB] 74s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3 armhf 3.12.2-0ubuntu1 [24.1 kB] 74s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-stdlib armhf 3.12.2-0ubuntu1 [9802 B] 74s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu2 [117 kB] 74s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu2 [78.7 kB] 74s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf groff-base armhf 1.23.0-3build1 [946 kB] 74s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-3.1build1 [56.5 kB] 74s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpgme11t64 armhf 1.18.0-4.1ubuntu3 [120 kB] 74s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-crypto3 armhf 3.1.0-1build1 [20.3 kB] 74s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B] 74s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB] 74s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dhcpcd-base armhf 1:10.0.6-1ubuntu2 [186 kB] 74s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-fs3 armhf 3.1.0-1build1 [34.4 kB] 74s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreiserfscore0t64 armhf 1:3.6.27-7.1 [66.2 kB] 74s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main armhf btrfs-progs armhf 6.6.3-1.1build1 [852 kB] 74s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu2 [201 kB] 74s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu2 [571 kB] 74s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-loop3 armhf 3.1.0-1build1 [6502 B] 74s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-mdraid3 armhf 3.1.0-1build1 [13.3 kB] 74s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-nvme3 armhf 3.1.0-1build1 [17.5 kB] 74s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnvme1t64 armhf 1.8-3 [67.5 kB] 74s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-part3 armhf 3.1.0-1build1 [16.4 kB] 74s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-swap3 armhf 3.1.0-1build1 [8894 B] 74s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev3 armhf 3.1.0-1build1 [42.9 kB] 75s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgudev-1.0-0 armhf 1:238-3ubuntu2 [13.6 kB] 75s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.3ubuntu2 [595 kB] 75s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbpf1 armhf 1:1.3.0-2build1 [146 kB] 75s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main armhf iproute2 armhf 6.1.0-1ubuntu5 [1060 kB] 75s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libelf1t64 armhf 0.190-1.1build2 [49.9 kB] 75s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1 [8018 B] 75s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lsof armhf 4.95.0-1build2 [248 kB] 75s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl2 armhf 1.3.0-3build2 [36.5 kB] 75s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1 [73.2 kB] 75s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-proxy armhf 1.31.2-0ubuntu2 [5748 B] 75s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-glib4 armhf 1.31.2-0ubuntu2 [216 kB] 75s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-common all 1.8.0-2build1 [4210 B] 75s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-0 armhf 1.8.0-2build1 [61.2 kB] 75s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnghttp2-14 armhf 1.59.0-1build1 [68.1 kB] 75s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssh-4 armhf 0.10.6-2build1 [169 kB] 75s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libusb-1.0-0 armhf 2:1.0.27-1 [48.7 kB] 75s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgusb2 armhf 0.4.8-1build1 [34.6 kB] 75s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmm-glib0 armhf 1.23.4-0ubuntu1 [214 kB] 75s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libprotobuf-c1 armhf 1.4.1-1ubuntu3 [17.7 kB] 75s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-2 armhf 2.1.28+dfsg1-5ubuntu1 [49.7 kB] 75s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libibverbs1 armhf 50.0-2build1 [57.9 kB] 75s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfido2-1 armhf 1.14.0-1build1 [75.8 kB] 75s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-3ubuntu3 [1280 kB] 75s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu2 [1216 kB] 75s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.39-0ubuntu6 [530 kB] 75s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main armhf file armhf 1:5.45-3 [21.1 kB] 75s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic-mgc armhf 1:5.45-3 [307 kB] 75s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic1t64 armhf 1:5.45-3 [81.4 kB] 76s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libplymouth5 armhf 24.004.60-1ubuntu6 [140 kB] 76s Get:207 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng16-16t64 armhf 1.6.43-3 [166 kB] 76s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-host armhf 1:9.18.24-0ubuntu3 [47.4 kB] 76s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-dnsutils armhf 1:9.18.24-0ubuntu3 [149 kB] 76s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-libs armhf 1:9.18.24-0ubuntu3 [1148 kB] 76s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuv1t64 armhf 1.48.0-1.1 [82.9 kB] 76s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu2 [41.7 kB] 76s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebconfclient0 armhf 0.271ubuntu2 [10.8 kB] 76s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage-common all 3.5-1build4 [10.1 kB] 76s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage2 armhf 3.5-1build4 [84.5 kB] 76s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main armhf install-info armhf 7.1-3build1 [60.5 kB] 76s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-19ubuntu1 [47.7 kB] 76s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu2 [14.7 kB] 76s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dmsetup armhf 2:1.02.185-3ubuntu2 [81.1 kB] 76s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main armhf eject armhf 2.39.3-9ubuntu2 [43.2 kB] 76s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main armhf krb5-locales all 1.20.1-5.1ubuntu1 [13.9 kB] 76s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbsd0 armhf 0.12.1-1 [36.6 kB] 76s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 76s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libslang2 armhf 2.3.3-3build1 [478 kB] 76s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main armhf locales all 2.39-0ubuntu6 [4232 kB] 77s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-tiny armhf 2:9.1.0016-1ubuntu5 [665 kB] 77s Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-common all 2:9.1.0016-1ubuntu5 [385 kB] 77s Get:228 http://ftpmaster.internal/ubuntu noble/main armhf xdg-user-dirs armhf 0.18-1 [17.3 kB] 77s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xxd armhf 2:9.1.0016-1ubuntu5 [62.4 kB] 77s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apparmor armhf 4.0.0-beta3-0ubuntu2 [562 kB] 77s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ftp all 20230507-2build1 [4724 B] 77s Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main armhf inetutils-telnet armhf 2:2.5-3ubuntu3 [90.7 kB] 77s Get:233 http://ftpmaster.internal/ubuntu noble-proposed/main armhf info armhf 7.1-3build1 [127 kB] 77s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmuu1 armhf 2:1.1.3-3build1 [8004 B] 77s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lshw armhf 02.19.git.2021.06.19.996aaad9c7-2build2 [310 kB] 77s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mtr-tiny armhf 0.95-1.1build1 [51.7 kB] 77s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu6 [9818 B] 77s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth armhf 24.004.60-1ubuntu6 [142 kB] 77s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.7-1 [176 kB] 77s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main armhf telnet all 0.17+2.5-3ubuntu3 [3682 B] 77s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main armhf usb.ids all 2024.03.18-1 [223 kB] 78s Get:242 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xz-utils armhf 5.6.0-0.2 [271 kB] 78s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf0 armhf 2.42-4ubuntu1 [87.7 kB] 78s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf-nobfd0 armhf 2.42-4ubuntu1 [88.0 kB] 78s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.42-4ubuntu1 [2925 kB] 78s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbinutils armhf 2.42-4ubuntu1 [464 kB] 78s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils armhf 2.42-4ubuntu1 [3078 B] 78s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-common armhf 2.42-4ubuntu1 [217 kB] 78s Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsframe1 armhf 2.42-4ubuntu1 [13.1 kB] 78s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bolt armhf 0.9.6-2build1 [138 kB] 78s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cryptsetup-bin armhf 2:2.7.0-1ubuntu2 [214 kB] 78s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.6ubuntu4 [1074 kB] 78s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.6ubuntu4 [268 kB] 78s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB] 78s Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ibverbs-providers armhf 50.0-2build1 [27.4 kB] 78s Get:256 http://ftpmaster.internal/ubuntu noble-proposed/main armhf jq armhf 1.7.1-3 [65.2 kB] 78s Get:257 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjq1 armhf 1.7.1-3 [156 kB] 78s Get:258 http://ftpmaster.internal/ubuntu noble/main armhf libatm1t64 armhf 1:2.5.1-5.1 [20.0 kB] 78s Get:259 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB] 78s Get:260 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libftdi1-2 armhf 1.5-6build4 [25.7 kB] 78s Get:261 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB] 78s Get:262 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules armhf 2.1.28+dfsg1-5ubuntu1 [61.3 kB] 78s Get:263 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-lib2to3 all 3.12.2-3ubuntu2 [79.3 kB] 78s Get:264 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pyrsistent armhf 0.20.0-1build1 [53.0 kB] 78s Get:265 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-typing-extensions all 4.10.0-1 [60.7 kB] 78s Get:266 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kpartx armhf 0.9.4-5ubuntu6 [31.5 kB] 79s Preconfiguring packages ... 79s Fetched 106 MB in 8s (13.6 MB/s) 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 79s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_armhf.deb ... 79s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ... 79s Setting up bsdutils (1:2.39.3-9ubuntu2) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 79s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_armhf.deb ... 79s Unpacking gcc-14-base:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 79s Setting up gcc-14-base:armhf (14-20240315-1ubuntu1) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 79s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_armhf.deb ... 79s Unpacking libgcc-s1:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 79s Setting up libgcc-s1:armhf (14-20240315-1ubuntu1) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 79s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_armhf.deb ... 79s Unpacking libstdc++6:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 80s Setting up libstdc++6:armhf (14-20240315-1ubuntu1) ... 80s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 80s Preparing to unpack .../libc6_2.39-0ubuntu6_armhf.deb ... 80s Unpacking libc6:armhf (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 80s Setting up libc6:armhf (2.39-0ubuntu6) ... 80s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 80s Preparing to unpack .../0-libbrotli1_1.1.0-2build1_armhf.deb ... 80s Unpacking libbrotli1:armhf (1.1.0-2build1) over (1.1.0-2) ... 80s Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-5.1ubuntu1_armhf.deb ... 80s Unpacking libgssapi-krb5-2:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 80s Preparing to unpack .../2-libkrb5-3_1.20.1-5.1ubuntu1_armhf.deb ... 80s Unpacking libkrb5-3:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 80s Preparing to unpack .../3-libkrb5support0_1.20.1-5.1ubuntu1_armhf.deb ... 80s Unpacking libkrb5support0:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 80s Preparing to unpack .../4-libk5crypto3_1.20.1-5.1ubuntu1_armhf.deb ... 80s Unpacking libk5crypto3:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 81s Preparing to unpack .../5-libcom-err2_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 81s Unpacking libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 81s Preparing to unpack .../6-zlib1g_1%3a1.3.dfsg-3.1ubuntu1_armhf.deb ... 81s Unpacking zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ... 81s Setting up zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) ... 81s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 81s Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-2build6_armhf.deb ... 81s Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ... 81s Preparing to unpack .../udisks2_2.10.1-6_armhf.deb ... 81s Unpacking udisks2 (2.10.1-6) over (2.10.1-1ubuntu2) ... 81s Preparing to unpack .../libudisks2-0_2.10.1-6_armhf.deb ... 81s Unpacking libudisks2-0:armhf (2.10.1-6) over (2.10.1-1ubuntu2) ... 81s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_armhf.deb ... 81s Unpacking libblkid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 81s Setting up libblkid1:armhf (2.39.3-9ubuntu2) ... 81s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 81s Preparing to unpack .../liblzma5_5.6.0-0.2_armhf.deb ... 81s Unpacking liblzma5:armhf (5.6.0-0.2) over (5.4.5-0.3) ... 81s Setting up liblzma5:armhf (5.6.0-0.2) ... 81s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 81s Preparing to unpack .../0-kmod_31+20240202-2ubuntu4_armhf.deb ... 81s Unpacking kmod (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 81s dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty 81s Preparing to unpack .../1-libkmod2_31+20240202-2ubuntu4_armhf.deb ... 81s Unpacking libkmod2:armhf (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ... 81s Preparing to unpack .../2-systemd-dev_255.4-1ubuntu5_all.deb ... 81s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 81s Preparing to unpack .../3-systemd-timesyncd_255.4-1ubuntu5_armhf.deb ... 81s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 81s Preparing to unpack .../4-dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ... 81s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 81s Preparing to unpack .../5-libaudit-common_1%3a3.1.2-2.1_all.deb ... 81s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ... 81s Setting up libaudit-common (1:3.1.2-2.1) ... 81s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 81s Preparing to unpack .../libcap-ng0_0.8.4-2build1_armhf.deb ... 81s Unpacking libcap-ng0:armhf (0.8.4-2build1) over (0.8.4-2) ... 81s Setting up libcap-ng0:armhf (0.8.4-2build1) ... 81s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 81s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_armhf.deb ... 81s Unpacking libaudit1:armhf (1:3.1.2-2.1) over (1:3.1.2-2) ... 81s Setting up libaudit1:armhf (1:3.1.2-2.1) ... 81s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 81s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_armhf.deb ... 81s Unpacking libpam0g:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 81s Setting up libpam0g:armhf (1.5.3-5ubuntu3) ... 81s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 81s Preparing to unpack .../libselinux1_3.5-2ubuntu1_armhf.deb ... 81s Unpacking libselinux1:armhf (3.5-2ubuntu1) over (3.5-2build1) ... 81s Setting up libselinux1:armhf (3.5-2ubuntu1) ... 82s dpkg: libcurl4:armhf: dependency problems, but removing anyway as you requested: 82s curl depends on libcurl4 (= 8.5.0-2ubuntu2). 82s 82s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58618 files and directories currently installed.) 82s Removing libcurl4:armhf (8.5.0-2ubuntu2) ... 82s Selecting previously unselected package libcurl4t64:armhf. 82s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58613 files and directories currently installed.) 82s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_armhf.deb ... 82s Unpacking libcurl4t64:armhf (8.5.0-2ubuntu7) ... 82s Preparing to unpack .../curl_8.5.0-2ubuntu7_armhf.deb ... 82s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 82s dpkg: libpsl5:armhf: dependency problems, but removing anyway as you requested: 82s wget depends on libpsl5 (>= 0.16.0). 82s libcurl3-gnutls:armhf depends on libpsl5 (>= 0.16.0). 82s 82s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58619 files and directories currently installed.) 82s Removing libpsl5:armhf (0.21.2-1build1) ... 82s Selecting previously unselected package libpsl5t64:armhf. 82s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58614 files and directories currently installed.) 82s Preparing to unpack .../libpsl5t64_0.21.2-1.1_armhf.deb ... 82s Unpacking libpsl5t64:armhf (0.21.2-1.1) ... 82s Preparing to unpack .../wget_1.21.4-1ubuntu2_armhf.deb ... 82s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ... 82s Preparing to unpack .../tnftp_20230507-2build1_armhf.deb ... 82s Unpacking tnftp (20230507-2build1) over (20230507-2) ... 82s dpkg: libpcap0.8:armhf: dependency problems, but removing anyway as you requested: 82s tcpdump depends on libpcap0.8 (>= 1.9.1). 82s 82s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58620 files and directories currently installed.) 82s Removing libpcap0.8:armhf (1.10.4-4ubuntu3) ... 82s Selecting previously unselected package libpcap0.8t64:armhf. 82s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58609 files and directories currently installed.) 82s Preparing to unpack .../00-libpcap0.8t64_1.10.4-4.1ubuntu1_armhf.deb ... 82s Unpacking libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ... 82s Preparing to unpack .../01-tcpdump_4.99.4-3ubuntu2_armhf.deb ... 82s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ... 82s Preparing to unpack .../02-libsystemd-shared_255.4-1ubuntu5_armhf.deb ... 82s Unpacking libsystemd-shared:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 82s Preparing to unpack .../03-systemd-resolved_255.4-1ubuntu5_armhf.deb ... 82s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 82s Preparing to unpack .../04-sudo_1.9.15p5-3ubuntu3_armhf.deb ... 82s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ... 82s Preparing to unpack .../05-rsync_3.2.7-1build1_armhf.deb ... 82s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ... 82s Preparing to unpack .../06-python3-cryptography_41.0.7-4build2_armhf.deb ... 82s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ... 82s Preparing to unpack .../07-openssl_3.0.13-0ubuntu2_armhf.deb ... 82s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 83s Preparing to unpack .../08-openssh-sftp-server_1%3a9.6p1-3ubuntu11_armhf.deb ... 83s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 83s Preparing to unpack .../09-openssh-client_1%3a9.6p1-3ubuntu11_armhf.deb ... 83s Unpacking openssh-client (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 83s Preparing to unpack .../10-openssh-server_1%3a9.6p1-3ubuntu11_armhf.deb ... 83s Unpacking openssh-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ... 83s Selecting previously unselected package linux-headers-6.8.0-20. 83s Preparing to unpack .../11-linux-headers-6.8.0-20_6.8.0-20.20_all.deb ... 83s Unpacking linux-headers-6.8.0-20 (6.8.0-20.20) ... 93s Selecting previously unselected package linux-headers-6.8.0-20-generic. 93s Preparing to unpack .../12-linux-headers-6.8.0-20-generic_6.8.0-20.20_armhf.deb ... 93s Unpacking linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 94s Preparing to unpack .../13-linux-headers-generic_6.8.0-20.20+1_armhf.deb ... 94s Unpacking linux-headers-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ... 94s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 89772 files and directories currently installed.) 94s Removing linux-headers-6.8.0-11-generic (6.8.0-11.11) ... 94s dpkg: libssl3:armhf: dependency problems, but removing anyway as you requested: 94s systemd depends on libssl3 (>= 3.0.0). 94s libssh-4:armhf depends on libssl3 (>= 3.0.0). 94s libsasl2-modules:armhf depends on libssl3 (>= 3.0.0). 94s libsasl2-2:armhf depends on libssl3 (>= 3.0.0). 94s libpython3.12-minimal:armhf depends on libssl3 (>= 3.0.0). 94s libpython3.11-minimal:armhf depends on libssl3 (>= 3.0.0). 94s libnvme1 depends on libssl3 (>= 3.0.0). 94s libfido2-1:armhf depends on libssl3 (>= 3.0.0). 94s libcryptsetup12:armhf depends on libssl3 (>= 3.0.0). 94s dhcpcd-base depends on libssl3 (>= 3.0.0). 94s bind9-libs:armhf depends on libssl3 (>= 3.0.0). 94s 94s Removing libssl3:armhf (3.0.10-1ubuntu4) ... 94s Selecting previously unselected package libssl3t64:armhf. 94s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78622 files and directories currently installed.) 94s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_armhf.deb ... 94s Unpacking libssl3t64:armhf (3.0.13-0ubuntu2) ... 94s Setting up libssl3t64:armhf (3.0.13-0ubuntu2) ... 94s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78635 files and directories currently installed.) 94s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_armhf.deb ... 94s Unpacking libnss-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 94s Preparing to unpack .../libudev1_255.4-1ubuntu5_armhf.deb ... 94s Unpacking libudev1:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 94s Setting up libudev1:armhf (255.4-1ubuntu5) ... 94s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78635 files and directories currently installed.) 94s Preparing to unpack .../systemd_255.4-1ubuntu5_armhf.deb ... 95s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 95s Preparing to unpack .../udev_255.4-1ubuntu5_armhf.deb ... 95s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 95s Preparing to unpack .../libsystemd0_255.4-1ubuntu5_armhf.deb ... 95s Unpacking libsystemd0:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 95s Setting up libsystemd0:armhf (255.4-1ubuntu5) ... 95s Setting up libkmod2:armhf (31+20240202-2ubuntu4) ... 95s Setting up libsystemd-shared:armhf (255.4-1ubuntu5) ... 95s Setting up systemd-dev (255.4-1ubuntu5) ... 95s Setting up systemd (255.4-1ubuntu5) ... 96s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78635 files and directories currently installed.) 96s Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_armhf.deb ... 96s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 96s Preparing to unpack .../libpam-systemd_255.4-1ubuntu5_armhf.deb ... 96s Unpacking libpam-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ... 96s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_armhf.deb ... 96s Unpacking libpam-modules-bin (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 96s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ... 96s pam_namespace.service is a disabled or a static unit not running, not starting it. 96s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78635 files and directories currently installed.) 96s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu3_armhf.deb ... 96s Unpacking libpam-modules:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ... 96s Setting up libpam-modules:armhf (1.5.3-5ubuntu3) ... 96s Installing new version of config file /etc/security/namespace.init ... 96s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 97s Preparing to unpack .../0-dbus-user-session_1.14.10-4ubuntu2_armhf.deb ... 97s Unpacking dbus-user-session (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 97s Preparing to unpack .../1-libapparmor1_4.0.0-beta3-0ubuntu2_armhf.deb ... 97s Unpacking libapparmor1:armhf (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 97s Preparing to unpack .../2-libexpat1_2.6.1-2_armhf.deb ... 97s Unpacking libexpat1:armhf (2.6.1-2) over (2.6.0-1) ... 97s Preparing to unpack .../3-dbus-system-bus-common_1.14.10-4ubuntu2_all.deb ... 97s Unpacking dbus-system-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 97s Preparing to unpack .../4-dbus-bin_1.14.10-4ubuntu2_armhf.deb ... 97s Unpacking dbus-bin (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 97s Preparing to unpack .../5-dbus_1.14.10-4ubuntu2_armhf.deb ... 97s Unpacking dbus (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 97s Preparing to unpack .../6-dbus-daemon_1.14.10-4ubuntu2_armhf.deb ... 97s Unpacking dbus-daemon (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 97s Preparing to unpack .../7-libdbus-1-3_1.14.10-4ubuntu2_armhf.deb ... 97s Unpacking libdbus-1-3:armhf (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ... 97s Preparing to unpack .../8-libmount1_2.39.3-9ubuntu2_armhf.deb ... 97s Unpacking libmount1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 97s Setting up libmount1:armhf (2.39.3-9ubuntu2) ... 97s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 97s Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_armhf.deb ... 97s Unpacking libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 97s Preparing to unpack .../libuuid1_2.39.3-9ubuntu2_armhf.deb ... 97s Unpacking libuuid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 97s Setting up libuuid1:armhf (2.39.3-9ubuntu2) ... 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 97s Preparing to unpack .../0-libcryptsetup12_2%3a2.7.0-1ubuntu2_armhf.deb ... 97s Unpacking libcryptsetup12:armhf (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 97s Preparing to unpack .../1-libfdisk1_2.39.3-9ubuntu2_armhf.deb ... 97s Unpacking libfdisk1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 97s Preparing to unpack .../2-mount_2.39.3-9ubuntu2_armhf.deb ... 97s Unpacking mount (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 98s Preparing to unpack .../3-libblockdev-utils3_3.1.0-1build1_armhf.deb ... 98s Unpacking libblockdev-utils3:armhf (3.1.0-1build1) over (3.1.0-1) ... 98s Preparing to unpack .../4-libvolume-key1_0.3.12-7build1_armhf.deb ... 98s Unpacking libvolume-key1:armhf (0.3.12-7build1) over (0.3.12-5build2) ... 98s Preparing to unpack .../5-libjcat1_0.2.0-2build2_armhf.deb ... 98s Unpacking libjcat1:armhf (0.2.0-2build2) over (0.2.0-2) ... 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78633 files and directories currently installed.) 98s Removing libgpgme11:armhf (1.18.0-4ubuntu1) ... 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78627 files and directories currently installed.) 98s Preparing to unpack .../parted_3.6-3.1build2_armhf.deb ... 98s Unpacking parted (3.6-3.1build2) over (3.6-3) ... 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78627 files and directories currently installed.) 98s Removing libparted2:armhf (3.6-3) ... 98s Selecting previously unselected package libparted2t64:armhf. 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 98s Preparing to unpack .../00-libparted2t64_3.6-3.1build2_armhf.deb ... 98s Unpacking libparted2t64:armhf (3.6-3.1build2) ... 98s Preparing to unpack .../01-python3.12_3.12.2-4build3_armhf.deb ... 98s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ... 98s Preparing to unpack .../02-python3.12-minimal_3.12.2-4build3_armhf.deb ... 98s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ... 98s Preparing to unpack .../03-libpython3.12-stdlib_3.12.2-4build3_armhf.deb ... 98s Unpacking libpython3.12-stdlib:armhf (3.12.2-4build3) over (3.12.2-1) ... 99s Preparing to unpack .../04-libpython3.12-minimal_3.12.2-4build3_armhf.deb ... 99s Unpacking libpython3.12-minimal:armhf (3.12.2-4build3) over (3.12.2-1) ... 99s Preparing to unpack .../05-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu1_armhf.deb ... 99s Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 99s Preparing to unpack .../06-python3.11_3.11.8-1build4_armhf.deb ... 99s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ... 99s Preparing to unpack .../07-python3.11-minimal_3.11.8-1build4_armhf.deb ... 99s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ... 99s Preparing to unpack .../08-libpython3.11-stdlib_3.11.8-1build4_armhf.deb ... 99s Unpacking libpython3.11-stdlib:armhf (3.11.8-1build4) over (3.11.8-1) ... 100s Preparing to unpack .../09-libpython3.11-minimal_3.11.8-1build4_armhf.deb ... 100s Unpacking libpython3.11-minimal:armhf (3.11.8-1build4) over (3.11.8-1) ... 100s Preparing to unpack .../10-libsqlite3-0_3.45.1-1ubuntu1_armhf.deb ... 100s Unpacking libsqlite3-0:armhf (3.45.1-1ubuntu1) over (3.45.1-1) ... 100s Preparing to unpack .../11-libtext-iconv-perl_1.7-8build2_armhf.deb ... 100s Unpacking libtext-iconv-perl:armhf (1.7-8build2) over (1.7-8build1) ... 101s Preparing to unpack .../12-libtext-charwidth-perl_0.04-11build2_armhf.deb ... 101s Unpacking libtext-charwidth-perl:armhf (0.04-11build2) over (0.04-11build1) ... 101s Preparing to unpack .../13-perl-modules-5.38_5.38.2-3.2_all.deb ... 101s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 101s dpkg: libperl5.38:armhf: dependency problems, but removing anyway as you requested: 101s perl depends on libperl5.38 (= 5.38.2-3). 101s 102s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78624 files and directories currently installed.) 102s Removing libperl5.38:armhf (5.38.2-3) ... 102s dpkg: libdb5.3:armhf: dependency problems, but removing anyway as you requested: 102s iproute2 depends on libdb5.3. 102s apt-utils depends on libdb5.3. 102s 102s Removing libdb5.3:armhf (5.3.28+dfsg2-4) ... 102s Selecting previously unselected package libdb5.3t64:armhf. 102s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78099 files and directories currently installed.) 102s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_armhf.deb ... 102s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-6) ... 102s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu2_armhf.deb ... 102s Unpacking python3-gdbm:armhf (3.12.2-3ubuntu2) over (3.11.5-1) ... 102s Preparing to unpack .../man-db_2.12.0-3build4_armhf.deb ... 102s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ... 102s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78105 files and directories currently installed.) 102s Removing libgdbm-compat4:armhf (1.23-5) ... 102s Removing libgdbm6:armhf (1.23-5) ... 102s Selecting previously unselected package libgdbm6t64:armhf. 102s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78095 files and directories currently installed.) 102s Preparing to unpack .../libgdbm6t64_1.23-5.1_armhf.deb ... 102s Unpacking libgdbm6t64:armhf (1.23-5.1) ... 102s Selecting previously unselected package libgdbm-compat4t64:armhf. 102s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_armhf.deb ... 102s Unpacking libgdbm-compat4t64:armhf (1.23-5.1) ... 102s Selecting previously unselected package libperl5.38t64:armhf. 102s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_armhf.deb ... 102s Unpacking libperl5.38t64:armhf (5.38.2-3.2) ... 102s Preparing to unpack .../perl_5.38.2-3.2_armhf.deb ... 102s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ... 102s Preparing to unpack .../perl-base_5.38.2-3.2_armhf.deb ... 102s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 103s Setting up perl-base (5.38.2-3.2) ... 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78626 files and directories currently installed.) 103s Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu4_armhf.deb ... 103s Unpacking liblocale-gettext-perl (1.07-6ubuntu4) over (1.07-6build1) ... 103s dpkg: libnettle8:armhf: dependency problems, but removing anyway as you requested: 103s libhogweed6:armhf depends on libnettle8. 103s libgnutls30:armhf depends on libnettle8 (>= 3.9~). 103s libcurl3-gnutls:armhf depends on libnettle8. 103s libarchive13:armhf depends on libnettle8. 103s 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78626 files and directories currently installed.) 103s Removing libnettle8:armhf (3.9.1-2) ... 103s Selecting previously unselected package libnettle8t64:armhf. 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78619 files and directories currently installed.) 103s Preparing to unpack .../libnettle8t64_3.9.1-2.2_armhf.deb ... 103s Unpacking libnettle8t64:armhf (3.9.1-2.2) ... 103s Setting up libnettle8t64:armhf (3.9.1-2.2) ... 103s dpkg: libhogweed6:armhf: dependency problems, but removing anyway as you requested: 103s libgnutls30:armhf depends on libhogweed6 (>= 3.6). 103s 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78627 files and directories currently installed.) 103s Removing libhogweed6:armhf (3.9.1-2) ... 103s Selecting previously unselected package libhogweed6t64:armhf. 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78622 files and directories currently installed.) 103s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_armhf.deb ... 103s Unpacking libhogweed6t64:armhf (3.9.1-2.2) ... 103s Setting up libhogweed6t64:armhf (3.9.1-2.2) ... 103s dpkg: libgnutls30:armhf: dependency problems, but removing anyway as you requested: 103s libldap2:armhf depends on libgnutls30 (>= 3.8.2). 103s libcurl3-gnutls:armhf depends on libgnutls30 (>= 3.8.2). 103s fwupd depends on libgnutls30 (>= 3.7.3). 103s dirmngr depends on libgnutls30 (>= 3.8.1). 103s apt depends on libgnutls30 (>= 3.8.1). 103s 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78628 files and directories currently installed.) 103s Removing libgnutls30:armhf (3.8.3-1ubuntu1) ... 103s Selecting previously unselected package libgnutls30t64:armhf. 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78619 files and directories currently installed.) 103s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_armhf.deb ... 103s Unpacking libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ... 103s Setting up libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ... 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78647 files and directories currently installed.) 103s Preparing to unpack .../libldap2_2.6.7+dfsg-1~exp1ubuntu6_armhf.deb ... 103s Unpacking libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 103s dpkg: libcurl3-gnutls:armhf: dependency problems, but removing anyway as you requested: 103s libfwupd2:armhf depends on libcurl3-gnutls (>= 7.63.0). 103s fwupd depends on libcurl3-gnutls (>= 7.63.0). 103s 103s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78647 files and directories currently installed.) 103s Removing libcurl3-gnutls:armhf (8.5.0-2ubuntu2) ... 104s Selecting previously unselected package libcurl3t64-gnutls:armhf. 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78640 files and directories currently installed.) 104s Preparing to unpack .../00-libcurl3t64-gnutls_8.5.0-2ubuntu7_armhf.deb ... 104s Unpacking libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ... 104s Preparing to unpack .../01-shared-mime-info_2.4-1build1_armhf.deb ... 104s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ... 104s Preparing to unpack .../02-gir1.2-girepository-2.0_1.79.1-1ubuntu6_armhf.deb ... 104s Unpacking gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ... 104s Preparing to unpack .../03-gir1.2-glib-2.0_2.79.3-3ubuntu5_armhf.deb ... 104s Unpacking gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 104s Preparing to unpack .../04-libgirepository-1.0-1_1.79.1-1ubuntu6_armhf.deb ... 104s Unpacking libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ... 104s Preparing to unpack .../05-python3-gi_3.47.0-3build1_armhf.deb ... 104s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ... 104s Preparing to unpack .../06-python3-dbus_1.3.2-5build2_armhf.deb ... 104s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ... 104s Selecting previously unselected package libnetplan1:armhf. 104s Preparing to unpack .../07-libnetplan1_1.0-1_armhf.deb ... 104s Unpacking libnetplan1:armhf (1.0-1) ... 104s Preparing to unpack .../08-python3-netplan_1.0-1_armhf.deb ... 104s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ... 104s Preparing to unpack .../09-netplan-generator_1.0-1_armhf.deb ... 104s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 104s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ... 104s Preparing to unpack .../10-initramfs-tools-bin_0.142ubuntu23_armhf.deb ... 104s Unpacking initramfs-tools-bin (0.142ubuntu23) over (0.142ubuntu20) ... 105s Preparing to unpack .../11-initramfs-tools-core_0.142ubuntu23_all.deb ... 105s Unpacking initramfs-tools-core (0.142ubuntu23) over (0.142ubuntu20) ... 105s Preparing to unpack .../12-initramfs-tools_0.142ubuntu23_all.deb ... 105s Unpacking initramfs-tools (0.142ubuntu23) over (0.142ubuntu20) ... 105s Preparing to unpack .../13-netplan.io_1.0-1_armhf.deb ... 105s Unpacking netplan.io (1.0-1) over (0.107.1-3) ... 105s Preparing to unpack .../14-libxmlb2_0.3.15-1build1_armhf.deb ... 105s Unpacking libxmlb2:armhf (0.3.15-1build1) over (0.3.15-1) ... 105s Preparing to unpack .../15-libqrtr-glib0_1.2.2-1ubuntu3_armhf.deb ... 105s Unpacking libqrtr-glib0:armhf (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ... 105s Preparing to unpack .../16-libqmi-glib5_1.35.2-0ubuntu1_armhf.deb ... 105s Unpacking libqmi-glib5:armhf (1.35.2-0ubuntu1) over (1.34.0-2) ... 105s Preparing to unpack .../17-libqmi-proxy_1.35.2-0ubuntu1_armhf.deb ... 105s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ... 105s Preparing to unpack .../18-libpolkit-agent-1-0_124-1ubuntu1_armhf.deb ... 105s Unpacking libpolkit-agent-1-0:armhf (124-1ubuntu1) over (124-1) ... 105s Preparing to unpack .../19-libpolkit-gobject-1-0_124-1ubuntu1_armhf.deb ... 105s Unpacking libpolkit-gobject-1-0:armhf (124-1ubuntu1) over (124-1) ... 105s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78651 files and directories currently installed.) 105s Removing libnetplan0:armhf (0.107.1-3) ... 105s dpkg: libglib2.0-0:armhf: dependency problems, but removing anyway as you requested: 105s libmm-glib0:armhf depends on libglib2.0-0 (>= 2.62.0). 105s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 105s libmbim-glib4:armhf depends on libglib2.0-0 (>= 2.56). 105s libjson-glib-1.0-0:armhf depends on libglib2.0-0 (>= 2.75.3). 105s libgusb2:armhf depends on libglib2.0-0 (>= 2.75.3). 105s libgudev-1.0-0:armhf depends on libglib2.0-0 (>= 2.38.0). 105s libfwupd2:armhf depends on libglib2.0-0 (>= 2.79.0). 105s libblockdev3:armhf depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-swap3:armhf depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-part3:armhf depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-nvme3:armhf depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-mdraid3:armhf depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-loop3:armhf depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-fs3:armhf depends on libglib2.0-0 (>= 2.42.2). 105s libblockdev-crypto3:armhf depends on libglib2.0-0 (>= 2.42.2). 105s fwupd depends on libglib2.0-0 (>= 2.79.0). 105s bolt depends on libglib2.0-0 (>= 2.56.0). 105s 105s Removing libglib2.0-0:armhf (2.79.2-1~ubuntu1) ... 105s Selecting previously unselected package libglib2.0-0t64:armhf. 105s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78622 files and directories currently installed.) 105s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_armhf.deb ... 105s 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... 105s removed '/var/lib/dpkg/info/libglib2.0-0:armhf.postrm' 105s Unpacking libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ... 105s Preparing to unpack .../libfwupd2_1.9.15-1_armhf.deb ... 105s Unpacking libfwupd2:armhf (1.9.15-1) over (1.9.14-1) ... 105s dpkg: libarchive13:armhf: dependency problems, but removing anyway as you requested: 105s fwupd depends on libarchive13 (>= 3.2.1). 105s 106s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78647 files and directories currently installed.) 106s Removing libarchive13:armhf (3.7.2-1ubuntu2) ... 106s Selecting previously unselected package libarchive13t64:armhf. 106s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78641 files and directories currently installed.) 106s Preparing to unpack .../libarchive13t64_3.7.2-1.1ubuntu2_armhf.deb ... 106s Unpacking libarchive13t64:armhf (3.7.2-1.1ubuntu2) ... 106s Preparing to unpack .../fwupd_1.9.15-1_armhf.deb ... 106s Unpacking fwupd (1.9.15-1) over (1.9.14-1) ... 106s Preparing to unpack .../apt-utils_2.7.14_armhf.deb ... 106s Unpacking apt-utils (2.7.14) over (2.7.12) ... 106s dpkg: libapt-pkg6.0:armhf: dependency problems, but removing anyway as you requested: 106s ubuntu-pro-client depends on libapt-pkg6.0 (>= 1.9~). 106s python3-apt depends on libapt-pkg6.0 (>= 2.7.11). 106s apt depends on libapt-pkg6.0 (>= 2.7.12). 106s 106s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78648 files and directories currently installed.) 106s Removing libapt-pkg6.0:armhf (2.7.12) ... 106s Selecting previously unselected package libapt-pkg6.0t64:armhf. 106s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78599 files and directories currently installed.) 106s Preparing to unpack .../libapt-pkg6.0t64_2.7.14_armhf.deb ... 106s Unpacking libapt-pkg6.0t64:armhf (2.7.14) ... 106s Setting up libapt-pkg6.0t64:armhf (2.7.14) ... 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78649 files and directories currently installed.) 107s Preparing to unpack .../archives/apt_2.7.14_armhf.deb ... 107s Unpacking apt (2.7.14) over (2.7.12) ... 107s Setting up apt (2.7.14) ... 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78649 files and directories currently installed.) 107s Preparing to unpack .../ubuntu-pro-client-l10n_31.2.1_armhf.deb ... 107s Unpacking ubuntu-pro-client-l10n (31.2.1) over (31.1) ... 108s Preparing to unpack .../ubuntu-pro-client_31.2.1_armhf.deb ... 108s Unpacking ubuntu-pro-client (31.2.1) over (31.1) ... 108s Preparing to unpack .../keyboxd_2.4.4-2ubuntu15_armhf.deb ... 108s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 108s dpkg: libnpth0:armhf: dependency problems, but removing anyway as you requested: 108s gpgv depends on libnpth0 (>= 0.90). 108s gpgsm depends on libnpth0 (>= 0.90). 108s gpg-agent depends on libnpth0 (>= 0.90). 108s gpg depends on libnpth0 (>= 0.90). 108s dirmngr depends on libnpth0 (>= 0.90). 108s 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78649 files and directories currently installed.) 108s Removing libnpth0:armhf (1.6-3build2) ... 108s Selecting previously unselected package libnpth0t64:armhf. 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78644 files and directories currently installed.) 108s Preparing to unpack .../libnpth0t64_1.6-3.1_armhf.deb ... 108s Unpacking libnpth0t64:armhf (1.6-3.1) ... 108s Setting up libnpth0t64:armhf (1.6-3.1) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78650 files and directories currently installed.) 108s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_armhf.deb ... 108s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 108s Setting up gpgv (2.4.4-2ubuntu15) ... 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78650 files and directories currently installed.) 108s Preparing to unpack .../gpg_2.4.4-2ubuntu15_armhf.deb ... 108s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 108s Preparing to unpack .../gpg-wks-client_2.4.4-2ubuntu15_armhf.deb ... 108s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 108s Preparing to unpack .../gnupg-utils_2.4.4-2ubuntu15_armhf.deb ... 108s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 108s Preparing to unpack .../gpg-agent_2.4.4-2ubuntu15_armhf.deb ... 108s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 108s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_armhf.deb ... 108s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 108s dpkg: libreadline8:armhf: dependency problems, but removing anyway as you requested: 108s gpgconf depends on libreadline8 (>= 6.0). 108s gawk depends on libreadline8 (>= 6.0). 108s fdisk depends on libreadline8 (>= 6.0). 108s 108s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78650 files and directories currently installed.) 108s Removing libreadline8:armhf (8.2-3) ... 108s Selecting previously unselected package libreadline8t64:armhf. 109s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78638 files and directories currently installed.) 109s Preparing to unpack .../libreadline8t64_8.2-3.1build1_armhf.deb ... 109s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' 109s 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' 109s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' 109s 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' 109s Unpacking libreadline8t64:armhf (8.2-3.1build1) ... 109s Setting up libreadline8t64:armhf (8.2-3.1build1) ... 109s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78658 files and directories currently installed.) 109s Preparing to unpack .../00-gawk_1%3a5.2.1-2build2_armhf.deb ... 109s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ... 109s Preparing to unpack .../01-fdisk_2.39.3-9ubuntu2_armhf.deb ... 109s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 109s Preparing to unpack .../02-gpgconf_2.4.4-2ubuntu15_armhf.deb ... 109s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 109s Preparing to unpack .../03-dirmngr_2.4.4-2ubuntu15_armhf.deb ... 109s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 109s Preparing to unpack .../04-gnupg_2.4.4-2ubuntu15_all.deb ... 109s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 109s Preparing to unpack .../05-python3-apt_2.7.6build1_armhf.deb ... 109s Unpacking python3-apt (2.7.6build1) over (2.7.6) ... 109s Preparing to unpack .../06-pinentry-curses_1.2.1-3ubuntu4_armhf.deb ... 109s Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-3ubuntu1) ... 109s Preparing to unpack .../07-python3-yaml_6.0.1-2build1_armhf.deb ... 109s Unpacking python3-yaml (6.0.1-2build1) over (6.0.1-2) ... 109s Preparing to unpack .../08-python-apt-common_2.7.6build1_all.deb ... 109s Unpacking python-apt-common (2.7.6build1) over (2.7.6) ... 109s Preparing to unpack .../09-python3-setuptools_68.1.2-2ubuntu1_all.deb ... 109s Unpacking python3-setuptools (68.1.2-2ubuntu1) over (68.1.2-2) ... 109s Preparing to unpack .../10-python3-pkg-resources_68.1.2-2ubuntu1_all.deb ... 110s Unpacking python3-pkg-resources (68.1.2-2ubuntu1) over (68.1.2-2) ... 110s Preparing to unpack .../11-dpkg_1.22.6ubuntu4_armhf.deb ... 110s Unpacking dpkg (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 110s Setting up dpkg (1.22.6ubuntu4) ... 110s Setting up libpython3.12-minimal:armhf (3.12.2-4build3) ... 110s Setting up libexpat1:armhf (2.6.1-2) ... 110s Setting up python3.12-minimal (3.12.2-4build3) ... 111s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78655 files and directories currently installed.) 111s Preparing to unpack .../python3-minimal_3.12.2-0ubuntu1_armhf.deb ... 111s Unpacking python3-minimal (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 111s Setting up python3-minimal (3.12.2-0ubuntu1) ... 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78655 files and directories currently installed.) 112s Preparing to unpack .../python3_3.12.2-0ubuntu1_armhf.deb ... 112s Unpacking python3 (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 112s Preparing to unpack .../libpython3-stdlib_3.12.2-0ubuntu1_armhf.deb ... 112s Unpacking libpython3-stdlib:armhf (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ... 112s Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu2_armhf.deb ... 112s Unpacking libsmartcols1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 112s Setting up libsmartcols1:armhf (2.39.3-9ubuntu2) ... 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78655 files and directories currently installed.) 112s Preparing to unpack .../0-bsdextrautils_2.39.3-9ubuntu2_armhf.deb ... 112s Unpacking bsdextrautils (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 112s Preparing to unpack .../1-groff-base_1.23.0-3build1_armhf.deb ... 112s Unpacking groff-base (1.23.0-3build1) over (1.23.0-3) ... 112s Preparing to unpack .../2-readline-common_8.2-3.1build1_all.deb ... 112s Unpacking readline-common (8.2-3.1build1) over (8.2-3) ... 112s Selecting previously unselected package libgpgme11t64:armhf. 112s Preparing to unpack .../3-libgpgme11t64_1.18.0-4.1ubuntu3_armhf.deb ... 112s Unpacking libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ... 112s Preparing to unpack .../4-libblockdev-crypto3_3.1.0-1build1_armhf.deb ... 112s Unpacking libblockdev-crypto3:armhf (3.1.0-1build1) over (3.1.0-1) ... 112s Preparing to unpack .../5-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ... 112s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 112s Preparing to unpack .../6-logsave_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 112s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 112s Preparing to unpack .../7-dhcpcd-base_1%3a10.0.6-1ubuntu2_armhf.deb ... 112s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ... 112s Preparing to unpack .../8-libblockdev-fs3_3.1.0-1build1_armhf.deb ... 112s Unpacking libblockdev-fs3:armhf (3.1.0-1build1) over (3.1.0-1) ... 112s dpkg: libreiserfscore0: dependency problems, but removing anyway as you requested: 112s btrfs-progs depends on libreiserfscore0 (>= 1:3.6.27). 112s 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78662 files and directories currently installed.) 112s Removing libreiserfscore0 (1:3.6.27-7) ... 112s Selecting previously unselected package libreiserfscore0t64. 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78657 files and directories currently installed.) 112s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_armhf.deb ... 112s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ... 112s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_armhf.deb ... 112s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ... 112s dpkg: libext2fs2:armhf: dependency problems, but removing anyway as you requested: 112s e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1). 112s 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78663 files and directories currently installed.) 113s Removing libext2fs2:armhf (1.47.0-2ubuntu1) ... 113s Selecting previously unselected package libext2fs2t64:armhf. 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78656 files and directories currently installed.) 113s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 113s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64' 113s 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' 113s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64' 113s 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' 113s Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ... 113s Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) ... 113s Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ... 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78672 files and directories currently installed.) 113s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 113s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 113s Preparing to unpack .../libblockdev-loop3_3.1.0-1build1_armhf.deb ... 113s Unpacking libblockdev-loop3:armhf (3.1.0-1build1) over (3.1.0-1) ... 113s Preparing to unpack .../libblockdev-mdraid3_3.1.0-1build1_armhf.deb ... 113s Unpacking libblockdev-mdraid3:armhf (3.1.0-1build1) over (3.1.0-1) ... 113s Preparing to unpack .../libblockdev-nvme3_3.1.0-1build1_armhf.deb ... 113s Unpacking libblockdev-nvme3:armhf (3.1.0-1build1) over (3.1.0-1) ... 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78672 files and directories currently installed.) 113s Removing libnvme1 (1.8-2) ... 113s Selecting previously unselected package libnvme1t64. 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78665 files and directories currently installed.) 113s Preparing to unpack .../0-libnvme1t64_1.8-3_armhf.deb ... 113s Unpacking libnvme1t64 (1.8-3) ... 113s Preparing to unpack .../1-libblockdev-part3_3.1.0-1build1_armhf.deb ... 113s Unpacking libblockdev-part3:armhf (3.1.0-1build1) over (3.1.0-1) ... 113s Preparing to unpack .../2-libblockdev-swap3_3.1.0-1build1_armhf.deb ... 113s Unpacking libblockdev-swap3:armhf (3.1.0-1build1) over (3.1.0-1) ... 113s Preparing to unpack .../3-libblockdev3_3.1.0-1build1_armhf.deb ... 113s Unpacking libblockdev3:armhf (3.1.0-1build1) over (3.1.0-1) ... 113s Preparing to unpack .../4-libgudev-1.0-0_1%3a238-3ubuntu2_armhf.deb ... 113s Unpacking libgudev-1.0-0:armhf (1:238-3ubuntu2) over (1:238-3) ... 113s Preparing to unpack .../5-libxml2_2.9.14+dfsg-1.3ubuntu2_armhf.deb ... 113s Unpacking libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) over (2.9.14+dfsg-1.3ubuntu1) ... 113s Preparing to unpack .../6-libbpf1_1%3a1.3.0-2build1_armhf.deb ... 113s Unpacking libbpf1:armhf (1:1.3.0-2build1) over (1:1.3.0-2) ... 113s Preparing to unpack .../7-iproute2_6.1.0-1ubuntu5_armhf.deb ... 113s Unpacking iproute2 (6.1.0-1ubuntu5) over (6.1.0-1ubuntu2) ... 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78673 files and directories currently installed.) 113s Removing libelf1:armhf (0.190-1) ... 113s Selecting previously unselected package libelf1t64:armhf. 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78668 files and directories currently installed.) 113s Preparing to unpack .../libelf1t64_0.190-1.1build2_armhf.deb ... 113s Unpacking libelf1t64:armhf (0.190-1.1build2) ... 114s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 114s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 114s Preparing to unpack .../lsof_4.95.0-1build2_armhf.deb ... 114s Unpacking lsof (4.95.0-1build2) over (4.95.0-1build1) ... 114s Preparing to unpack .../libnsl2_1.3.0-3build2_armhf.deb ... 114s Unpacking libnsl2:armhf (1.3.0-3build2) over (1.3.0-3) ... 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78673 files and directories currently installed.) 114s Removing libtirpc3:armhf (1.3.4+ds-1build1) ... 114s Selecting previously unselected package libtirpc3t64:armhf. 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78667 files and directories currently installed.) 114s Preparing to unpack .../00-libtirpc3t64_1.3.4+ds-1.1_armhf.deb ... 114s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' 114s 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' 114s Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1) ... 114s Preparing to unpack .../01-libmbim-proxy_1.31.2-0ubuntu2_armhf.deb ... 114s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ... 114s Preparing to unpack .../02-libmbim-glib4_1.31.2-0ubuntu2_armhf.deb ... 114s Unpacking libmbim-glib4:armhf (1.31.2-0ubuntu2) over (1.30.0-1) ... 114s Preparing to unpack .../03-libjson-glib-1.0-common_1.8.0-2build1_all.deb ... 114s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ... 114s Preparing to unpack .../04-libjson-glib-1.0-0_1.8.0-2build1_armhf.deb ... 114s Unpacking libjson-glib-1.0-0:armhf (1.8.0-2build1) over (1.8.0-2) ... 114s Preparing to unpack .../05-libnghttp2-14_1.59.0-1build1_armhf.deb ... 114s Unpacking libnghttp2-14:armhf (1.59.0-1build1) over (1.59.0-1) ... 114s Preparing to unpack .../06-libssh-4_0.10.6-2build1_armhf.deb ... 114s Unpacking libssh-4:armhf (0.10.6-2build1) over (0.10.6-2) ... 114s Preparing to unpack .../07-libusb-1.0-0_2%3a1.0.27-1_armhf.deb ... 114s Unpacking libusb-1.0-0:armhf (2:1.0.27-1) over (2:1.0.26-1) ... 114s Preparing to unpack .../08-libgusb2_0.4.8-1build1_armhf.deb ... 114s Unpacking libgusb2:armhf (0.4.8-1build1) over (0.4.8-1) ... 114s Preparing to unpack .../09-libmm-glib0_1.23.4-0ubuntu1_armhf.deb ... 114s Unpacking libmm-glib0:armhf (1.23.4-0ubuntu1) over (1.22.0-3) ... 114s Preparing to unpack .../10-libprotobuf-c1_1.4.1-1ubuntu3_armhf.deb ... 114s Unpacking libprotobuf-c1:armhf (1.4.1-1ubuntu3) over (1.4.1-1ubuntu2) ... 114s Preparing to unpack .../11-libsasl2-2_2.1.28+dfsg1-5ubuntu1_armhf.deb ... 114s Unpacking libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 114s Preparing to unpack .../12-libibverbs1_50.0-2build1_armhf.deb ... 114s Unpacking libibverbs1:armhf (50.0-2build1) over (50.0-2) ... 114s Preparing to unpack .../13-libfido2-1_1.14.0-1build1_armhf.deb ... 114s Unpacking libfido2-1:armhf (1.14.0-1build1) over (1.14.0-1) ... 115s Preparing to unpack .../14-coreutils_9.4-3ubuntu3_armhf.deb ... 115s Unpacking coreutils (9.4-3ubuntu3) over (9.4-2ubuntu4) ... 115s Setting up coreutils (9.4-3ubuntu3) ... 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78678 files and directories currently installed.) 115s Preparing to unpack .../util-linux_2.39.3-9ubuntu2_armhf.deb ... 115s Unpacking util-linux (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 115s Setting up util-linux (2.39.3-9ubuntu2) ... 116s fstrim.service is a disabled or a static unit not running, not starting it. 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78678 files and directories currently installed.) 116s Preparing to unpack .../libc-bin_2.39-0ubuntu6_armhf.deb ... 116s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 116s Setting up libc-bin (2.39-0ubuntu6) ... 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78678 files and directories currently installed.) 116s Removing libatm1:armhf (1:2.5.1-5) ... 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78673 files and directories currently installed.) 116s Preparing to unpack .../file_1%3a5.45-3_armhf.deb ... 116s Unpacking file (1:5.45-3) over (1:5.45-2) ... 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78673 files and directories currently installed.) 116s Removing libmagic1:armhf (1:5.45-2) ... 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78663 files and directories currently installed.) 116s Preparing to unpack .../libmagic-mgc_1%3a5.45-3_armhf.deb ... 116s Unpacking libmagic-mgc (1:5.45-3) over (1:5.45-2) ... 117s Selecting previously unselected package libmagic1t64:armhf. 117s Preparing to unpack .../libmagic1t64_1%3a5.45-3_armhf.deb ... 117s Unpacking libmagic1t64:armhf (1:5.45-3) ... 117s Preparing to unpack .../libplymouth5_24.004.60-1ubuntu6_armhf.deb ... 117s Unpacking libplymouth5:armhf (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78674 files and directories currently installed.) 117s Removing libpng16-16:armhf (1.6.43-1) ... 117s Selecting previously unselected package libpng16-16t64:armhf. 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78664 files and directories currently installed.) 117s Preparing to unpack .../libpng16-16t64_1.6.43-3_armhf.deb ... 117s Unpacking libpng16-16t64:armhf (1.6.43-3) ... 117s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_armhf.deb ... 117s Unpacking bind9-host (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 117s Preparing to unpack .../bind9-dnsutils_1%3a9.18.24-0ubuntu3_armhf.deb ... 117s Unpacking bind9-dnsutils (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 117s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_armhf.deb ... 117s Unpacking bind9-libs:armhf (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ... 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78675 files and directories currently installed.) 117s Removing libuv1:armhf (1.48.0-1) ... 117s Selecting previously unselected package libuv1t64:armhf. 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78670 files and directories currently installed.) 117s Preparing to unpack .../libuv1t64_1.48.0-1.1_armhf.deb ... 117s Unpacking libuv1t64:armhf (1.48.0-1.1) ... 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78676 files and directories currently installed.) 117s Removing python3-distutils (3.11.5-1) ... 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 117s Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu2_armhf.deb ... 117s Unpacking uuid-runtime (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 117s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_armhf.deb ... 117s Unpacking libdebconfclient0:armhf (0.271ubuntu2) over (0.271ubuntu1) ... 117s Setting up libdebconfclient0:armhf (0.271ubuntu2) ... 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 117s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ... 117s Unpacking libsemanage-common (3.5-1build4) over (3.5-1build2) ... 117s Setting up libsemanage-common (3.5-1build4) ... 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 117s Preparing to unpack .../libsemanage2_3.5-1build4_armhf.deb ... 117s Unpacking libsemanage2:armhf (3.5-1build4) over (3.5-1build2) ... 117s Setting up libsemanage2:armhf (3.5-1build4) ... 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 117s Preparing to unpack .../install-info_7.1-3build1_armhf.deb ... 117s Unpacking install-info (7.1-3build1) over (7.1-3) ... 117s Setting up install-info (7.1-3build1) ... 118s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78621 files and directories currently installed.) 118s Preparing to unpack .../00-gcc-13-base_13.2.0-19ubuntu1_armhf.deb ... 118s Unpacking gcc-13-base:armhf (13.2.0-19ubuntu1) over (13.2.0-17ubuntu2) ... 118s Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu2_armhf.deb ... 118s Unpacking libss2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ... 118s Preparing to unpack .../02-dmsetup_2%3a1.02.185-3ubuntu2_armhf.deb ... 118s Unpacking dmsetup (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ... 118s Preparing to unpack .../03-eject_2.39.3-9ubuntu2_armhf.deb ... 118s Unpacking eject (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ... 118s Preparing to unpack .../04-krb5-locales_1.20.1-5.1ubuntu1_all.deb ... 118s Unpacking krb5-locales (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ... 118s Preparing to unpack .../05-libbsd0_0.12.1-1_armhf.deb ... 118s Unpacking libbsd0:armhf (0.12.1-1) over (0.11.8-1) ... 118s Preparing to unpack .../06-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 118s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 118s Preparing to unpack .../07-libslang2_2.3.3-3build1_armhf.deb ... 118s Unpacking libslang2:armhf (2.3.3-3build1) over (2.3.3-3) ... 118s Preparing to unpack .../08-locales_2.39-0ubuntu6_all.deb ... 118s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 119s Preparing to unpack .../09-vim-tiny_2%3a9.1.0016-1ubuntu5_armhf.deb ... 119s Unpacking vim-tiny (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 119s Preparing to unpack .../10-vim-common_2%3a9.1.0016-1ubuntu5_all.deb ... 119s Unpacking vim-common (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 119s Selecting previously unselected package xdg-user-dirs. 119s Preparing to unpack .../11-xdg-user-dirs_0.18-1_armhf.deb ... 119s Unpacking xdg-user-dirs (0.18-1) ... 119s Preparing to unpack .../12-xxd_2%3a9.1.0016-1ubuntu5_armhf.deb ... 119s Unpacking xxd (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ... 119s Preparing to unpack .../13-apparmor_4.0.0-beta3-0ubuntu2_armhf.deb ... 120s Unpacking apparmor (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ... 120s Preparing to unpack .../14-ftp_20230507-2build1_all.deb ... 120s Unpacking ftp (20230507-2build1) over (20230507-2) ... 120s Preparing to unpack .../15-inetutils-telnet_2%3a2.5-3ubuntu3_armhf.deb ... 120s Unpacking inetutils-telnet (2:2.5-3ubuntu3) over (2:2.5-3ubuntu1) ... 120s Preparing to unpack .../16-info_7.1-3build1_armhf.deb ... 120s Unpacking info (7.1-3build1) over (7.1-3) ... 120s Preparing to unpack .../17-libxmuu1_2%3a1.1.3-3build1_armhf.deb ... 120s Unpacking libxmuu1:armhf (2:1.1.3-3build1) over (2:1.1.3-3) ... 120s Preparing to unpack .../18-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_armhf.deb ... 120s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ... 120s Preparing to unpack .../19-mtr-tiny_0.95-1.1build1_armhf.deb ... 120s Unpacking mtr-tiny (0.95-1.1build1) over (0.95-1.1) ... 120s Preparing to unpack .../20-plymouth-theme-ubuntu-text_24.004.60-1ubuntu6_armhf.deb ... 120s Unpacking plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 120s Preparing to unpack .../21-plymouth_24.004.60-1ubuntu6_armhf.deb ... 121s Unpacking plymouth (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ... 121s Preparing to unpack .../22-psmisc_23.7-1_armhf.deb ... 121s Unpacking psmisc (23.7-1) over (23.6-2) ... 121s Preparing to unpack .../23-telnet_0.17+2.5-3ubuntu3_all.deb ... 121s Unpacking telnet (0.17+2.5-3ubuntu3) over (0.17+2.5-3ubuntu1) ... 121s Preparing to unpack .../24-usb.ids_2024.03.18-1_all.deb ... 121s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ... 121s Preparing to unpack .../25-xz-utils_5.6.0-0.2_armhf.deb ... 121s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ... 121s Preparing to unpack .../26-libctf0_2.42-4ubuntu1_armhf.deb ... 121s Unpacking libctf0:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 121s Preparing to unpack .../27-libctf-nobfd0_2.42-4ubuntu1_armhf.deb ... 121s Unpacking libctf-nobfd0:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 121s Preparing to unpack .../28-binutils-arm-linux-gnueabihf_2.42-4ubuntu1_armhf.deb ... 121s Unpacking binutils-arm-linux-gnueabihf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 121s Preparing to unpack .../29-libbinutils_2.42-4ubuntu1_armhf.deb ... 121s Unpacking libbinutils:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 121s Preparing to unpack .../30-binutils_2.42-4ubuntu1_armhf.deb ... 121s Unpacking binutils (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 121s Preparing to unpack .../31-binutils-common_2.42-4ubuntu1_armhf.deb ... 121s Unpacking binutils-common:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 121s Preparing to unpack .../32-libsframe1_2.42-4ubuntu1_armhf.deb ... 121s Unpacking libsframe1:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ... 121s Preparing to unpack .../33-bolt_0.9.6-2build1_armhf.deb ... 121s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ... 121s Preparing to unpack .../34-cryptsetup-bin_2%3a2.7.0-1ubuntu2_armhf.deb ... 121s Unpacking cryptsetup-bin (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ... 122s Preparing to unpack .../35-dpkg-dev_1.22.6ubuntu4_all.deb ... 122s Unpacking dpkg-dev (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 122s Preparing to unpack .../36-libdpkg-perl_1.22.6ubuntu4_all.deb ... 122s Unpacking libdpkg-perl (1.22.6ubuntu4) over (1.22.4ubuntu5) ... 122s Preparing to unpack .../37-gnupg-l10n_2.4.4-2ubuntu15_all.deb ... 122s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ... 122s Preparing to unpack .../38-ibverbs-providers_50.0-2build1_armhf.deb ... 122s Unpacking ibverbs-providers:armhf (50.0-2build1) over (50.0-2) ... 122s Preparing to unpack .../39-jq_1.7.1-3_armhf.deb ... 122s Unpacking jq (1.7.1-3) over (1.7.1-2) ... 122s Preparing to unpack .../40-libjq1_1.7.1-3_armhf.deb ... 122s Unpacking libjq1:armhf (1.7.1-3) over (1.7.1-2) ... 122s Selecting previously unselected package libatm1t64:armhf. 122s Preparing to unpack .../41-libatm1t64_1%3a2.5.1-5.1_armhf.deb ... 122s Unpacking libatm1t64:armhf (1:2.5.1-5.1) ... 122s Preparing to unpack .../42-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ... 122s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 123s Preparing to unpack .../43-libftdi1-2_1.5-6build4_armhf.deb ... 123s Unpacking libftdi1-2:armhf (1.5-6build4) over (1.5-6build3) ... 123s Preparing to unpack .../44-libldap-common_2.6.7+dfsg-1~exp1ubuntu6_all.deb ... 123s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ... 123s Preparing to unpack .../45-libsasl2-modules_2.1.28+dfsg1-5ubuntu1_armhf.deb ... 123s Unpacking libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ... 123s Preparing to unpack .../46-python3-lib2to3_3.12.2-3ubuntu2_all.deb ... 123s Unpacking python3-lib2to3 (3.12.2-3ubuntu2) over (3.11.5-1) ... 123s Preparing to unpack .../47-python3-pyrsistent_0.20.0-1build1_armhf.deb ... 123s Unpacking python3-pyrsistent:armhf (0.20.0-1build1) over (0.20.0-1) ... 123s Preparing to unpack .../48-python3-typing-extensions_4.10.0-1_all.deb ... 123s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ... 123s Preparing to unpack .../49-kpartx_0.9.4-5ubuntu6_armhf.deb ... 123s Unpacking kpartx (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ... 123s Setting up pinentry-curses (1.2.1-3ubuntu4) ... 123s Setting up libtext-iconv-perl:armhf (1.7-8build2) ... 123s Setting up libtext-charwidth-perl:armhf (0.04-11build2) ... 123s Setting up libibverbs1:armhf (50.0-2build1) ... 123s Setting up systemd-sysv (255.4-1ubuntu5) ... 123s Setting up libapparmor1:armhf (4.0.0-beta3-0ubuntu2) ... 123s Setting up libatm1t64:armhf (1:2.5.1-5.1) ... 123s Setting up libgdbm6t64:armhf (1.23-5.1) ... 123s Setting up bsdextrautils (2.39.3-9ubuntu2) ... 123s Setting up libgdbm-compat4t64:armhf (1.23-5.1) ... 123s Setting up xdg-user-dirs (0.18-1) ... 123s Setting up ibverbs-providers:armhf (50.0-2build1) ... 123s Setting up linux-headers-6.8.0-20 (6.8.0-20.20) ... 123s Setting up libmagic-mgc (1:5.45-3) ... 123s Setting up gawk (1:5.2.1-2build2) ... 123s Setting up psmisc (23.7-1) ... 123s Setting up libjq1:armhf (1.7.1-3) ... 123s Setting up libtirpc-common (1.3.4+ds-1.1) ... 123s Setting up libbrotli1:armhf (1.1.0-2build1) ... 123s Setting up libsqlite3-0:armhf (3.45.1-1ubuntu1) ... 123s Setting up libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) ... 123s Setting up libuv1t64:armhf (1.48.0-1.1) ... 123s Setting up libmagic1t64:armhf (1:5.45-3) ... 123s Setting up binutils-common:armhf (2.42-4ubuntu1) ... 123s Setting up libpsl5t64:armhf (0.21.2-1.1) ... 123s Setting up libnghttp2-14:armhf (1.59.0-1build1) ... 123s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ... 123s Setting up libctf-nobfd0:armhf (2.42-4ubuntu1) ... 123s Setting up libnss-systemd:armhf (255.4-1ubuntu5) ... 123s Setting up krb5-locales (1.20.1-5.1ubuntu1) ... 123s Setting up file (1:5.45-3) ... 123s Setting up kmod (31+20240202-2ubuntu4) ... 124s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ... 124s Setting up locales (2.39-0ubuntu6) ... 124s Generating locales (this might take a while)... 127s en_US.UTF-8... done 127s Generation complete. 127s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ... 127s Setting up libprotobuf-c1:armhf (1.4.1-1ubuntu3) ... 127s Setting up xxd (2:9.1.0016-1ubuntu5) ... 127s Setting up libsframe1:armhf (2.42-4ubuntu1) ... 127s Setting up libelf1t64:armhf (0.190-1.1build2) ... 127s Setting up libkrb5support0:armhf (1.20.1-5.1ubuntu1) ... 127s Setting up linux-headers-6.8.0-20-generic (6.8.0-20.20) ... 127s Setting up eject (2.39.3-9ubuntu2) ... 127s Setting up apparmor (4.0.0-beta3-0ubuntu2) ... 127s Installing new version of config file /etc/apparmor.d/abstractions/authentication ... 127s Installing new version of config file /etc/apparmor.d/abstractions/crypto ... 127s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ... 127s Installing new version of config file /etc/apparmor.d/abstractions/openssl ... 127s Installing new version of config file /etc/apparmor.d/code ... 127s Installing new version of config file /etc/apparmor.d/firefox ... 127s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 127s 127s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 127s 127s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 127s 128s sysctl: cannot stat /proc/sys/kernel/apparmor_restrict_unprivileged_userns: No such file or directory 128s Reloading AppArmor profiles 128s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "busybox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 128s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 128s 129s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "nautilus". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "toybox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 129s 129s Error: At least one profile failed to load 129s Setting up libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ... 129s No schema files found: doing nothing. 129s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 129s Setting up vim-common (2:9.1.0016-1ubuntu5) ... 129s Setting up gcc-13-base:armhf (13.2.0-19ubuntu1) ... 129s Setting up libqrtr-glib0:armhf (1.2.2-1ubuntu3) ... 129s Setting up libslang2:armhf (2.3.3-3build1) ... 129s Setting up libnvme1t64 (1.8-3) ... 129s Setting up mtr-tiny (0.95-1.1build1) ... 129s Setting up gnupg-l10n (2.4.4-2ubuntu15) ... 129s Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) ... 129s Setting up libdbus-1-3:armhf (1.14.10-4ubuntu2) ... 129s Setting up xz-utils (5.6.0-0.2) ... 129s Setting up perl-modules-5.38 (5.38.2-3.2) ... 129s Setting up libblockdev-utils3:armhf (3.1.0-1build1) ... 129s Setting up libpng16-16t64:armhf (1.6.43-3) ... 129s Setting up systemd-timesyncd (255.4-1ubuntu5) ... 129s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ... 129s Setting up udev (255.4-1ubuntu5) ... 130s Setting up libss2:armhf (1.47.0-2.4~exp1ubuntu2) ... 130s Setting up usb.ids (2024.03.18-1) ... 130s Setting up sudo (1.9.15p5-3ubuntu3) ... 130s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ... 130s Setting up gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) ... 130s Setting up libk5crypto3:armhf (1.20.1-5.1ubuntu1) ... 130s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ... 130s Setting up libfdisk1:armhf (2.39.3-9ubuntu2) ... 130s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-6) ... 130s Setting up libblockdev-nvme3:armhf (3.1.0-1build1) ... 130s Setting up libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) ... 130s Setting up libblockdev-fs3:armhf (3.1.0-1build1) ... 130s Setting up python-apt-common (2.7.6build1) ... 130s Setting up mount (2.39.3-9ubuntu2) ... 130s Setting up dmsetup (2:1.02.185-3ubuntu2) ... 130s Setting up uuid-runtime (2.39.3-9ubuntu2) ... 131s uuidd.service is a disabled or a static unit not running, not starting it. 131s Setting up libmm-glib0:armhf (1.23.4-0ubuntu1) ... 131s Setting up groff-base (1.23.0-3build1) ... 131s Setting up libplymouth5:armhf (24.004.60-1ubuntu6) ... 131s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ... 131s Setting up kpartx (0.9.4-5ubuntu6) ... 131s Setting up jq (1.7.1-3) ... 131s Setting up gpgconf (2.4.4-2ubuntu15) ... 131s Setting up libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ... 131s Setting up libcryptsetup12:armhf (2:2.7.0-1ubuntu2) ... 131s Setting up libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) ... 131s Setting up libjson-glib-1.0-common (1.8.0-2build1) ... 131s Setting up libkrb5-3:armhf (1.20.1-5.1ubuntu1) ... 131s Setting up libpython3.11-minimal:armhf (3.11.8-1build4) ... 131s Setting up libusb-1.0-0:armhf (2:1.0.27-1) ... 131s Setting up libperl5.38t64:armhf (5.38.2-3.2) ... 131s Setting up tnftp (20230507-2build1) ... 131s Setting up libbinutils:armhf (2.42-4ubuntu1) ... 131s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ... 131s Setting up libfido2-1:armhf (1.14.0-1build1) ... 131s Setting up openssl (3.0.13-0ubuntu2) ... 131s Setting up libbsd0:armhf (0.12.1-1) ... 131s Setting up readline-common (8.2-3.1build1) ... 131s Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) ... 131s Setting up libxmuu1:armhf (2:1.1.3-3build1) ... 131s Setting up dbus-bin (1.14.10-4ubuntu2) ... 131s Setting up info (7.1-3build1) ... 131s Setting up liblocale-gettext-perl (1.07-6ubuntu4) ... 131s Setting up gpg (2.4.4-2ubuntu15) ... 131s Setting up libgudev-1.0-0:armhf (1:238-3ubuntu2) ... 131s Setting up libpolkit-gobject-1-0:armhf (124-1ubuntu1) ... 131s Setting up libbpf1:armhf (1:1.3.0-2build1) ... 131s Setting up libmbim-glib4:armhf (1.31.2-0ubuntu2) ... 131s Setting up rsync (3.2.7-1build1) ... 132s rsync.service is a disabled or a static unit not running, not starting it. 132s Setting up libudisks2-0:armhf (2.10.1-6) ... 132s Setting up bolt (0.9.6-2build1) ... 132s bolt.service is a disabled or a static unit not running, not starting it. 132s Setting up gnupg-utils (2.4.4-2ubuntu15) ... 132s Setting up initramfs-tools-bin (0.142ubuntu23) ... 132s Setting up libctf0:armhf (2.42-4ubuntu1) ... 132s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ... 132s Setting up python3.11-minimal (3.11.8-1build4) ... 134s Setting up tcpdump (4.99.4-3ubuntu2) ... 134s apparmor_parser: Unable to replace "tcpdump". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 134s 134s Setting up apt-utils (2.7.14) ... 134s Setting up gpg-agent (2.4.4-2ubuntu15) ... 135s Setting up libpython3.12-stdlib:armhf (3.12.2-4build3) ... 135s Setting up libblockdev-mdraid3:armhf (3.1.0-1build1) ... 135s Setting up wget (1.21.4-1ubuntu2) ... 135s Setting up libblockdev-swap3:armhf (3.1.0-1build1) ... 135s Setting up plymouth (24.004.60-1ubuntu6) ... 135s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 135s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 135s Setting up libxmlb2:armhf (0.3.15-1build1) ... 135s Setting up btrfs-progs (6.6.3-1.1build1) ... 135s Setting up libpython3.11-stdlib:armhf (3.11.8-1build4) ... 135s Setting up python3.12 (3.12.2-4build3) ... 137s Setting up libblockdev-loop3:armhf (3.1.0-1build1) ... 137s Setting up gpgsm (2.4.4-2ubuntu15) ... 137s Setting up inetutils-telnet (2:2.5-3ubuntu3) ... 137s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ... 137s update-initramfs: deferring update (trigger activated) 137s e2scrub_all.service is a disabled or a static unit not running, not starting it. 137s Setting up libparted2t64:armhf (3.6-3.1build2) ... 137s Setting up linux-headers-generic (6.8.0-20.20+1) ... 137s Setting up dbus-daemon (1.14.10-4ubuntu2) ... 137s Setting up libmbim-proxy (1.31.2-0ubuntu2) ... 137s Setting up vim-tiny (2:9.1.0016-1ubuntu5) ... 137s Setting up libnetplan1:armhf (1.0-1) ... 137s Setting up man-db (2.12.0-3build4) ... 138s Updating database of manual pages ... 139s apparmor_parser: Unable to replace "/usr/bin/man". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 139s 139s man-db.service is a disabled or a static unit not running, not starting it. 139s Setting up libblockdev3:armhf (3.1.0-1build1) ... 139s Setting up fdisk (2.39.3-9ubuntu2) ... 139s Setting up libjson-glib-1.0-0:armhf (1.8.0-2build1) ... 139s Setting up libblockdev-part3:armhf (3.1.0-1build1) ... 139s Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) ... 139s Setting up libftdi1-2:armhf (1.5-6build4) ... 139s Setting up perl (5.38.2-3.2) ... 139s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) ... 139s update-initramfs: deferring update (trigger activated) 139s Setting up gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) ... 139s Setting up dbus (1.14.10-4ubuntu2) ... 139s A reboot is required to replace the running dbus-daemon. 139s Please reboot the system when convenient. 140s Setting up shared-mime-info (2.4-1build1) ... 140s Setting up libgssapi-krb5-2:armhf (1.20.1-5.1ubuntu1) ... 140s Setting up ftp (20230507-2build1) ... 140s Setting up keyboxd (2.4.4-2ubuntu15) ... 140s Setting up libdpkg-perl (1.22.6ubuntu4) ... 140s Setting up libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) ... 140s Setting up libssh-4:armhf (0.10.6-2build1) ... 140s Setting up libpam-systemd:armhf (255.4-1ubuntu5) ... 140s Setting up libpolkit-agent-1-0:armhf (124-1ubuntu1) ... 140s Setting up libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ... 140s Setting up netplan-generator (1.0-1) ... 140s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 140s Setting up initramfs-tools-core (0.142ubuntu23) ... 140s Setting up binutils-arm-linux-gnueabihf (2.42-4ubuntu1) ... 140s Setting up libarchive13t64:armhf (3.7.2-1.1ubuntu2) ... 140s Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) ... 140s Setting up libpython3-stdlib:armhf (3.12.2-0ubuntu1) ... 140s Setting up systemd-resolved (255.4-1ubuntu5) ... 141s Setting up python3.11 (3.11.8-1build4) ... 142s Setting up telnet (0.17+2.5-3ubuntu3) ... 142s Setting up initramfs-tools (0.142ubuntu23) ... 142s update-initramfs: deferring update (trigger activated) 142s Setting up libcurl4t64:armhf (8.5.0-2ubuntu7) ... 142s Setting up bind9-libs:armhf (1:9.18.24-0ubuntu3) ... 142s Setting up libtirpc3t64:armhf (1.3.4+ds-1.1) ... 142s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ... 142s Setting up iproute2 (6.1.0-1ubuntu5) ... 142s Setting up openssh-client (1:9.6p1-3ubuntu11) ... 142s Setting up libgusb2:armhf (0.4.8-1build1) ... 142s Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ... 142s Setting up parted (3.6-3.1build2) ... 142s Setting up libqmi-glib5:armhf (1.35.2-0ubuntu1) ... 142s Setting up python3 (3.12.2-0ubuntu1) ... 142s Setting up binutils (2.42-4ubuntu1) ... 142s Setting up libjcat1:armhf (0.2.0-2build2) ... 142s Setting up dpkg-dev (1.22.6ubuntu4) ... 142s Setting up dirmngr (2.4.4-2ubuntu15) ... 142s Setting up dbus-user-session (1.14.10-4ubuntu2) ... 142s Setting up python3-cryptography (41.0.7-4build2) ... 143s Setting up python3-gi (3.47.0-3build1) ... 143s Setting up python3-typing-extensions (4.10.0-1) ... 143s Setting up lsof (4.95.0-1build2) ... 143s Setting up python3-pyrsistent:armhf (0.20.0-1build1) ... 143s Setting up libnsl2:armhf (1.3.0-3build2) ... 143s Setting up gnupg (2.4.4-2ubuntu15) ... 143s Setting up python3-netplan (1.0-1) ... 143s Setting up curl (8.5.0-2ubuntu7) ... 143s Setting up libvolume-key1:armhf (0.3.12-7build1) ... 143s Setting up bind9-host (1:9.18.24-0ubuntu3) ... 143s Setting up python3-lib2to3 (3.12.2-3ubuntu2) ... 144s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... 144s Setting up openssh-sftp-server (1:9.6p1-3ubuntu11) ... 144s Setting up python3-dbus (1.3.2-5build2) ... 144s Setting up python3-setuptools (68.1.2-2ubuntu1) ... 145s Setting up gpg-wks-client (2.4.4-2ubuntu15) ... 145s Setting up openssh-server (1:9.6p1-3ubuntu11) ... 145s Replacing config file /etc/ssh/sshd_config with new version 146s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket. 147s Setting up libblockdev-crypto3:armhf (3.1.0-1build1) ... 147s Setting up python3-gdbm:armhf (3.12.2-3ubuntu2) ... 147s Setting up python3-apt (2.7.6build1) ... 147s Setting up libfwupd2:armhf (1.9.15-1) ... 147s Setting up python3-yaml (6.0.1-2build1) ... 148s Setting up libqmi-proxy (1.35.2-0ubuntu1) ... 148s Setting up netplan.io (1.0-1) ... 148s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ... 148s Setting up ubuntu-pro-client (31.2.1) ... 148s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 148s 149s Setting up fwupd (1.9.15-1) ... 149s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 149s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 149s fwupd.service is a disabled or a static unit not running, not starting it. 149s Setting up ubuntu-pro-client-l10n (31.2.1) ... 149s Setting up udisks2 (2.10.1-6) ... 149s vda: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/uevent': Permission denied 149s vda1: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda1/uevent': Permission denied 149s vda15: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda15/uevent': Permission denied 149s vda2: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda2/uevent': Permission denied 149s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied 149s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied 149s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 149s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 149s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 149s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 149s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 149s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 150s Processing triggers for ufw (0.36.2-5) ... 150s Processing triggers for systemd (255.4-1ubuntu5) ... 150s Processing triggers for install-info (7.1-3build1) ... 150s Processing triggers for libc-bin (2.39-0ubuntu6) ... 150s Processing triggers for initramfs-tools (0.142ubuntu23) ... 151s Reading package lists... 152s Building dependency tree... 152s Reading state information... 154s The following packages will be REMOVED: 154s linux-headers-6.8.0-11* python3-lib2to3* 154s 0 upgraded, 0 newly installed, 2 to remove and 1 not upgraded. 154s After this operation, 85.8 MB disk space will be freed. 154s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78592 files and directories currently installed.) 154s Removing linux-headers-6.8.0-11 (6.8.0-11.11) ... 155s Removing python3-lib2to3 (3.12.2-3ubuntu2) ... 157s autopkgtest [23:44:00]: rebooting testbed after setup commands that affected boot 194s autopkgtest [23:44:37]: testbed running kernel: Linux 5.15.0-101-generic #111-Ubuntu SMP Wed Mar 6 18:01:01 UTC 2024 219s autopkgtest [23:45:02]: @@@@@@@@@@@@@@@@@@@@ apt-source htslib 235s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe htslib 1.19+ds-1.1build2 (dsc) [2584 B] 235s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe htslib 1.19+ds-1.1build2 (tar) [1522 kB] 235s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe htslib 1.19+ds-1.1build2 (diff) [21.4 kB] 235s gpgv: Signature made Sat Mar 16 06:59:33 2024 UTC 235s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 235s gpgv: issuer "steve.langasek@ubuntu.com" 235s gpgv: Can't check signature: No public key 235s dpkg-source: warning: cannot verify inline signature for ./htslib_1.19+ds-1.1build2.dsc: no acceptable signature found 236s autopkgtest [23:45:19]: testing package htslib version 1.19+ds-1.1build2 238s autopkgtest [23:45:21]: build not needed 240s autopkgtest [23:45:23]: test run-unit-test: preparing testbed 250s Reading package lists... 250s Building dependency tree... 250s Reading state information... 252s Starting pkgProblemResolver with broken count: 0 252s Starting 2 pkgProblemResolver with broken count: 0 252s Done 252s The following additional packages will be installed: 252s autoconf automake autopoint autotools-dev build-essential cpp cpp-13 252s cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper debugedit 252s dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 252s g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-13 252s gcc-13-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext htslib-test 252s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 252s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 252s libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 252s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev 252s libhts3t64 libhtscodecs-dev libhtscodecs2 libisl23 liblzma-dev libmpc3 252s libssl-dev libstdc++-13-dev libsub-override-perl libtool libubsan1 252s linux-libc-dev m4 po-debconf rpcsvc-proto tabix zlib1g-dev 252s Suggested packages: 252s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-13-locales 252s cpp-13-doc dh-make gcc-13-doc gcc-multilib manpages-dev flex bison gdb 252s gcc-doc gdb-arm-linux-gnueabihf gettext-doc libasprintf-dev libgettextpo-dev 252s glibc-doc libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev 252s librtmp-dev libssh2-1-dev pkg-config liblzma-doc libssl-doc libstdc++-13-doc 252s libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl 252s Recommended packages: 252s bzip2-doc manpages manpages-dev libc-devtools libarchive-cpio-perl 252s libltdl-dev libmail-sendmail-perl 252s The following NEW packages will be installed: 252s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 252s cpp cpp-13 cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper 252s debugedit dh-autoreconf dh-strip-nondeterminism dwz g++ g++-13 252s g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-13 252s gcc-13-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext htslib-test 252s intltool-debian libarchive-zip-perl libasan8 libatomic1 libbz2-dev 252s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev 252s libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 252s libfile-stripnondeterminism-perl libgcc-13-dev libgomp1 libhts-dev 252s libhts3t64 libhtscodecs-dev libhtscodecs2 libisl23 liblzma-dev libmpc3 252s libssl-dev libstdc++-13-dev libsub-override-perl libtool libubsan1 252s linux-libc-dev m4 po-debconf rpcsvc-proto tabix zlib1g-dev 252s 0 upgraded, 60 newly installed, 0 to remove and 1 not upgraded. 252s Need to get 62.1 MB/62.1 MB of archives. 252s After this operation, 183 MB of additional disk space will be used. 252s Get:1 /tmp/autopkgtest.DZoMuI/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [828 B] 252s Get:2 http://ftpmaster.internal/ubuntu noble/main armhf m4 armhf 1.4.19-4 [235 kB] 252s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf autoconf all 2.71-3 [339 kB] 252s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf autotools-dev all 20220109.1 [44.9 kB] 252s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] 252s Get:6 http://ftpmaster.internal/ubuntu noble/main armhf autopoint all 0.21-14ubuntu1 [422 kB] 252s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-dev-bin armhf 2.39-0ubuntu6 [19.1 kB] 252s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-libc-dev armhf 6.8.0-20.20 [1555 kB] 252s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libcrypt-dev armhf 1:4.4.36-4 [136 kB] 252s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu6 [63.7 kB] 252s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6-dev armhf 2.39-0ubuntu6 [1351 kB] 252s Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libisl23 armhf 0.26-3 [595 kB] 252s Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libmpc3 armhf 1.3.1-1 [46.4 kB] 252s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cpp-13-arm-linux-gnueabihf armhf 13.2.0-19ubuntu1 [8753 kB] 252s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cpp-13 armhf 13.2.0-19ubuntu1 [1036 B] 252s Get:16 http://ftpmaster.internal/ubuntu noble/main armhf cpp-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [5320 B] 252s Get:17 http://ftpmaster.internal/ubuntu noble/main armhf cpp armhf 4:13.2.0-7ubuntu1 [22.4 kB] 252s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcc1-0 armhf 14-20240315-1ubuntu1 [39.0 kB] 252s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgomp1 armhf 14-20240315-1ubuntu1 [125 kB] 252s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libatomic1 armhf 14-20240315-1ubuntu1 [7824 B] 252s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libasan8 armhf 14-20240315-1ubuntu1 [2941 kB] 253s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libubsan1 armhf 14-20240315-1ubuntu1 [1152 kB] 253s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-13-dev armhf 13.2.0-19ubuntu1 [900 kB] 253s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-arm-linux-gnueabihf armhf 13.2.0-19ubuntu1 [16.8 MB] 253s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13 armhf 13.2.0-19ubuntu1 [448 kB] 253s Get:26 http://ftpmaster.internal/ubuntu noble/main armhf gcc-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [1220 B] 253s Get:27 http://ftpmaster.internal/ubuntu noble/main armhf gcc armhf 4:13.2.0-7ubuntu1 [5022 B] 253s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++-13-dev armhf 13.2.0-19ubuntu1 [2403 kB] 253s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf g++-13-arm-linux-gnueabihf armhf 13.2.0-19ubuntu1 [9935 kB] 253s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf g++-13 armhf 13.2.0-19ubuntu1 [14.5 kB] 253s Get:31 http://ftpmaster.internal/ubuntu noble/main armhf g++-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [966 B] 253s Get:32 http://ftpmaster.internal/ubuntu noble/main armhf g++ armhf 4:13.2.0-7ubuntu1 [1090 B] 253s Get:33 http://ftpmaster.internal/ubuntu noble/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 253s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] 253s Get:35 http://ftpmaster.internal/ubuntu noble/main armhf libtool all 2.4.7-7 [166 kB] 253s Get:36 http://ftpmaster.internal/ubuntu noble/main armhf dh-autoreconf all 20 [16.1 kB] 253s Get:37 http://ftpmaster.internal/ubuntu noble/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 253s Get:38 http://ftpmaster.internal/ubuntu noble/main armhf libsub-override-perl all 0.10-1 [10.0 kB] 253s Get:39 http://ftpmaster.internal/ubuntu noble/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] 253s Get:40 http://ftpmaster.internal/ubuntu noble/main armhf dh-strip-nondeterminism all 1.13.1-1 [5362 B] 253s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdw1t64 armhf 0.190-1.1build2 [235 kB] 253s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debugedit armhf 1:5.0-5build1 [42.2 kB] 253s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dwz armhf 0.15-1build5 [116 kB] 253s Get:44 http://ftpmaster.internal/ubuntu noble/main armhf gettext armhf 0.21-14ubuntu1 [800 kB] 253s Get:45 http://ftpmaster.internal/ubuntu noble/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 253s Get:46 http://ftpmaster.internal/ubuntu noble/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 253s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debhelper all 13.14.1ubuntu5 [869 kB] 253s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf htslib-test all 1.19+ds-1.1build2 [1141 kB] 253s Get:49 http://ftpmaster.internal/ubuntu noble/main armhf libbz2-dev armhf 1.0.8-5ubuntu1 [30.4 kB] 254s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl4-gnutls-dev armhf 8.5.0-2ubuntu7 [408 kB] 254s Get:51 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB] 254s Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate-dev armhf 1.19-1 [48.4 kB] 254s Get:53 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.6.0-1 [65.9 kB] 254s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libhts3t64 armhf 1.19+ds-1.1build2 [389 kB] 254s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma-dev armhf 5.6.0-0.2 [166 kB] 254s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1ubuntu1 [880 kB] 254s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libhts-dev armhf 1.19+ds-1.1build2 [1731 kB] 254s Get:58 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs-dev armhf 1.6.0-1 [2956 kB] 254s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl-dev armhf 3.0.13-0ubuntu2 [2084 kB] 254s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf tabix armhf 1.19+ds-1.1build2 [428 kB] 254s Fetched 62.1 MB in 2s (25.9 MB/s) 254s Selecting previously unselected package m4. 254s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58435 files and directories currently installed.) 254s Preparing to unpack .../00-m4_1.4.19-4_armhf.deb ... 254s Unpacking m4 (1.4.19-4) ... 254s Selecting previously unselected package autoconf. 254s Preparing to unpack .../01-autoconf_2.71-3_all.deb ... 254s Unpacking autoconf (2.71-3) ... 254s Selecting previously unselected package autotools-dev. 254s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 254s Unpacking autotools-dev (20220109.1) ... 254s Selecting previously unselected package automake. 254s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 254s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 254s Selecting previously unselected package autopoint. 254s Preparing to unpack .../04-autopoint_0.21-14ubuntu1_all.deb ... 254s Unpacking autopoint (0.21-14ubuntu1) ... 254s Selecting previously unselected package libc-dev-bin. 254s Preparing to unpack .../05-libc-dev-bin_2.39-0ubuntu6_armhf.deb ... 254s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 254s Selecting previously unselected package linux-libc-dev:armhf. 254s Preparing to unpack .../06-linux-libc-dev_6.8.0-20.20_armhf.deb ... 254s Unpacking linux-libc-dev:armhf (6.8.0-20.20) ... 255s Selecting previously unselected package libcrypt-dev:armhf. 255s Preparing to unpack .../07-libcrypt-dev_1%3a4.4.36-4_armhf.deb ... 255s Unpacking libcrypt-dev:armhf (1:4.4.36-4) ... 255s Selecting previously unselected package rpcsvc-proto. 255s Preparing to unpack .../08-rpcsvc-proto_1.4.2-0ubuntu6_armhf.deb ... 255s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 255s Selecting previously unselected package libc6-dev:armhf. 255s Preparing to unpack .../09-libc6-dev_2.39-0ubuntu6_armhf.deb ... 255s Unpacking libc6-dev:armhf (2.39-0ubuntu6) ... 255s Selecting previously unselected package libisl23:armhf. 255s Preparing to unpack .../10-libisl23_0.26-3_armhf.deb ... 255s Unpacking libisl23:armhf (0.26-3) ... 255s Selecting previously unselected package libmpc3:armhf. 256s Preparing to unpack .../11-libmpc3_1.3.1-1_armhf.deb ... 256s Unpacking libmpc3:armhf (1.3.1-1) ... 256s Selecting previously unselected package cpp-13-arm-linux-gnueabihf. 256s Preparing to unpack .../12-cpp-13-arm-linux-gnueabihf_13.2.0-19ubuntu1_armhf.deb ... 256s Unpacking cpp-13-arm-linux-gnueabihf (13.2.0-19ubuntu1) ... 256s Selecting previously unselected package cpp-13. 256s Preparing to unpack .../13-cpp-13_13.2.0-19ubuntu1_armhf.deb ... 256s Unpacking cpp-13 (13.2.0-19ubuntu1) ... 256s Selecting previously unselected package cpp-arm-linux-gnueabihf. 256s Preparing to unpack .../14-cpp-arm-linux-gnueabihf_4%3a13.2.0-7ubuntu1_armhf.deb ... 256s Unpacking cpp-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... 256s Selecting previously unselected package cpp. 256s Preparing to unpack .../15-cpp_4%3a13.2.0-7ubuntu1_armhf.deb ... 256s Unpacking cpp (4:13.2.0-7ubuntu1) ... 256s Selecting previously unselected package libcc1-0:armhf. 256s Preparing to unpack .../16-libcc1-0_14-20240315-1ubuntu1_armhf.deb ... 256s Unpacking libcc1-0:armhf (14-20240315-1ubuntu1) ... 256s Selecting previously unselected package libgomp1:armhf. 256s Preparing to unpack .../17-libgomp1_14-20240315-1ubuntu1_armhf.deb ... 256s Unpacking libgomp1:armhf (14-20240315-1ubuntu1) ... 256s Selecting previously unselected package libatomic1:armhf. 256s Preparing to unpack .../18-libatomic1_14-20240315-1ubuntu1_armhf.deb ... 256s Unpacking libatomic1:armhf (14-20240315-1ubuntu1) ... 256s Selecting previously unselected package libasan8:armhf. 256s Preparing to unpack .../19-libasan8_14-20240315-1ubuntu1_armhf.deb ... 256s Unpacking libasan8:armhf (14-20240315-1ubuntu1) ... 256s Selecting previously unselected package libubsan1:armhf. 256s Preparing to unpack .../20-libubsan1_14-20240315-1ubuntu1_armhf.deb ... 256s Unpacking libubsan1:armhf (14-20240315-1ubuntu1) ... 256s Selecting previously unselected package libgcc-13-dev:armhf. 256s Preparing to unpack .../21-libgcc-13-dev_13.2.0-19ubuntu1_armhf.deb ... 256s Unpacking libgcc-13-dev:armhf (13.2.0-19ubuntu1) ... 256s Selecting previously unselected package gcc-13-arm-linux-gnueabihf. 256s Preparing to unpack .../22-gcc-13-arm-linux-gnueabihf_13.2.0-19ubuntu1_armhf.deb ... 256s Unpacking gcc-13-arm-linux-gnueabihf (13.2.0-19ubuntu1) ... 256s Selecting previously unselected package gcc-13. 256s Preparing to unpack .../23-gcc-13_13.2.0-19ubuntu1_armhf.deb ... 256s Unpacking gcc-13 (13.2.0-19ubuntu1) ... 256s 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.../34-dh-autoreconf_20_all.deb ... 256s Unpacking dh-autoreconf (20) ... 256s Selecting previously unselected package libarchive-zip-perl. 256s Preparing to unpack .../35-libarchive-zip-perl_1.68-1_all.deb ... 256s Unpacking libarchive-zip-perl (1.68-1) ... 256s Selecting previously unselected package libsub-override-perl. 256s Preparing to unpack .../36-libsub-override-perl_0.10-1_all.deb ... 256s Unpacking libsub-override-perl (0.10-1) ... 256s Selecting previously unselected package libfile-stripnondeterminism-perl. 256s Preparing to unpack .../37-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 256s Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 257s Selecting previously unselected package dh-strip-nondeterminism. 257s Preparing to unpack .../38-dh-strip-nondeterminism_1.13.1-1_all.deb ... 257s Unpacking dh-strip-nondeterminism (1.13.1-1) ... 257s Selecting previously unselected package libdw1t64:armhf. 257s Preparing to unpack .../39-libdw1t64_0.190-1.1build2_armhf.deb ... 257s Unpacking libdw1t64:armhf (0.190-1.1build2) ... 257s Selecting previously unselected package debugedit. 257s Preparing to unpack .../40-debugedit_1%3a5.0-5build1_armhf.deb ... 257s Unpacking debugedit (1:5.0-5build1) ... 258s Selecting previously unselected package dwz. 258s Preparing to unpack .../41-dwz_0.15-1build5_armhf.deb ... 258s Unpacking dwz (0.15-1build5) ... 258s Selecting previously unselected package gettext. 258s Preparing to unpack .../42-gettext_0.21-14ubuntu1_armhf.deb ... 258s Unpacking gettext (0.21-14ubuntu1) ... 258s Selecting previously unselected package intltool-debian. 258s Preparing to unpack .../43-intltool-debian_0.35.0+20060710.6_all.deb ... 258s Unpacking intltool-debian (0.35.0+20060710.6) ... 258s Selecting previously unselected package po-debconf. 258s Preparing to unpack .../44-po-debconf_1.0.21+nmu1_all.deb ... 258s Unpacking po-debconf (1.0.21+nmu1) ... 258s Selecting previously unselected package debhelper. 258s Preparing to unpack .../45-debhelper_13.14.1ubuntu5_all.deb ... 258s Unpacking debhelper (13.14.1ubuntu5) ... 258s Selecting previously unselected package htslib-test. 258s Preparing to unpack .../46-htslib-test_1.19+ds-1.1build2_all.deb ... 258s Unpacking htslib-test (1.19+ds-1.1build2) ... 258s Selecting previously unselected package libbz2-dev:armhf. 258s Preparing to unpack .../47-libbz2-dev_1.0.8-5ubuntu1_armhf.deb ... 258s Unpacking libbz2-dev:armhf (1.0.8-5ubuntu1) ... 258s Selecting previously unselected package libcurl4-gnutls-dev:armhf. 258s Preparing to unpack .../48-libcurl4-gnutls-dev_8.5.0-2ubuntu7_armhf.deb ... 258s Unpacking libcurl4-gnutls-dev:armhf (8.5.0-2ubuntu7) ... 258s Selecting previously unselected package libdeflate0:armhf. 258s Preparing to unpack .../49-libdeflate0_1.19-1_armhf.deb ... 258s Unpacking libdeflate0:armhf (1.19-1) ... 258s Selecting previously unselected package libdeflate-dev:armhf. 258s Preparing to unpack .../50-libdeflate-dev_1.19-1_armhf.deb ... 258s Unpacking libdeflate-dev:armhf (1.19-1) ... 258s Selecting previously unselected package libhtscodecs2:armhf. 258s Preparing to unpack .../51-libhtscodecs2_1.6.0-1_armhf.deb ... 258s Unpacking libhtscodecs2:armhf (1.6.0-1) ... 258s Selecting previously unselected package libhts3t64:armhf. 258s Preparing to unpack .../52-libhts3t64_1.19+ds-1.1build2_armhf.deb ... 258s Unpacking libhts3t64:armhf (1.19+ds-1.1build2) ... 258s Selecting previously unselected package liblzma-dev:armhf. 258s Preparing to unpack .../53-liblzma-dev_5.6.0-0.2_armhf.deb ... 258s Unpacking liblzma-dev:armhf (5.6.0-0.2) ... 258s Selecting previously unselected package zlib1g-dev:armhf. 258s Preparing to unpack .../54-zlib1g-dev_1%3a1.3.dfsg-3.1ubuntu1_armhf.deb ... 258s Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu1) ... 258s Selecting previously unselected package libhts-dev:armhf. 258s Preparing to unpack .../55-libhts-dev_1.19+ds-1.1build2_armhf.deb ... 258s Unpacking libhts-dev:armhf (1.19+ds-1.1build2) ... 258s Selecting previously unselected package libhtscodecs-dev:armhf. 258s Preparing to unpack .../56-libhtscodecs-dev_1.6.0-1_armhf.deb ... 258s Unpacking libhtscodecs-dev:armhf (1.6.0-1) ... 258s Selecting previously unselected package libssl-dev:armhf. 258s Preparing to unpack .../57-libssl-dev_3.0.13-0ubuntu2_armhf.deb ... 258s Unpacking libssl-dev:armhf (3.0.13-0ubuntu2) ... 258s Selecting previously unselected package tabix. 258s Preparing to unpack .../58-tabix_1.19+ds-1.1build2_armhf.deb ... 258s Unpacking tabix (1.19+ds-1.1build2) ... 258s Selecting previously unselected package autopkgtest-satdep. 258s Preparing to unpack .../59-1-autopkgtest-satdep.deb ... 258s Unpacking autopkgtest-satdep (0) ... 258s Setting up libhtscodecs2:armhf (1.6.0-1) ... 258s Setting up libarchive-zip-perl (1.68-1) ... 258s Setting up htslib-test (1.19+ds-1.1build2) ... 258s Setting up libdebhelper-perl (13.14.1ubuntu5) ... 258s Setting up libdeflate0:armhf (1.19-1) ... 258s Setting up linux-libc-dev:armhf (6.8.0-20.20) ... 258s Setting up m4 (1.4.19-4) ... 258s Setting up libgomp1:armhf (14-20240315-1ubuntu1) ... 258s Setting up libcurl4-gnutls-dev:armhf (8.5.0-2ubuntu7) ... 258s Setting up libdw1t64:armhf (0.190-1.1build2) ... 258s Setting up libhtscodecs-dev:armhf (1.6.0-1) ... 258s Setting up autotools-dev (20220109.1) ... 258s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 258s Setting up libssl-dev:armhf (3.0.13-0ubuntu2) ... 258s Setting up libmpc3:armhf (1.3.1-1) ... 258s Setting up libatomic1:armhf (14-20240315-1ubuntu1) ... 258s Setting up autopoint (0.21-14ubuntu1) ... 258s Setting up autoconf (2.71-3) ... 258s Setting up liblzma-dev:armhf (5.6.0-0.2) ... 258s Setting up libubsan1:armhf (14-20240315-1ubuntu1) ... 258s Setting up dwz (0.15-1build5) ... 258s Setting up libcrypt-dev:armhf (1:4.4.36-4) ... 258s Setting up libasan8:armhf (14-20240315-1ubuntu1) ... 258s Setting up debugedit (1:5.0-5build1) ... 258s Setting up libhts3t64:armhf (1.19+ds-1.1build2) ... 258s Setting up libsub-override-perl (0.10-1) ... 258s Setting up libisl23:armhf (0.26-3) ... 258s Setting up libc-dev-bin (2.39-0ubuntu6) ... 258s Setting up libdeflate-dev:armhf (1.19-1) ... 258s Setting up tabix (1.19+ds-1.1build2) ... 258s Setting up libcc1-0:armhf (14-20240315-1ubuntu1) ... 258s Setting up automake (1:1.16.5-1.3ubuntu1) ... 258s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 258s Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 258s Setting up gettext (0.21-14ubuntu1) ... 258s Setting up cpp-13-arm-linux-gnueabihf (13.2.0-19ubuntu1) ... 258s Setting up intltool-debian (0.35.0+20060710.6) ... 258s Setting up dh-strip-nondeterminism (1.13.1-1) ... 258s Setting up libgcc-13-dev:armhf (13.2.0-19ubuntu1) ... 258s Setting up libc6-dev:armhf (2.39-0ubuntu6) ... 258s Setting up cpp-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... 258s Setting up libstdc++-13-dev:armhf (13.2.0-19ubuntu1) ... 258s Setting up libbz2-dev:armhf (1.0.8-5ubuntu1) ... 258s Setting up cpp-13 (13.2.0-19ubuntu1) ... 258s Setting up po-debconf (1.0.21+nmu1) ... 258s Setting up gcc-13-arm-linux-gnueabihf (13.2.0-19ubuntu1) ... 258s Setting up gcc-13 (13.2.0-19ubuntu1) ... 258s Setting up zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu1) ... 258s Setting up cpp (4:13.2.0-7ubuntu1) ... 258s Setting up gcc-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... 258s Setting up g++-13-arm-linux-gnueabihf (13.2.0-19ubuntu1) ... 258s Setting up g++-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... 258s Setting up g++-13 (13.2.0-19ubuntu1) ... 258s Setting up libtool (2.4.7-7) ... 258s Setting up libhts-dev:armhf (1.19+ds-1.1build2) ... 258s Setting up gcc (4:13.2.0-7ubuntu1) ... 258s Setting up dh-autoreconf (20) ... 258s Setting up g++ (4:13.2.0-7ubuntu1) ... 258s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 258s Setting up build-essential (12.10ubuntu1) ... 258s Setting up debhelper (13.14.1ubuntu5) ... 258s Setting up autopkgtest-satdep (0) ... 258s Processing triggers for man-db (2.12.0-3build4) ... 258s Processing triggers for install-info (7.1-3build1) ... 259s Processing triggers for libc-bin (2.39-0ubuntu6) ... 276s (Reading database ... 63284 files and directories currently installed.) 276s Removing autopkgtest-satdep (0) ... 282s autopkgtest [23:46:05]: test run-unit-test: [----------------------- 283s + pkg=htslib 283s + '[' /tmp/autopkgtest.DZoMuI/autopkgtest_tmp = '' ']' 283s + cp -aL /usr/share/htslib-test/Makefile /usr/share/htslib-test/annot-tsv.c /usr/share/htslib-test/bcf_sr_sort.c /usr/share/htslib-test/bcf_sr_sort.h /usr/share/htslib-test/bgzf.c /usr/share/htslib-test/bgzip.c /usr/share/htslib-test/config.h /usr/share/htslib-test/config.mk /usr/share/htslib-test/config_vars.h /usr/share/htslib-test/cram /usr/share/htslib-test/errmod.c /usr/share/htslib-test/faidx.c /usr/share/htslib-test/fuzz_settings.h /usr/share/htslib-test/header.c /usr/share/htslib-test/header.h /usr/share/htslib-test/hfile.c /usr/share/htslib-test/hfile_gcs.c /usr/share/htslib-test/hfile_internal.h /usr/share/htslib-test/hfile_libcurl.c /usr/share/htslib-test/hfile_s3.c /usr/share/htslib-test/hfile_s3_write.c /usr/share/htslib-test/hts.c /usr/share/htslib-test/hts_expr.c /usr/share/htslib-test/hts_internal.h /usr/share/htslib-test/hts_os.c /usr/share/htslib-test/hts_time_funcs.h /usr/share/htslib-test/htscodecs.mk /usr/share/htslib-test/htscodecs_bundled.mk /usr/share/htslib-test/htscodecs_external.mk /usr/share/htslib-test/htsfile.c /usr/share/htslib-test/htslib.mk /usr/share/htslib-test/htslib_static.mk /usr/share/htslib-test/htslib_vars.mk /usr/share/htslib-test/kfunc.c /usr/share/htslib-test/kstring.c /usr/share/htslib-test/md5.c /usr/share/htslib-test/multipart.c /usr/share/htslib-test/os /usr/share/htslib-test/plugin.c /usr/share/htslib-test/probaln.c /usr/share/htslib-test/realn.c /usr/share/htslib-test/regidx.c /usr/share/htslib-test/region.c /usr/share/htslib-test/sam.c /usr/share/htslib-test/sam_internal.h /usr/share/htslib-test/sam_mods.c /usr/share/htslib-test/synced_bcf_reader.c /usr/share/htslib-test/tabix.c /usr/share/htslib-test/tbx.c /usr/share/htslib-test/test /usr/share/htslib-test/textutils.c /usr/share/htslib-test/textutils_internal.h /usr/share/htslib-test/thread_pool.c /usr/share/htslib-test/thread_pool_internal.h /usr/share/htslib-test/vcf.c /usr/share/htslib-test/vcf_sweep.c /usr/share/htslib-test/vcfutils.c /usr/share/htslib-test/version.h /usr/share/htslib-test/version.sh /tmp/autopkgtest.DZoMuI/autopkgtest_tmp 283s + cp -aL htslib.pc.in /tmp/autopkgtest.DZoMuI/autopkgtest_tmp 283s + cp -aL htslib.map /tmp/autopkgtest.DZoMuI/autopkgtest_tmp 283s + cd /tmp/autopkgtest.DZoMuI/autopkgtest_tmp 283s + sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk 283s + sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk 283s + CFLAGS='-O2 -fno-strict-aliasing -fno-code-hoisting' 283s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kfunc.o kfunc.c 283s + grep sse /proc/cpuinfo 283s + export CFLAGS 283s + make -e check 284s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kstring.o kstring.c 284s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bcf_sr_sort.o bcf_sr_sort.c 284s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzf.o bgzf.c 285s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o errmod.o errmod.c 286s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o faidx.o faidx.c 286s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o header.o header.c 288s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hfile.o hfile.c 288s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts.o hts.c 291s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_expr.o hts_expr.c 291s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_os.o hts_os.c 291s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o md5.o md5.c 291s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o multipart.o multipart.c 292s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o probaln.o probaln.c 292s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o realn.o realn.c 292s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o regidx.o regidx.c 293s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o region.o region.c 293s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam.o sam.c 296s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_mods.o sam_mods.c 297s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o synced_bcf_reader.o synced_bcf_reader.c 297s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf_sweep.o vcf_sweep.c 298s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tbx.o tbx.c 298s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o textutils.o textutils.c 298s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o thread_pool.o thread_pool.c 298s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf.o vcf.c 303s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcfutils.o vcfutils.c 304s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_codecs.o cram/cram_codecs.c 305s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_decode.o cram/cram_decode.c 307s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_encode.o cram/cram_encode.c 309s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_external.o cram/cram_external.c 310s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_index.o cram/cram_index.c 310s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_io.o cram/cram_io.c 312s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_stats.o cram/cram_stats.c 313s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/mFILE.o cram/mFILE.c 313s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/open_trace_file.o cram/open_trace_file.c 313s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/pooled_alloc.o cram/pooled_alloc.c 313s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/string_alloc.o cram/string_alloc.c 313s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c 313s ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o 313s ranlib libhts.a 313s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kfunc.pico kfunc.c 313s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kstring.pico kstring.c 314s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c 314s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bgzf.pico bgzf.c 315s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o errmod.pico errmod.c 316s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o faidx.pico faidx.c 316s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o header.pico header.c 317s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile.pico hfile.c 318s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts.pico hts.c 321s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_expr.pico hts_expr.c 321s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_os.pico hts_os.c 321s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o md5.pico md5.c 321s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o multipart.pico multipart.c 321s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o probaln.pico probaln.c 322s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o realn.pico realn.c 322s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o regidx.pico regidx.c 322s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o region.pico region.c 323s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam.pico sam.c 326s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam_mods.pico sam_mods.c 327s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c 327s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf_sweep.pico vcf_sweep.c 327s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o tbx.pico tbx.c 328s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o textutils.pico textutils.c 328s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o thread_pool.pico thread_pool.c 328s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf.pico vcf.c 333s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcfutils.pico vcfutils.c 334s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c 335s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c 337s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c 339s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_external.pico cram/cram_external.c 339s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_index.pico cram/cram_index.c 340s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_io.pico cram/cram_io.c 342s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c 342s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/mFILE.pico cram/mFILE.c 342s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c 343s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c 343s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c 343s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c 343s gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 343s ln -sf libhts.so libhts.so.3 343s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o annot-tsv.o annot-tsv.c 343s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 344s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzip.o bgzip.c 344s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 344s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o htsfile.o htsfile.c 344s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 344s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tabix.o tabix.c 344s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 344s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c 345s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread 345s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_gcs.pico hfile_gcs.c 345s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 345s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3.pico hfile_s3.c 346s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread 346s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c 347s gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread 347s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hts_endian.o test/hts_endian.c 347s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm 347s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fieldarith.o test/fieldarith.c 347s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 347s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hfile.o test/hfile.c 347s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 347s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup.o test/pileup.c 348s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 348s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup_mod.o test/pileup_mod.c 348s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 348s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/plugins-dlhts.o test/plugins-dlhts.c 348s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm 348s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/sam.o test/sam.c 349s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 349s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_bgzf.o test/test_bgzf.c 349s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 350s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_expr.o test/test_expr.c 350s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 350s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_faidx.o test/test_faidx.c 350s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 350s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kfunc.o test/test_kfunc.c 350s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 350s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kstring.o test/test_kstring.c 350s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 350s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_mod.o test/test_mod.c 350s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 350s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_realn.o test/test_realn.c 351s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 351s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-regidx.o test/test-regidx.c 351s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 351s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_str2int.o test/test_str2int.c 351s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 351s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_time_funcs.o test/test_time_funcs.c 351s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o 351s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_view.o test/test_view.c 352s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 352s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_index.o test/test_index.c 352s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 352s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-api.o test/test-vcf-api.c 352s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 352s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c 352s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 352s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-sr.o test/test-bcf-sr.c 352s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 352s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c 352s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-translate.o test/test-bcf-translate.c 353s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 353s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-parse-reg.o test/test-parse-reg.c 353s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 353s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_introspection.o test/test_introspection.c 353s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 353s gcc -O2 -fno-strict-aliasing -fno-code-hoisting -I. -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c 357s gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread 357s sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp 357s sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk 357s sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc 357s test/hts_endian 357s test/test_expr 357s test/test_kfunc 357s test/test_kstring 357s test/test_str2int 357s test/test_time_funcs 358s test/fieldarith test/fieldarith.sam 358s test/hfile 358s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 358s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ 358s fi 358s if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ 358s HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ 358s fi 359s test/test_bgzf test/bgziptest.txt 359s test/test-parse-reg -t test/colons.bam 359s cd test/faidx && ./test-faidx.sh faidx.tst 359s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead 359s Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead 359s Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" 359s Expected error: [E::hts_parse_region] Unexpected string "x" after region 359s Expected error: [E::hts_parse_region] Unexpected string "y" after region 359s Expected error: [E::hts_parse_region] Unexpected string "chr3" after region 359s Testing faidx... 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 359s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai 359s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 359s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 359s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 359s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent 359s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 359s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 359s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 359s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 360s PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 360s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 360s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 360s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 360s PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 360s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai 360s PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 360s 360s Expected passes: 25 360s Unexpected passes: 0 360s Expected failures: 0 360s Unexpected failures: 0 360s cd test/sam_filter && ./filter.sh filter.tst 360s Testing sam_filter... 360s PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam 360s PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam 360s PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam 360s PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam 360s PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam 360s PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam 360s PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam 360s PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' 360s PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' 360s PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' 360s PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' 360s PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' 360s PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' 360s PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' 360s PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' 360s PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' 360s PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' 360s PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' 360s 360s Expected passes: 18 360s Unexpected passes: 0 360s Expected failures: 0 360s Unexpected failures: 0 360s cd test/tabix && ./test-tabix.sh tabix.tst 360s Testing tabix... 360s PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz 360s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 360s PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 360s PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz 360s PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 360s PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 360s PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) 360s PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz 360s PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 360s PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz 360s PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 360s PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz 360s PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 360s PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 360s 360s Expected passes: 14 360s Unexpected passes: 0 360s Expected failures: 0 360s Unexpected failures: 0 360s cd test/mpileup && ./test-pileup.sh mpileup.tst 360s Testing (m)pileup... 360s PASS : $pileup mp_D.sam 360s PASS : $pileup -m mp_D.sam 360s PASS : $pileup mp_DI.sam 360s PASS : $pileup -m mp_DI.sam 360s PASS : $pileup mp_I.sam 360s PASS : $pileup -m mp_I.sam 360s PASS : $pileup mp_P.sam 360s PASS : $pileup -m mp_P.sam 360s PASS : $pileup mp_ID.sam 360s PASS : $pileup -m mp_ID.sam 360s PASS : $pileup mp_N.sam 360s PASS : $pileup -m mp_N.sam 360s PASS : $pileup mp_N2.sam 360s PASS : $pileup -m mp_N2.sam 360s PASS : $pileup c1#pad1.sam 360s PASS : $pileup -m c1#pad1.sam 360s PASS : $pileup c1#pad2.sam 360s PASS : $pileup -m c1#pad2.sam 360s PASS : $pileup c1#pad3.sam 360s PASS : $pileup -m c1#pad3.sam 360s PASS : $pileup -m small.bam 360s 360s Expected passes: 21 360s Unexpected passes: 0 360s Expected failures: 0 360s Unexpected failures: 0 360s cd test/fastq && ./test-fastq.sh 360s Testing fastq support 360s PASS : $tview minimal.fq 360s PASS : $tview minimal.fa 360s PASS : $tview multiline.fq 360s PASS : $tview multiline.fa 360s PASS : $tview -i fastq_aux longline.fq 360s PASS : $tview single.fq 360s PASS : $tview single.fa 360s PASS : $tview -i fastq_aux single.fq 360s PASS : $tview -i fastq_aux single.fa 360s PASS : $tview interleaved.fq 360s PASS : $tview interleaved.fa 360s PASS : $tview -i fastq_aux interleaved.fq 360s PASS : $tview -i fastq_aux interleaved.fa 360s PASS : $tview -i fastq_casava interleaved_casava.fq 360s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq 360s PASS : $tview -i fastq_casava interleaved_casava.fa 360s PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa 360s PASS : $tview -i fastq_casava filter_casava.fq 360s PASS : $tview -i fastq_casava filter_casava.fa 360s PASS : $tview -i fastq_aux r1.fq 360s PASS : $tview -i fastq_aux r2.fq 360s PASS : $tview -i fastq_aux r1.fa 360s PASS : $tview -i fastq_aux r2.fa 360s PASS : $tview -i fastq_name2 name2.fq 360s PASS : $tview -i fastq_name2 name2.fa 361s PASS : $tview -f minimal.sam 361s PASS : $tview -F minimal.sam 361s PASS : $tview -f -o fastq_aux single_aux.sam 361s PASS : $tview -F -o fastq_aux single_aux.sam 361s PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam 361s PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam 361s PASS : $tview -f -o fastq_casava inter_casava.sam 361s PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 361s PASS : $tview -F -o fastq_casava inter_casava.sam 361s PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam 361s PASS : $tview -f -o fastq_casava filter_casava.sam 361s PASS : $tview -F -o fastq_casava filter_casava.sam 361s PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam 361s PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam 361s PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam 361s PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam 361s 361s Expected passes: 41 361s Unexpected passes: 0 361s Expected failures: 0 361s Unexpected failures: 0 361s cd test/base_mods && ./base-mods.sh base-mods.tst 361s Testing base-modifications... 361s PASS : $test_mod MM-chebi.sam 361s PASS : $test_mod MM-double.sam 361s PASS : $test_mod MM-multi.sam 361s PASS : $test_mod MM-explicit.sam 361s PASS : $test_mod -x MM-explicit.sam 361s PASS : $test_mod -f 1 MM-explicit.sam 361s PASS : $test_mod MM-not-all-modded.sam 361s PASS : $pileup_mod < MM-pileup.sam 361s PASS : $pileup_mod < MM-pileup2.sam 361s PASS : $pileup_mod < MM-MNp.sam 361s PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) 361s PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) 361s 361s Expected passes: 12 361s Unexpected passes: 0 361s Expected failures: 0 361s Unexpected failures: 0 361s REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq 361s (Expect trailing 'x' message for " -1,001x") 361s [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] 361s (Expect trailing 'k' message for "1.5e+3k") 361s [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] 361s (Expect dropped fraction message for "12.3456k") 361s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 361s [W::hts_parse_decimal] Discarding fractional part of 12.3456k 361s (Expect invalid numeric message for "A") 361s [W::hts_parse_decimal] Invalid numeric value A[truncated] 361s (Expect invalid numeric message for "G") 361s [W::hts_parse_decimal] Invalid numeric value G[truncated] 361s (Expect invalid numeric message for " +/-") 361s [W::hts_parse_decimal] Invalid numeric value +/-[truncated] 361s (Expect invalid numeric message for " -.e+9999") 361s [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] 361s test/test-regidx 361s cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 361s bgzip round-trip no threads: .. ok 361s 361s bgzip text mode round-trip no threads: .. ok 361s 361s bgzip -b no threads: .. ok 361s 361s bgzip -b -I no threads: .. ok 361s 362s bgzip multifile no threads: .. ok 362s 362s bgzip round-trip 4 threads: .. ok 362s 362s bgzip text mode round-trip 4 threads: .. ok 362s 362s bgzip -b 4 threads: .. ok 362s 362s bgzip -b -I 4 threads: .. ok 362s 362s bgzip multifile 4 threads: .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/4_dn6B0Y4l/index.bam.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.bam 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.bam 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -b -m 0 -x /tmp/4_dn6B0Y4l/index.bam.bai /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.bam 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -b /tmp/4_dn6B0Y4l/index.bam 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/4_dn6B0Y4l/index.sam.gz.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/4_dn6B0Y4l/index.sam.gz.bai /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -b /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/4_dn6B0Y4l/index.sam.gz.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index_dos.sam > /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/4_dn6B0Y4l/index.sam.gz.bai /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index_dos.sam > /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -b /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -C -x /tmp/4_dn6B0Y4l/index.cram.crai /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.cram 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index /tmp/4_dn6B0Y4l/index.cram 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -b -m 14 -x /tmp/4_dn6B0Y4l/index.bcf.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.vcf > /tmp/4_dn6B0Y4l/index.bcf 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.bcf 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -z -m 14 -x /tmp/4_dn6B0Y4l/index.vcf.gz.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.vcf > /tmp/4_dn6B0Y4l/index.vcf.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.vcf.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -l 0 -z -m 0 -x /tmp/4_dn6B0Y4l/index.vcf.gz.tbi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.vcf > /tmp/4_dn6B0Y4l/index.vcf.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -t /tmp/4_dn6B0Y4l/index.vcf.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/tabix /tmp/4_dn6B0Y4l/index.vcf.gz##idx##/tmp/4_dn6B0Y4l/index.vcf.gz.tbi 1:10000060-10000060 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/4_dn6B0Y4l/index2.bam 1:1000000-1000000 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/4_dn6B0Y4l/index2.bam 1:2000000-2000000 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/4_dn6B0Y4l/index2.bam 2:1000000-1000000 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/4_dn6B0Y4l/index2.bam 2:2000000-2000000 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/4_dn6B0Y4l/index.bam.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.bam 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.bam 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 0 -x /tmp/4_dn6B0Y4l/index.bam.bai /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.bam 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -b /tmp/4_dn6B0Y4l/index.bam 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/4_dn6B0Y4l/index.sam.gz.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/4_dn6B0Y4l/index.sam.gz.bai /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -b /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/4_dn6B0Y4l/index.sam.gz.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index_dos.sam > /tmp/4_dn6B0Y4l/index.sam.gz 362s .. ok 362s 362s test_index: 362s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.sam.gz 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/4_dn6B0Y4l/index.sam.gz.bai /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index_dos.sam > /tmp/4_dn6B0Y4l/index.sam.gz 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -b /tmp/4_dn6B0Y4l/index.sam.gz 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -C -x /tmp/4_dn6B0Y4l/index.cram.crai /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.sam > /tmp/4_dn6B0Y4l/index.cram 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index /tmp/4_dn6B0Y4l/index.cram 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -b -m 14 -x /tmp/4_dn6B0Y4l/index.bcf.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.vcf > /tmp/4_dn6B0Y4l/index.bcf 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.bcf 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 14 -x /tmp/4_dn6B0Y4l/index.vcf.gz.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.vcf > /tmp/4_dn6B0Y4l/index.vcf.gz 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c /tmp/4_dn6B0Y4l/index.vcf.gz 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -@4 -l 0 -z -m 0 -x /tmp/4_dn6B0Y4l/index.vcf.gz.tbi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/index.vcf > /tmp/4_dn6B0Y4l/index.vcf.gz 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -t /tmp/4_dn6B0Y4l/index.vcf.gz 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/tabix /tmp/4_dn6B0Y4l/index.vcf.gz##idx##/tmp/4_dn6B0Y4l/index.vcf.gz.tbi 1:10000060-10000060 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/4_dn6B0Y4l/index2.bam 1:1000000-1000000 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/4_dn6B0Y4l/index2.bam 1:2000000-2000000 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/4_dn6B0Y4l/index2.bam 2:1000000-1000000 363s .. ok 363s 363s test_index: 363s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/4_dn6B0Y4l/index2.bam 2:2000000-2000000 363s .. ok 363s 363s test_view testing multi-ref CRAM modes: 363s ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 363s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 363s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 363s ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 363s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 363s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 363s ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 363s ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ 363s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 363s .. ok 363s 363s test_view testing multi-ref CRAM modes: 363s ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 363s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 363s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 363s ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 363s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 363s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 363s ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram 363s ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ 363s ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ 364s .. ok 364s 364s test_view testing auxf#values.sam, ref auxf.fa: 364s ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 364s ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 364s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 364s ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 364s ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 364s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 364s ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 364s ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 364s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 364s ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 364s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 364s .. ok 364s 364s test_view testing c1#bounds.sam, ref c1.fa: 364s ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 364s ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 364s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 364s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 364s ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 364s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 364s ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 364s ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 364s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 364s .. ok 364s 364s test_view testing c1#clip.sam, ref c1.fa: 364s ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 364s ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 364s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 364s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 364s ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 364s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 364s ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 364s ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 364s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 364s .. ok 364s 364s test_view testing c1#noseq.sam, ref c1.fa: 364s ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 364s ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 364s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 364s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 364s ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 364s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 364s ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 364s ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 364s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 364s .. ok 364s 364s test_view testing c1#pad1.sam, ref c1.fa: 364s ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 364s ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 364s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 364s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 364s ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 364s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 364s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 364s ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 364s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 364s .. ok 364s 364s test_view testing c1#pad2.sam, ref c1.fa: 364s ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 364s ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 364s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 364s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 364s ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 364s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 364s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 364s ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 364s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 364s .. ok 364s 364s test_view testing c1#pad3.sam, ref c1.fa: 364s ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 364s ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 364s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 364s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 364s ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 364s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 364s ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 364s ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 364s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 364s .. ok 364s 364s test_view testing c1#unknown.sam, ref c1.fa: 364s ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 364s ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 364s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 364s ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 364s ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 364s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 364s ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 364s ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 364s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 364s .. ok 364s 364s test_view testing c2#pad.sam, ref c2.fa: 364s ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 364s ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 364s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 364s ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 364s ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 364s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 365s ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 365s ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 365s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 365s .. ok 365s 365s test_view testing ce#1.sam, ref ce.fa: 365s ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam 365s ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ 365s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 365s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 365s ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 365s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 365s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 365s ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 365s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 365s .. ok 365s 365s test_view testing ce#1000.sam, ref ce.fa: 365s ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam 365s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 365s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 365s ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 365s ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 365s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 365s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 365s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 365s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 365s ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 365s ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 365s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 365s ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 365s ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 365s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 365s .. ok 365s 365s test_view testing ce#2.sam, ref ce.fa: 365s ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam 365s ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ 365s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 365s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 365s ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 365s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 365s ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 365s ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 365s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 365s .. ok 365s 365s test_view testing ce#5.sam, ref ce.fa: 365s ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam 365s ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ 365s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 365s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 365s ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 365s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 365s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 365s ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 365s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 365s .. ok 365s 365s test_view testing ce#5b.sam, ref ce.fa: 365s ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 365s ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 365s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 365s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 365s ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 365s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 365s ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 365s ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 365s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 365s ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 365s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 365s .. ok 365s 365s test_view testing ce#large_seq.sam, ref ce.fa: 365s ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 365s ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 365s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 365s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 366s ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 366s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 366s ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 366s ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 366s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 366s .. ok 366s 366s test_view testing ce#supp.sam, ref ce.fa: 366s ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 366s ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 366s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 366s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 366s ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 366s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 366s ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 366s ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 366s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 366s .. ok 366s 366s test_view testing ce#tag_depadded.sam, ref ce.fa: 366s ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 366s ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 366s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 366s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 366s ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 366s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 366s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 366s ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 366s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 366s .. ok 366s 366s test_view testing ce#tag_padded.sam, ref ce.fa: 366s ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 366s ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 366s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 366s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 366s ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 366s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 366s ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 366s ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 366s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 366s .. ok 366s 366s test_view testing ce#unmap.sam, ref ce.fa: 366s ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 366s ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 366s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 366s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 366s ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 366s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 366s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 366s ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 366s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 366s .. ok 366s 366s test_view testing ce#unmap1.sam, ref ce.fa: 366s ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 366s ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 366s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 366s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 367s ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 367s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 367s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 367s ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 367s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 367s .. ok 367s 367s test_view testing ce#unmap2.sam, ref ce.fa: 367s ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 367s ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 367s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 367s ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 367s ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 367s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 367s ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 367s ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 367s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 367s .. ok 367s 367s test_view testing md#1.sam, ref md.fa: 367s ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam 367s ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ 367s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 367s ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 367s ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ 367s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 367s ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 367s ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 367s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 367s .. ok 367s 367s test_view testing xx#blank.sam, ref xx.fa: 367s ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 367s ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 367s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 367s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 367s ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 367s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 367s ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 367s ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 367s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 367s .. ok 367s 367s test_view testing xx#large_aux.sam, ref xx.fa: 367s ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 367s ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 367s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 367s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 367s ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 367s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 367s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 367s ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 367s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 367s ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 367s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 367s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 367s .. ok 367s 367s test_view testing xx#large_aux2.sam, ref xx.fa: 367s ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 367s ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 367s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 367s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 367s ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 367s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 367s ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 367s ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 367s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 367s .. ok 367s 367s test_view testing xx#MD.sam, ref xx.fa: 367s ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 367s ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 367s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 367s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 367s ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 367s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 367s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 367s ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 367s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 367s .. ok 367s 367s test_view testing xx#MD2.sam, ref xx.fa: 367s ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 367s ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 367s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 367s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 367s ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 367s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 367s ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 367s ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 367s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 367s .. ok 367s 367s test_view testing xx#minimal.sam, ref xx.fa: 367s ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 367s ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 367s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 367s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 368s ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 368s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 368s ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 368s ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 368s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 368s .. ok 368s 368s test_view testing xx#pair.sam, ref xx.fa: 368s ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 368s ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 368s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 368s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 368s ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 368s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 368s ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 368s ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 368s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 368s .. ok 368s 368s test_view testing xx#repeated.sam, ref xx.fa: 368s ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 368s ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 368s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 368s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 368s ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 368s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 368s ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 368s ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 368s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 368s .. ok 368s 368s test_view testing xx#rg.sam, ref xx.fa: 368s ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 368s ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 368s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 368s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 368s ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 368s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 368s ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 368s ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 368s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 368s .. ok 368s 368s test_view testing xx#tlen.sam, ref xx.fa: 368s ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 368s ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 368s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 368s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 368s ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 368s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 368s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 368s ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 368s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 368s .. ok 368s 368s test_view testing xx#tlen2.sam, ref xx.fa: 368s ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 368s ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 368s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 368s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 368s ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 368s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 368s ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 368s ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 368s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 368s .. ok 368s 368s test_view testing xx#triplet.sam, ref xx.fa: 368s ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 368s ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 368s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 368s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 368s ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 368s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 368s ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 368s ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 368s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 368s .. ok 368s 368s test_view testing xx#unsorted.sam, ref xx.fa: 368s ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 368s ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 368s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 368s ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 368s ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 368s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 368s ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 368s ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 368s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 368s .. ok 368s 368s test_view testing embed_ref=2: 368s ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam 368s [W::cram_get_ref] Failed to populate reference for id 0 368s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 368s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 368s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 368s ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 368s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 368s .. ok 368s 368s test_view testing region queries: 368s ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 368s ./compare_sam.pl range.tmp range.out 368s ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 368s ./compare_sam.pl range.tmp range.out 368s .. ok 368s 368s test_view testing BAM files with absent @SQ lines: 368s ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 368s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 368s ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 368s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 368s .. ok 368s 368s test_view testing large (> 2Gbases) positions: 368s ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 368s ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 369s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 369s test_view: 369s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 369s .. ok 369s 369s ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 369s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 369s ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 369s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 369s .. ok 369s 369s test_view testing auxf#values.sam, ref auxf.fa: 369s ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam 369s ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ 369s ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ 369s ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram 369s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 369s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 369s ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram 369s ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ 369s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ 369s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram 369s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 369s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 369s ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram 369s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 369s This is a technology demonstration that should not be used for archival data. 369s ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ 369s ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ 369s ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ 369s ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ 369s .. ok 369s 369s test_view testing c1#bounds.sam, ref c1.fa: 369s ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam 369s ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ 369s ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ 369s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram 369s ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ 369s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ 369s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram 369s ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ 369s ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ 369s .. ok 369s 369s test_view testing c1#clip.sam, ref c1.fa: 369s ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam 369s ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ 369s ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ 369s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram 369s ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ 369s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ 369s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram 369s ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ 369s ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ 369s .. ok 369s 369s test_view testing c1#noseq.sam, ref c1.fa: 369s ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam 369s ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ 369s ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ 369s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram 370s ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ 370s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ 370s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram 370s ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ 370s ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ 370s .. ok 370s 370s test_view testing c1#pad1.sam, ref c1.fa: 370s ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam 370s ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ 370s ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ 370s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram 370s ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ 370s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ 370s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram 370s ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ 370s ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ 370s .. ok 370s 370s test_view testing c1#pad2.sam, ref c1.fa: 370s ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam 370s ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ 370s ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ 370s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram 370s ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ 370s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ 370s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram 370s ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ 370s ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ 370s .. ok 370s 370s test_view testing c1#pad3.sam, ref c1.fa: 370s ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam 370s ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ 370s ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ 370s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram 370s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 370s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 370s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram 370s ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ 370s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ 370s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram 370s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 370s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 370s ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram 370s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 370s This is a technology demonstration that should not be used for archival data. 371s ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ 371s ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ 371s .. ok 371s 371s test_view testing c1#unknown.sam, ref c1.fa: 371s ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam 371s ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ 371s ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ 371s ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram 371s ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ 371s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ 371s ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram 371s ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ 371s ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ 371s .. ok 371s 371s test_view testing c2#pad.sam, ref c2.fa: 371s ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam 371s ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ 371s ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ 371s ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram 371s ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ 371s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ 371s ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram 371s ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ 371s ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ 371s .. ok 371s 371s test_view testing ce#1.sam, ref ce.fa: 371s ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam 371s ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ 371s ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ 371s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram 371s ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ 371s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ 371s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram 371s ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ 371s ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ 371s .. ok 371s 371s test_view testing ce#1000.sam, ref ce.fa: 371s ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam 371s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 371s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 371s ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam 371s ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ 371s ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ 371s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram 371s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 371s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 371s ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram 371s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 371s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 372s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram 372s ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ 372s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ 372s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms 372s ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ 372s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ 372s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram 372s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 372s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 372s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram 372s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 372s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 372s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram 372s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 372s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 372s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram 372s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 372s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 372s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram 372s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 372s This is a technology demonstration that should not be used for archival data. 373s ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ 373s ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ 373s .. ok 373s 373s test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: 373s ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam 373s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ 373s ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ 373s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram 373s ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ 373s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ 373s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram 373s ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 373s ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ 373s .. ok 373s 373s test_view testing ce#2.sam, ref ce.fa: 373s ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam 373s ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ 373s ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ 373s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram 373s ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ 373s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ 373s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram 373s ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ 373s ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ 373s .. ok 373s 373s test_view testing ce#5.sam, ref ce.fa: 373s ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam 373s ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ 373s ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ 373s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram 373s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 373s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 373s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram 373s ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ 373s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ 373s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms 373s ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ 373s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ 373s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram 374s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 374s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 374s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram 374s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 374s This is a technology demonstration that should not be used for archival data. 374s ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ 374s ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ 374s .. ok 374s 374s test_view testing ce#5b.sam, ref ce.fa: 374s ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam 374s ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ 374s ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ 374s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram 374s ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ 374s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ 374s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram 374s ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ 374s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ 374s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms 374s ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ 374s ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ 374s ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ 374s ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ 374s .. ok 374s 374s test_view testing ce#large_seq.sam, ref ce.fa: 374s ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam 374s ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ 374s ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ 374s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram 374s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 374s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 374s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram 375s ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ 375s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ 375s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 375s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 375s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 375s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram 375s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 375s This is a technology demonstration that should not be used for archival data. 376s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 376s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 376s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram 376s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 376s This is a technology demonstration that should not be used for archival data. 376s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 376s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 376s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram 376s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 376s This is a technology demonstration that should not be used for archival data. 376s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 376s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 377s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram 377s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 377s This is a technology demonstration that should not be used for archival data. 377s ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ 377s ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ 377s .. ok 377s 377s test_view testing ce#supp.sam, ref ce.fa: 377s ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam 377s ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ 377s ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ 377s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram 377s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 377s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 377s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram 377s ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ 378s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ 378s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram 378s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 378s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 378s ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram 378s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 378s This is a technology demonstration that should not be used for archival data. 378s ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ 378s ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ 378s .. ok 378s 378s test_view testing ce#tag_depadded.sam, ref ce.fa: 378s ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam 378s ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ 378s ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ 378s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram 378s ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ 378s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ 378s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram 378s ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ 378s ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ 378s .. ok 378s 378s test_view testing ce#tag_padded.sam, ref ce.fa: 378s ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam 378s ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ 378s ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ 378s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram 378s ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ 378s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ 378s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram 378s ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ 378s ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ 378s .. ok 378s 378s test_view testing ce#unmap.sam, ref ce.fa: 378s ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam 378s ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ 378s ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ 378s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram 378s ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ 378s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ 378s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram 378s ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ 378s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ 378s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms 378s ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ 378s ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ 378s .. ok 378s 378s test_view testing ce#unmap1.sam, ref ce.fa: 378s ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam 378s ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ 378s ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ 378s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram 378s ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ 378s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ 378s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram 378s ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ 379s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ 379s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms 379s ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ 379s ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ 379s .. ok 379s 379s test_view testing ce#unmap2.sam, ref ce.fa: 379s ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam 379s ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ 379s ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ 379s ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram 379s ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ 379s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ 379s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram 379s ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ 379s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ 379s ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms 379s ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ 379s ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ 379s .. ok 379s 379s test_view testing md#1.sam, ref md.fa: 379s ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam 379s ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ 379s ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ 379s ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram 379s ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ 379s ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ 379s ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram 379s ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ 379s ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ 379s .. ok 379s 379s test_view testing xx#blank.sam, ref xx.fa: 379s ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam 379s ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ 379s ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ 379s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram 379s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 379s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 379s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram 379s ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ 379s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ 379s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms 379s ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ 379s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ 379s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram 379s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 379s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 379s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram 379s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 379s This is a technology demonstration that should not be used for archival data. 379s ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ 379s ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ 379s .. ok 379s 379s test_view testing xx#large_aux.sam, ref xx.fa: 379s ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam 379s ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ 379s ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ 379s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram 379s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 379s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 379s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram 379s ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ 379s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ 379s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 380s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 380s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 380s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram 380s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 380s This is a technology demonstration that should not be used for archival data. 380s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 380s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 380s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram 380s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 380s This is a technology demonstration that should not be used for archival data. 380s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 380s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 380s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 380s This is a technology demonstration that should not be used for archival data. 380s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram 380s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 380s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 380s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram 380s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 380s This is a technology demonstration that should not be used for archival data. 380s ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ 380s ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ 380s ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ 380s [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 380s ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ 380s .. ok 380s 380s test_view testing xx#large_aux2.sam, ref xx.fa: 380s ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam 380s ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ 380s ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ 380s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram 380s ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ 380s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ 380s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram 380s ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ 380s ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ 380s .. ok 380s 380s test_view testing xx#MD.sam, ref xx.fa: 380s ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam 380s ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ 380s ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ 380s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram 380s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 380s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 380s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram 380s ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ 380s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ 381s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram 381s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 381s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 381s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram 381s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 381s This is a technology demonstration that should not be used for archival data. 381s ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 381s ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ 381s .. ok 381s 381s test_view testing xx#MD2.sam, ref xx.fa: 381s ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam 381s ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ 381s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ 381s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram 381s ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 381s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ 381s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram 381s ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ 381s ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ 381s .. ok 381s 381s test_view testing xx#minimal.sam, ref xx.fa: 381s ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam 381s ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ 381s ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ 381s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram 381s ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ 381s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ 381s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram 381s ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ 381s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ 381s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms 381s ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ 381s ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ 381s .. ok 381s 381s test_view testing xx#pair.sam, ref xx.fa: 381s ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam 381s ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ 381s ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ 381s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram 381s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 381s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 381s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram 381s ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ 381s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ 381s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram 381s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 381s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 381s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram 381s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 381s This is a technology demonstration that should not be used for archival data. 382s ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ 382s ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ 382s .. ok 382s 382s test_view testing xx#repeated.sam, ref xx.fa: 382s ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam 382s ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ 382s ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ 382s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram 382s ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ 382s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ 382s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram 382s ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ 382s ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ 382s .. ok 382s 382s test_view testing xx#rg.sam, ref xx.fa: 382s ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam 382s ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ 382s ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ 382s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram 382s ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ 382s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ 382s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram 382s ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ 382s ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ 382s .. ok 382s 382s test_view testing xx#tlen.sam, ref xx.fa: 382s ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam 382s ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ 382s ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ 382s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram 382s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 382s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 382s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram 382s ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ 382s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ 382s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms 382s ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ 382s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ 382s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram 382s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 382s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 382s ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram 382s [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. 382s This is a technology demonstration that should not be used for archival data. 382s ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ 382s ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ 382s .. ok 382s 382s test_view testing xx#tlen2.sam, ref xx.fa: 382s ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam 382s ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ 382s ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ 382s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram 382s ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ 382s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ 382s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram 382s ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ 383s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ 383s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms 383s ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ 383s ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ 383s .. ok 383s 383s test_view testing xx#triplet.sam, ref xx.fa: 383s ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam 383s ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ 383s ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ 383s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram 383s ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ 383s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ 383s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram 383s ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ 383s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ 383s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms 383s ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ 383s ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ 383s .. ok 383s 383s test_view testing xx#unsorted.sam, ref xx.fa: 383s ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam 383s ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ 383s ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ 383s ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram 383s ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ 383s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ 383s ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram 383s ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ 383s ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ 383s .. ok 383s 383s test_view testing embed_ref=2: 383s ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam 383s [W::cram_get_ref] Failed to populate reference for id 0 383s [W::cram_write_SAM_hdr] No M5 tags present and could not find reference 383s [W::cram_write_SAM_hdr] Enabling embed_ref=2 option 383s [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference 383s ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram 383s ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam 383s .. ok 383s 383s test_view testing region queries: 383s ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 383s ./compare_sam.pl range.tmp range.out 383s ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp 383s ./compare_sam.pl range.tmp range.out 383s .. ok 383s 383s test_view testing BAM files with absent @SQ lines: 383s ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam 383s ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam 383s ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I 383s ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam 383s .. ok 383s 383s test_view testing large (> 2Gbases) positions: 383s ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam 383s ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz 383s ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ 383s test_view: 383s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_index -c longrefs/longref.tmp.sam.gz 383s .. ok 383s 383s ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 383s ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam 383s ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 383s ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam 383s .. ok 383s 383s 383s test_MD testing xx#MD.sam, ref xx.fa: 383s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 383s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 384s ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ 384s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 384s ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 384s ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ 384s Checking for MD/NM in xx#MD.sam 384s ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram 384s ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ 384s ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ 384s .. ok 384s 384s 384s test_MD testing xx#MD2.sam, ref xx.fa: 384s ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 384s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 384s ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ 384s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 384s ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 384s ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ 384s ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram 384s ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ 384s ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ 384s .. ok 384s 384s test_vcf_api: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-vcf-api /tmp/4_dn6B0Y4l/test-vcf-api.bcf 384s .. ok 384s 384s test_bcf2vcf: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/tabix/vcf_file.bcf 384s .. ok 384s 384s test_vcf_sweep: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-vcf-sweep /tmp/4_dn6B0Y4l/test-vcf-api.bcf 384s .. ok 384s 384s test_vcf_various: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/htsfile -ch /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-vcf-hdr-in.vcf 384s .. ok 384s 384s test_vcf_various: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/formatcols.vcf 384s .. ok 384s 384s test_vcf_various: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/noroundtrip.vcf 384s .. ok 384s 384s test_vcf_various: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/formatmissing.vcf 384s .. ok 384s 384s test_vcf_various: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/htsfile -c /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/vcf_meta_meta.vcf 384s .. ok 384s 384s test_vcf_various: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/modhdr.vcf.gz chr22:1-2 384s .. ok 384s 384s test-bcf-sr: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 74452500 384s .. ok 384s 384s test-bcf-sr: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 34270147 384s .. ok 384s 384s test-bcf-sr: 384s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 11108528 385s .. ok 385s 385s test-bcf-sr: 385s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 42233895 385s .. ok 385s 385s test-bcf-sr: 385s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 8111117 385s .. ok 385s 385s test-bcf-sr: 385s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 85644070 386s .. ok 386s 386s test-bcf-sr: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 49879942 386s .. ok 386s 386s test-bcf-sr: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 47881429 386s .. ok 386s 386s test-bcf-sr: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 69081244 386s .. ok 386s 386s test-bcf-sr: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr.pl -t /tmp/4_dn6B0Y4l -s 83459376 386s .. ok 386s 386s test_bcf_sr_no_index: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/merge.noidx.b.vcf /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/4_dn6B0Y4l/no_index_1.err 386s .. ok 386s 386s test_bcf_sr_no_index: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/4_dn6B0Y4l/no_index_2.out 2> /tmp/4_dn6B0Y4l/no_index_2.err (expected fail) 386s .. ok 386s 386s test_bcf_sr_no_index: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/4_dn6B0Y4l/no_index_3.out 2> /tmp/4_dn6B0Y4l/no_index_3.err (expected fail) 386s .. ok 386s 386s test_bcf_sr_no_index: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr --no-index -p all --args /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/merge.noidx.rec_order.vcf /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/merge.noidx.a.vcf > /tmp/4_dn6B0Y4l/no_index_4.out 2> /tmp/4_dn6B0Y4l/no_index_4.err (expected fail) 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -b -p /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf -x /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf.csi /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bcf-sr/weird-chr-names.vcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_1.out.vcf -r '1' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_2.out.vcf -r '1:1-2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_4.out.vcf -r '1:1-1' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_5.out.vcf -r '{1:1}' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf (expected fail) 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_14.out.vcf -t '1' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 386s Failed to set regions 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_15.out.vcf -t '1:1-2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_17.out.vcf -t '1:1-1' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_18.out.vcf -t '{1:1}' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf 386s .. ok 386s 386s test_bcf_sr_range: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-sr -O vcf -o /tmp/4_dn6B0Y4l/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/4_dn6B0Y4l/weird-chr-names.vcf.bcf (expected fail) 386s .. ok 386s 386s test_command: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf-translate - 386s [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 386s Failed to set targets 386s .. ok 386s 386s test_convert_padded_header: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/4_dn6B0Y4l/headernul0.bam 386s .. ok 386s 386s test_convert_padded_header: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/4_dn6B0Y4l/headernul1.bam 386s .. ok 386s 386s test_convert_padded_header: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_view -t ce.fa -C /tmp/4_dn6B0Y4l/headernul678.bam 386s .. ok 386s 386s test_rebgzip: Alternate zlib/deflate library detected 386s test_rebgzip: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/bgzip -I /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bgziptest.txt.tmp.gz.gzi -c -g /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/bgziptest.txt 386s .. ok 386s 386s test-logging: 386s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-logging.pl 386s .. ok 386s 386s test_plugin_loading: 386s HTS_PATH=/tmp/autopkgtest.DZoMuI/autopkgtest_tmp /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/with-shlib.sh /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/htsfile https://localhost:99999/invalid_port 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn01.sam -o - 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02.sam -o - 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn01.sam -o - 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02.sam -o - 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn01.fa -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn01.sam -o - 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -e -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02.sam -o - 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -r -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02-r.sam -o - 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -a -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02_exp.sam -o - 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02.fa -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn02_exp-a.sam -o - 387s .. ok 387s 387s test_realn: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test_realn -f /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn03.fa -e -i /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/realn03.sam -o - 387s .. ok 387s 387s test-bcf_set_variant_type: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/test-bcf_set_variant_type 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -c chr,beg,end -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl,value:overlap,value -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -O 0.5 -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -rO 0.5 -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.1.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.1.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.2.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.2.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.3.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.3.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.3.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.3.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.3.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl:overlap -a nbp,frac -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.3.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.4.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.4.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.4.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.4.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.4.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.4.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.5.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.5.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.5.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.5.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.5.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.5.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.6.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.6.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.6.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.6.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.6.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.6.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.7.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.7.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.7.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.7.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.7.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.7.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.8.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.8.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.8.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.8.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.8.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.8.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.9.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.9.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.9.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.9.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.9.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.9.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -f smpl -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -x -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -x -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -x -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -m smpl -f smpl -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -m smpl -f smpl -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -m smpl -f smpl -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -m smpl -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -m smpl -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -m smpl -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -m smpl -x -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -m smpl -x -s /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt 387s .. ok 387s 387s run_annot_tsv: 387s cat /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/src.10.txt | /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/annot-tsv -m smpl -x -t /tmp/autopkgtest.DZoMuI/autopkgtest_tmp/test/annot-tsv/dst.10.txt 387s .. ok 387s 387s 387s Number of tests: 387s total .. 291 387s passed .. 291 387s failed .. 0 387s 387s + echo PASS 387s PASS 387s autopkgtest [23:47:50]: test run-unit-test: -----------------------] 391s autopkgtest [23:47:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 391s run-unit-test PASS 395s autopkgtest [23:47:58]: @@@@@@@@@@@@@@@@@@@@ summary 395s run-unit-test PASS