Start: 2024-03-24 16:00:47 GMT [testing] Package: bio-eagle Source: bio-eagle (2.4.1-3) Version: 2.4.1-3+b1 Installed-Size: 619 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-iostreams1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3 (>= 1.10), libopenblas0, libstdc++6 (>= 5.2) Recommends: med-config (>= 2.1) Suggests: bio-eagle-examples Description: Haplotype phasing within a genotyped cohort or using a phased reference panel Homepage: https://data.broadinstitute.org/alkesgroup/Eagle/ Description-md5: ea6e8307bcd12f756aab2c02e5d41b0e Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, use::analysing Section: science Priority: optional Filename: pool/main/b/bio-eagle/bio-eagle_2.4.1-3+b1_amd64.deb Size: 224080 MD5sum: 344ae770ea5281c881a1010052c1af4b SHA256: 3a3432961525c3962316ef2fb4b45697a9537f1a6b0988ad3efaa31067baaf04 [sid] Package: bio-eagle Source: bio-eagle (2.4.1-3) Version: 2.4.1-3+b3 Installed-Size: 654 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-iostreams1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libopenblas0, libstdc++6 (>= 13.1) Recommends: med-config (>= 2.1) Suggests: bio-eagle-examples Description: Haplotype phasing within a genotyped cohort or using a phased reference panel Homepage: https://data.broadinstitute.org/alkesgroup/Eagle/ Description-md5: ea6e8307bcd12f756aab2c02e5d41b0e Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, use::analysing Section: science Priority: optional Filename: pool/main/b/bio-eagle/bio-eagle_2.4.1-3+b3_amd64.deb Size: 232980 MD5sum: aad00e37f4b044c1eabee069a63f6e02 SHA256: 681e170773c0bbeacd1b9e2b22e09a767f14d417fbc6a270ae5e6bf266e53260 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt bio-eagle=2.4.1-3+b3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt bio-eagle=2.4.1-3+b3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpdwsnhara 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpdwsnhara 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/pts'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/pts'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/ptmx'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/ptmx'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/console'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/console'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/shm'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/shm'] 0m0.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.6s DEBUG: Created policy-rc.d and chmodded it. 0m0.6s DEBUG: Created resolv.conf. 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpdwsnhara/tmp/scripts/ 0m0.6s INFO: Running scripts post_chroot_unpack 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', 'update'] 0m1.8s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s DUMP: 0942a352c5bc637c4fdbc12bf31cd5ba - 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s INFO: Running scripts post_setup 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u5 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u4 install ok installed libc6:amd64 libc6 2.36-9+deb12u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.22-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.22-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m4.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m4.4s INFO: Running scripts is_testable 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s INFO: Running scripts pre_test 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_test_root_password'] 0m4.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_test_root_password'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'show', '--no-all-versions', 'bio-eagle'] 0m4.8s DUMP: Package: bio-eagle Source: bio-eagle (2.4.1-3) Version: 2.4.1-3+b1 Installed-Size: 619 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-iostreams1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3 (>= 1.10), libopenblas0, libstdc++6 (>= 5.2) Recommends: med-config (>= 2.1) Suggests: bio-eagle-examples Description-en: Haplotype phasing within a genotyped cohort or using a phased reference panel Eagle estimates haplotype phase either within a genotyped cohort or using a phased reference panel. The basic idea of the Eagle1 algorithm is to harness identity-by-descent among distant relatives??which is pervasive at very large sample sizes but rare among smaller numbers of samples??to rapidly call phase using a fast scoring approach. In contrast, the Eagle2 algorithm analyzes a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. . Please note: The executable was renamed to bio-eagle because of a name clash. Please read more about this in /usr/share/doc/bio-eagle/README.Debian. Description-md5: ea6e8307bcd12f756aab2c02e5d41b0e Homepage: https://data.broadinstitute.org/alkesgroup/Eagle/ Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, use::analysing Section: science Priority: optional Filename: pool/main/b/bio-eagle/bio-eagle_2.4.1-3+b1_amd64.deb Size: 224080 MD5sum: 344ae770ea5281c881a1010052c1af4b SHA256: 3a3432961525c3962316ef2fb4b45697a9537f1a6b0988ad3efaa31067baaf04 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'show', '--no-all-versions', 'bio-eagle'] 0m4.8s INFO: apt-cache knows about the following packages: bio-eagle 0m4.8s INFO: Running scripts pre_install 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy'] 0m4.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.5,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy', 'bio-eagle'] 0m5.0s DUMP: bio-eagle: Installed: (none) Candidate: 2.4.1-3+b1 Version table: 2.4.1-3+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy', 'bio-eagle'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', 'install', 'bio-eagle'] 0m8.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libboost-iostreams1.74.0 libboost-program-options1.74.0 libbrotli1 libcurl3-gnutls libdeflate0 libgfortran5 libgomp1 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libnghttp2-14 libopenblas0 libopenblas0-pthread libpsl5 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl3 Suggested packages: bio-eagle-examples krb5-doc krb5-user Recommended packages: med-config ca-certificates krb5-locales libldap-common publicsuffix libsasl2-modules The following NEW packages will be installed: bio-eagle libboost-iostreams1.74.0 libboost-program-options1.74.0 libbrotli1 libcurl3-gnutls libdeflate0 libgfortran5 libgomp1 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libnghttp2-14 libopenblas0 libopenblas0-pthread libpsl5 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl3 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. Need to get 13.1 MB of archives. After this operation, 66.2 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74.0 amd64 1.74.0+ds1-21 [240 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-21 [329 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:8 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u5 [385 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 bio-eagle amd64 2.4.1-3+b1 [224 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.1 MB in 1s (25.5 MB/s) Selecting previously unselected package libboost-iostreams1.74.0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6102 files and directories currently installed.) Preparing to unpack .../00-libboost-iostreams1.74.0_1.74.0+ds1-21_amd64.deb ... Unpacking libboost-iostreams1.74.0:amd64 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-program-options1.74.0:amd64. Preparing to unpack .../01-libboost-program-options1.74.0_1.74.0+ds1-21_amd64.deb ... Unpacking libboost-program-options1.74.0:amd64 (1.74.0+ds1-21) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../02-libgomp1_12.2.0-14_amd64.deb ... Unpacking libgomp1:amd64 (12.2.0-14) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../03-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../07-libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.20.1-2+deb12u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../10-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../11-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../12-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../13-libnghttp2-14_1.52.0-1+deb12u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../14-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../15-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../16-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../17-libcurl3-gnutls_7.88.1-10+deb12u5_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.88.1-10+deb12u5) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../18-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../19-libhtscodecs2_1.3.0-4_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.3.0-4) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../20-libhts3_1.16+ds-3_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../21-libquadmath0_12.2.0-14_amd64.deb ... Unpacking libquadmath0:amd64 (12.2.0-14) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../22-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package libopenblas0-pthread:amd64. Preparing to unpack .../23-libopenblas0-pthread_0.3.21+ds-4_amd64.deb ... Unpacking libopenblas0-pthread:amd64 (0.3.21+ds-4) ... Selecting previously unselected package libopenblas0:amd64. Preparing to unpack .../24-libopenblas0_0.3.21+ds-4_amd64.deb ... Unpacking libopenblas0:amd64 (0.3.21+ds-4) ... Selecting previously unselected package bio-eagle. Preparing to unpack .../25-bio-eagle_2.4.1-3+b1_amd64.deb ... Unpacking bio-eagle (2.4.1-3+b1) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost-iostreams1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libboost-program-options1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libssl3:amd64 (3.0.11-1~deb12u2) ... Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u5) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up bio-eagle (2.4.1-3+b1) ... Processing triggers for libc-bin (2.36-9+deb12u4) ... 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', 'install', 'bio-eagle'] 0m8.7s INFO: Running scripts post_install 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_install_exceptions'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_install_exceptions'] 0m8.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m9.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m9.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpdwsnhara to sid 0m9.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m9.0s INFO: Running scripts pre_distupgrade 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', 'update'] 0m13.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9955 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7222 kB] Fetched 17.4 MB in 3s (5224 kB/s) Reading package lists... 0m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', 'update'] 0m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-yf', 'dist-upgrade'] 0m30.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libboost-iostreams1.74.0 libboost-program-options1.74.0 libquadmath0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libcurl3-gnutls libdb5.3 libext2fs2 libgnutls30 libhogweed6 libhts3 libnettle8 libpsl5 libssh2-1 libssl3 The following NEW packages will be installed: gcc-14-base libapt-pkg6.0t64 libboost-iostreams1.83.0 libboost-program-options1.83.0 libcurl3t64-gnutls libdb5.3t64 libext2fs2t64 libgnutls30t64 libhogweed6t64 libhts3t64 libnettle8t64 libpsl5t64 libssh2-1t64 libssl3t64 libunistring5 The following packages will be upgraded: adduser apt base-files base-passwd bash bio-eagle bsdutils coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils gcc-12-base gpgv grep gzip hostname init-system-helpers libacl1 libattr1 libaudit-common libaudit1 libblkid1 libboost-iostreams1.74.0 libboost-program-options1.74.0 libbrotli1 libbz2-1.0 libc-bin libc6 libcap-ng0 libcap2 libcom-err2 libcrypt1 libdebconfclient0 libdeflate0 libffi8 libgcc-s1 libgcrypt20 libgfortran5 libgmp10 libgomp1 libgpg-error0 libgssapi-krb5-2 libhtscodecs2 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 liblz4-1 liblzma5 libmd0 libmount1 libnghttp2-14 libopenblas0 libopenblas0-pthread libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libss2 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libudev1 libuuid1 libxxhash0 libzstd1 login logsave mawk mount ncurses-base ncurses-bin passwd perl-base sed sysvinit-utils tar tzdata usr-is-merged util-linux util-linux-extra zlib1g 102 upgraded, 15 newly installed, 11 to remove and 0 not upgraded. Need to get 46.3 MB of archives. After this operation, 11.6 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.17 [89.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-10 [97.3 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15.1 [2752 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15.1 [602 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240315-1 [42.9 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240315-1 [72.2 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:10 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:11 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b3 [58.5 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:16 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:17 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.0-0.2 [250 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1+b1 [364 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:23 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3.2 [1643 kB] Get:24 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-6 [67.7 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2+b1 [75.0 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-6 [697 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240315-1 [713 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.9.1-2.2 [296 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.9.1-2.2 [328 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.2-1 [425 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.3-1.1+b1 [1426 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.1.5-1.1 [2058 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b1 [215 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.6.0-4 [421 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.14 [986 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [38.0 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1+b1 [126 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b3 [10.2 kB] Get:50 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:52 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b3 [90.3 kB] Get:54 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:55 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:56 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-3 [649 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http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:70 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1+b1 [74.1 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:73 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Get:74 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:75 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.6 [1510 kB] Get:76 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:77 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:78 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:79 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:80 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.12-1.1 [133 kB] Get:81 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:82 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:84 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:85 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-10 [159 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-10 [191 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-10 [117 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-10 [30.1 kB] Get:90 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-10 [155 kB] Get:91 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-10 [1231 kB] Get:92 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 39 [5572 B] Get:93 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:94 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:95 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:96 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.4 [20.1 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.4 [206 kB] Get:98 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.4 [571 kB] Get:99 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-10 [143 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:104 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:105 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-2.1 [253 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libboost-program-options1.83.0 amd64 1.83.0-2.1 [345 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240315-1 [136 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240315-1 [836 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libopenblas0-pthread amd64 0.3.26+ds-1 [6807 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libopenblas0 amd64 0.3.26+ds-1 [37.5 kB] Get:112 http://deb.debian.org/debian sid/main amd64 bio-eagle amd64 2.4.1-3+b3 [233 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240315-1 [147 kB] Get:114 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-15 [41.8 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libboost-iostreams1.74.0 amd64 1.74.0+ds1-23.1 [239 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-23.1 [331 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2.4 [25.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 46.3 MB in 0s (100.0 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6300 files and directories currently installed.) Preparing to unpack .../base-files_13_amd64.deb ... Unpacking base-files (13) over (12.4+deb12u5) ... Setting up base-files (13) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (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 ... 6303 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-2_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.3-2) over (1.10.1-3) ... Setting up libgcrypt20:amd64 (1.10.3-2) ... (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 ... 6304 files and directories currently installed.) Preparing to unpack .../liblzma5_5.6.0-0.2_amd64.deb ... Unpacking liblzma5:amd64 (5.6.0-0.2) over (5.4.1-0.2) ... Setting up liblzma5:amd64 (5.6.0-0.2) ... (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 ... 6305 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ... Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.0.9-1) ... Setting up libaudit-common (1:3.1.2-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6305 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.4-2_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.4-2) over (0.8.3-1+b3) ... Setting up libcap-ng0:amd64 (0.8.4-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6304 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-2.1) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.2-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6304 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-4) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6304 files and directories currently installed.) Preparing to unpack .../perl-base_5.38.2-3.2_amd64.deb ... Unpacking perl-base (5.38.2-3.2) over (5.36.0-7+deb12u1) ... Setting up perl-base (5.38.2-3.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6308 files and directories currently installed.) Preparing to unpack .../debconf_1.5.86_all.deb ... Unpacking debconf (1.5.86) over (1.5.82) ... Setting up debconf (1.5.86) ... Installing new version of config file /etc/debconf.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.3-6_amd64.deb ... Unpacking libpam0g:amd64 (1.5.3-6) over (1.5.2-6+deb12u1) ... Setting up libpam0g:amd64 (1.5.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6306 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4+b1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4+b1) over (10.42-1) ... Setting up libpcre2-8-0:amd64 (10.42-4+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-2+b1_amd64.deb ... Unpacking libselinux1:amd64 (3.5-2+b1) over (3.4-1+b6) ... Setting up libselinux1:amd64 (3.5-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6308 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-6_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-6) over (1.5.2-6+deb12u1) ... Setting up libpam-modules-bin (1.5.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-6_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-6) over (1.5.2-6+deb12u1) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu/security': Directory not empty Setting up libpam-modules:amd64 (1.5.3-6) ... Installing new version of config file /etc/security/namespace.init ... dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libsasl2-modules-db:amd64 depends on libdb5.3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6304 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-1) ... Selecting previously unselected package libdb5.3t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6298 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) over (2.1.28+dfsg-10) ... Preparing to unpack .../libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) over (2.1.28+dfsg-10) ... Preparing to unpack .../libldap-2.5-0_2.5.16+dfsg-2_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.16+dfsg-2) over (2.5.13+dfsg-5) ... Preparing to unpack .../libstdc++6_14-20240315-1_amd64.deb ... Unpacking libstdc++6:amd64 (14-20240315-1) over (12.2.0-14) ... Setting up libstdc++6:amd64 (14-20240315-1) ... dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested: libhogweed6:amd64 depends on libnettle8. libgnutls30:amd64 depends on libnettle8 (>= 3.7~). libcurl3-gnutls:amd64 depends on libnettle8. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6302 files and directories currently installed.) Removing libnettle8:amd64 (3.8.1-2) ... Selecting previously unselected package libnettle8t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6294 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.2_amd64.deb ... Unpacking libnettle8t64:amd64 (3.9.1-2.2) ... Setting up libnettle8t64:amd64 (3.9.1-2.2) ... dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested: libgnutls30:amd64 depends on libhogweed6 (>= 3.6). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6303 files and directories currently installed.) Removing libhogweed6:amd64 (3.8.1-2) ... Selecting previously unselected package libhogweed6t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6297 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.9.1-2.2) ... Setting up libhogweed6t64:amd64 (3.9.1-2.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6304 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-4_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.3-4) over (0.24.1-2) ... Setting up libp11-kit0:amd64 (0.25.3-4) ... Selecting previously unselected package libunistring5:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6304 files and directories currently installed.) Preparing to unpack .../libunistring5_1.2-1_amd64.deb ... Unpacking libunistring5:amd64 (1.2-1) ... Setting up libunistring5:amd64 (1.2-1) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: libcurl3-gnutls:amd64 depends on libgnutls30 (>= 3.7.5). apt depends on libgnutls30 (>= 3.7.5). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6310 files and directories currently installed.) Removing libgnutls30:amd64 (3.7.9-2+deb12u2) ... Selecting previously unselected package libgnutls30t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6281 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1+b1_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.3-1.1+b1) ... Setting up libgnutls30t64:amd64 (3.8.3-1.1+b1) ... dpkg: libpsl5:amd64: dependency problems, but removing anyway as you requested: libcurl3-gnutls:amd64 depends on libpsl5 (>= 0.16.0). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6311 files and directories currently installed.) Removing libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package libpsl5t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6305 files and directories currently installed.) Preparing to unpack .../libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... dpkg: libssh2-1:amd64: dependency problems, but removing anyway as you requested: libcurl3-gnutls:amd64 depends on libssh2-1 (>= 1.7.0). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6312 files and directories currently installed.) Removing libssh2-1:amd64 (1.10.0-3+b1) ... dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: libkrb5-3:amd64 depends on libssl3 (>= 3.0.0). libhts3:amd64 depends on libssl3 (>= 3.0.0). Removing libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libssl3t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6291 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.1.5-1.1_amd64.deb ... Unpacking libssl3t64:amd64 (3.1.5-1.1) ... Setting up libssl3t64:amd64 (3.1.5-1.1) ... Selecting previously unselected package libssh2-1t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6306 files and directories currently installed.) Preparing to unpack .../libssh2-1t64_1.11.0-4.1+b1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b1) ... dpkg: libcurl3-gnutls:amd64: dependency problems, but removing anyway as you requested: libhts3:amd64 depends on libcurl3-gnutls (>= 7.18.0). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6316 files and directories currently installed.) Removing libcurl3-gnutls:amd64 (7.88.1-10+deb12u5) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6308 files and directories currently installed.) Preparing to unpack .../libcurl3t64-gnutls_8.6.0-4_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.6.0-4) ... dpkg: libhts3:amd64: dependency problems, but removing anyway as you requested: bio-eagle depends on libhts3 (>= 1.10). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6316 files and directories currently installed.) Removing libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package libhts3t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6301 files and directories currently installed.) Preparing to unpack .../libhts3t64_1.19+ds-1.1+b1_amd64.deb ... Unpacking libhts3t64:amd64 (1.19+ds-1.1+b1) ... dpkg: libapt-pkg6.0:amd64: dependency problems, but removing anyway as you requested: apt depends on libapt-pkg6.0 (>= 2.6.1). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6318 files and directories currently installed.) Removing libapt-pkg6.0:amd64 (2.6.1) ... Selecting previously unselected package libapt-pkg6.0t64:amd64. (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 ... 6314 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-1) over (2.5.4-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-1) ... (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 ... 6309 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.7-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.7-2) over (2.3.3-1+b1) ... Setting up libidn2-0:amd64 (2.3.7-2) ... (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 ... 6310 files and directories currently installed.) Preparing to unpack .../00-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) over (1.0.9-2+b6) ... Preparing to unpack .../01-libgssapi-krb5-2_1.20.1-6_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6) over (1.20.1-2+deb12u1) ... Preparing to unpack .../02-libkrb5-3_1.20.1-6_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6) over (1.20.1-2+deb12u1) ... Preparing to unpack .../03-libk5crypto3_1.20.1-6_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6) over (1.20.1-2+deb12u1) ... Preparing to unpack .../04-libkrb5support0_1.20.1-6_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6) over (1.20.1-2+deb12u1) ... Preparing to unpack .../05-libcom-err2_1.47.0-2.4_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.0-2.4) over (1.47.0-2) ... Preparing to unpack .../06-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) over (1.6.3-2) ... Preparing to unpack .../07-libnghttp2-14_1.59.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.59.0-1+b1) over (1.52.0-1+deb12u1) ... Preparing to unpack .../08-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) over (1.14-1) ... Preparing to unpack .../09-libhtscodecs2_1.6.0-1+b1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.0-1+b1) over (1.3.0-4) ... Preparing to unpack .../10-coreutils_9.4-3.1_amd64.deb ... 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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 ... 6320 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.22.6_amd64.deb ... Unpacking dpkg (1.22.6) over (1.21.22) ... Setting up dpkg (1.22.6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6308 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-6_amd64.deb ... Unpacking dash (0.5.12-6) over (0.5.12-2) ... Setting up dash (0.5.12-6) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (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 ... 6308 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-5_amd64.deb ... Unpacking findutils (4.9.0-5) over (4.9.0-4) ... Setting up findutils (4.9.0-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6308 files and directories currently installed.) Preparing to unpack .../archives/grep_3.11-4_amd64.deb ... Unpacking grep (3.11-4) over (3.8-5) ... Setting up grep (3.11-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6308 files and directories currently installed.) Preparing to unpack .../gzip_1.12-1.1_amd64.deb ... Unpacking gzip (1.12-1.1) over (1.12-1) ... dpkg: warning: old file '/bin/uncompress' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') dpkg: warning: old file '/bin/gunzip' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') Setting up gzip (1.12-1.1) ... (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 ... 6307 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.4-4) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1_amd64.deb ... Unpacking ncurses-bin (6.4+20240113-1) over (6.4-4) ... Setting up ncurses-bin (6.4+20240113-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-2_amd64.deb ... Unpacking sed (4.9-2) over (4.9-1) ... Setting up sed (4.9-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Preparing to unpack .../libblkid1_2.39.3-10_amd64.deb ... Unpacking libblkid1:amd64 (2.39.3-10) over (2.38.1-5+b1) ... Setting up libblkid1:amd64 (2.39.3-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6306 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-10_amd64.deb ... Unpacking libmount1:amd64 (2.39.3-10) over (2.38.1-5+b1) ... Setting up libmount1:amd64 (2.39.3-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6305 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.3-10_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.3-10) over (2.38.1-5+b1) ... Setting up libsmartcols1:amd64 (2.39.3-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6304 files and directories currently installed.) Preparing to unpack .../libuuid1_2.39.3-10_amd64.deb ... Unpacking libuuid1:amd64 (2.39.3-10) over (2.38.1-5+b1) ... Setting up libuuid1:amd64 (2.39.3-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6303 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.39.3-10_amd64.deb ... Unpacking util-linux-extra (2.39.3-10) over (2.38.1-5+b1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/etc/init.d': Directory not empty Setting up util-linux-extra (2.39.3-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.3-10_amd64.deb ... Unpacking util-linux (2.39.3-10) over (2.38.1-5+b1) ... Setting up util-linux (2.39.3-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6309 files and directories currently installed.) Preparing to unpack .../usr-is-merged_39_all.deb ... Unpacking usr-is-merged (39) over (37~deb12u1) ... Setting up usr-is-merged (39) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6309 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.66_all.deb ... Unpacking init-system-helpers (1.66) over (1.65.2) ... Setting up init-system-helpers (1.66) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6309 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4+20240113-1_all.deb ... Unpacking ncurses-base (6.4+20240113-1) over (6.4-4) ... Setting up ncurses-base (6.4+20240113-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-7_amd64.deb ... Unpacking sysvinit-utils (3.08-7) over (3.06-4) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.08-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2.4_amd64.deb ... Unpacking logsave (1.47.0-2.4) over (1.47.0-2) ... dpkg: libext2fs2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 1.47.0-2). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6307 files and directories currently installed.) Removing libext2fs2:amd64 (1.47.0-2) ... Selecting previously unselected package libext2fs2t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6300 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.0-2.4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.0-2.4) ... Setting up libcom-err2:amd64 (1.47.0-2.4) ... Setting up libext2fs2t64:amd64 (1.47.0-2.4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6316 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2.4_amd64.deb ... Unpacking e2fsprogs (1.47.0-2.4) over (1.47.0-2) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../mount_2.39.3-10_amd64.deb ... Unpacking mount (2.39.3-10) over (2.38.1-5+b1) ... Preparing to unpack .../libpam-runtime_1.5.3-6_all.deb ... Unpacking libpam-runtime (1.5.3-6) over (1.5.2-6+deb12u1) ... Setting up libpam-runtime (1.5.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6312 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.2-1_amd64.deb ... Unpacking libacl1:amd64 (2.3.2-1) over (2.3.1-3) ... Setting up libacl1:amd64 (2.3.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6312 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.2-1_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.2-1) over (1:2.5.1-4) ... Setting up libattr1:amd64 (1:2.5.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6312 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2_amd64.deb ... Unpacking libmd0:amd64 (1.1.0-2) over (1.0.4-2) ... Setting up libmd0:amd64 (1.1.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6312 files and directories currently installed.) Preparing to unpack .../00-mawk_1.3.4.20240123-1_amd64.deb ... Unpacking mawk (1.3.4.20240123-1) over (1.3.4.20200120-3.1) ... Preparing to unpack .../01-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) over (2024a-0+deb12u1) ... Selecting previously unselected package libboost-iostreams1.83.0:amd64. Preparing to unpack .../02-libboost-iostreams1.83.0_1.83.0-2.1_amd64.deb ... Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-2.1) ... Selecting previously unselected package libboost-program-options1.83.0:amd64. Preparing to unpack .../03-libboost-program-options1.83.0_1.83.0-2.1_amd64.deb ... Unpacking libboost-program-options1.83.0:amd64 (1.83.0-2.1) ... Preparing to unpack .../04-libgomp1_14-20240315-1_amd64.deb ... Unpacking libgomp1:amd64 (14-20240315-1) over (12.2.0-14) ... Preparing to unpack .../05-libgfortran5_14-20240315-1_amd64.deb ... Unpacking libgfortran5:amd64 (14-20240315-1) over (12.2.0-14) ... Preparing to unpack .../06-libopenblas0-pthread_0.3.26+ds-1_amd64.deb ... Unpacking libopenblas0-pthread:amd64 (0.3.26+ds-1) over (0.3.21+ds-4) ... Preparing to unpack .../07-libopenblas0_0.3.26+ds-1_amd64.deb ... Unpacking libopenblas0:amd64 (0.3.26+ds-1) over (0.3.21+ds-4) ... Preparing to unpack .../08-bio-eagle_2.4.1-3+b3_amd64.deb ... Unpacking bio-eagle (2.4.1-3+b3) over (2.4.1-3+b1) ... Preparing to unpack .../09-libquadmath0_14-20240315-1_amd64.deb ... Unpacking libquadmath0:amd64 (14-20240315-1) over (12.2.0-14) ... Preparing to unpack .../10-gcc-12-base_12.3.0-15_amd64.deb ... Unpacking gcc-12-base:amd64 (12.3.0-15) over (12.2.0-14) ... Preparing to unpack .../11-libboost-iostreams1.74.0_1.74.0+ds1-23.1_amd64.deb ... Unpacking libboost-iostreams1.74.0:amd64 (1.74.0+ds1-23.1) over (1.74.0+ds1-21) ... Preparing to unpack .../12-libboost-program-options1.74.0_1.74.0+ds1-23.1_amd64.deb ... Unpacking libboost-program-options1.74.0:amd64 (1.74.0+ds1-23.1) over (1.74.0+ds1-21) ... Preparing to unpack .../13-libss2_1.47.0-2.4_amd64.deb ... Unpacking libss2:amd64 (1.47.0-2.4) over (1.47.0-2) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up libboost-program-options1.83.0:amd64 (1.83.0-2.1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libboost-iostreams1.74.0:amd64 (1.74.0+ds1-23.1) ... Setting up libboost-program-options1.74.0:amd64 (1.74.0+ds1-23.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.59.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up libgomp1:amd64 (14-20240315-1) ... Setting up libkrb5support0:amd64 (1.20.1-6) ... Setting up gcc-12-base:amd64 (12.3.0-15) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Mar 24 16:01:17 UTC 2024. Universal Time is now: Sun Mar 24 16:01:17 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) ... Setting up libboost-iostreams1.83.0:amd64 (1.83.0-2.1) ... Setting up libquadmath0:amd64 (14-20240315-1) ... Setting up libss2:amd64 (1.47.0-2.4) ... Setting up libk5crypto3:amd64 (1.20.1-6) ... Setting up logsave (1.47.0-2.4) ... Setting up libgfortran5:amd64 (14-20240315-1) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Setting up mount (2.39.3-10) ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:amd64 (1.20.1-6) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Setting up libopenblas0-pthread:amd64 (0.3.26+ds-1) ... Setting up e2fsprogs (1.47.0-2.4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libopenblas0:amd64 (0.3.26+ds-1) ... Setting up libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Setting up libcurl3t64-gnutls:amd64 (8.6.0-4) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up bio-eagle (2.4.1-3+b3) ... Processing triggers for debianutils (5.17) ... Processing triggers for libc-bin (2.37-15.1) ... 0m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-yf', 'dist-upgrade'] 0m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m31.5s DUMP: 702bd09d5889134ee611c3fab54d4ded - 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'show', '--no-all-versions', 'bio-eagle'] 0m31.9s DUMP: Package: bio-eagle Source: bio-eagle (2.4.1-3) Version: 2.4.1-3+b3 Installed-Size: 654 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-iostreams1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libopenblas0, libstdc++6 (>= 13.1) Recommends: med-config (>= 2.1) Suggests: bio-eagle-examples Description-en: Haplotype phasing within a genotyped cohort or using a phased reference panel Eagle estimates haplotype phase either within a genotyped cohort or using a phased reference panel. The basic idea of the Eagle1 algorithm is to harness identity-by-descent among distant relatives??which is pervasive at very large sample sizes but rare among smaller numbers of samples??to rapidly call phase using a fast scoring approach. In contrast, the Eagle2 algorithm analyzes a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. . Please note: The executable was renamed to bio-eagle because of a name clash. Please read more about this in /usr/share/doc/bio-eagle/README.Debian. Description-md5: ea6e8307bcd12f756aab2c02e5d41b0e Homepage: https://data.broadinstitute.org/alkesgroup/Eagle/ Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, use::analysing Section: science Priority: optional Filename: pool/main/b/bio-eagle/bio-eagle_2.4.1-3+b3_amd64.deb Size: 232980 MD5sum: aad00e37f4b044c1eabee069a63f6e02 SHA256: 681e170773c0bbeacd1b9e2b22e09a767f14d417fbc6a270ae5e6bf266e53260 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'show', '--no-all-versions', 'bio-eagle'] 0m31.9s INFO: apt-cache knows about the following packages: bio-eagle 0m31.9s INFO: Running scripts pre_install 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_database-server'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_database-server'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_exceptions'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_exceptions'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_extras'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_extras'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy'] 0m32.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy'] 0m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy', 'bio-eagle'] 0m32.0s DUMP: bio-eagle: Installed: 2.4.1-3+b3 Candidate: 2.4.1-3+b3 Version table: *** 2.4.1-3+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy', 'bio-eagle'] 0m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', 'install', 'bio-eagle'] 0m32.9s DUMP: Reading package lists... Building dependency tree... Reading state information... bio-eagle is already the newest version (2.4.1-3+b3). The following packages were automatically installed and are no longer required: libboost-iostreams1.74.0 libboost-program-options1.74.0 libquadmath0 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', 'install', 'bio-eagle'] 0m32.9s INFO: Running scripts post_install 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_install_exceptions'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_install_exceptions'] 0m32.9s INFO: Running scripts post_distupgrade 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_exceptions'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_exceptions'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_zz_backports'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_distupgrade_zz_backports'] 0m32.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m33.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m33.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m33.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m33.6s INFO: Running scripts pre_install 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_database-server'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_database-server'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_exceptions'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_exceptions'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_extras'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_extras'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy'] 0m33.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy'] 0m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy', 'bio-eagle'] 0m33.8s DUMP: bio-eagle: Installed: 2.4.1-3+b3 Candidate: 2.4.1-3+b3 Version table: *** 2.4.1-3+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-cache', 'policy', 'bio-eagle'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', 'install', 'bio-eagle=2.4.1-3+b3'] 0m34.6s DUMP: Reading package lists... Building dependency tree... Reading state information... bio-eagle is already the newest version (2.4.1-3+b3). The following packages were automatically installed and are no longer required: libboost-iostreams1.74.0 libboost-program-options1.74.0 libquadmath0 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', 'install', 'bio-eagle=2.4.1-3+b3'] 0m34.6s INFO: Running scripts post_install 0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_install_exceptions'] 0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_install_exceptions'] 0m34.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m35.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m35.0s INFO: /bin converted to /usr/bin by /usr merge 0m35.0s INFO: /lib converted to /usr/lib by /usr merge 0m35.0s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m35.0s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m35.0s INFO: /sbin converted to /usr/sbin by /usr merge 0m35.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', '-ac', '--ignore-obsolete'] 0m36.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', '-ac', '--ignore-obsolete'] 0m36.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m36.4s DUMP: 0.15.6 0m36.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m36.4s INFO: Running adequate version 0.15.6 now. 0m36.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'bio-eagle'] 0m36.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'bio-eagle'] 0m36.5s INFO: Running scripts pre_remove 0m36.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_exceptions'] 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/pre_remove_exceptions'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m38.1s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.14 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bio-eagle bio-eagle 2.4.1-3+b3 install ok installed bsdutils bsdutils 1:2.39.3-10 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-15 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240315-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.39.3-10 install ok installed libboost-iostreams1.74.0:amd64 libboost-iostreams1.74.0 1.74.0+ds1-23.1 install ok installed libboost-iostreams1.83.0:amd64 libboost-iostreams1.83.0 1.83.0-2.1 install ok installed libboost-program-options1.74.0:amd64 libboost-program-options1.74.0 1.74.0+ds1-23.1 install ok installed libboost-program-options1.83.0:amd64 libboost-program-options1.83.0 1.83.0-2.1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.6.0-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libdeflate0:amd64 libdeflate0 1.20-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240315-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgfortran5:amd64 libgfortran5 14-20240315-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.3-1.1+b1 install ok installed libgomp1:amd64 libgomp1 14-20240315-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-6 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libhts3t64:amd64 libhts3t64 1.19+ds-1.1+b1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-6 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-6 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-6 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.16+dfsg-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.6.0-0.2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-10 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1+b1 install ok installed libopenblas0:amd64 libopenblas0 0.3.26+ds-1 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.26+ds-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libquadmath0:amd64 libquadmath0 14-20240315-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b3 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-6 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-10 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstdc++6:amd64 libstdc++6 14-20240315-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.39.3-10 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.39.3-10 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-10 install ok installed util-linux-extra util-linux-extra 2.39.3-10 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libboost-iostreams1.74.0:amd64-', 'libboost-iostreams1.83.0:amd64-', 'libboost-program-options1.74.0:amd64-', 'libboost-program-options1.83.0:amd64-', 'libbrotli1:amd64-', 'libcurl3t64-gnutls:amd64-', 'libdb5.3t64:amd64-', 'libdeflate0:amd64-', 'libgfortran5:amd64-', 'libgomp1:amd64-', 'libgssapi-krb5-2:amd64-', 'libhts3t64:amd64-', 'libhtscodecs2:amd64-', 'libk5crypto3:amd64-', 'libkeyutils1:amd64-', 'libkrb5-3:amd64-', 'libkrb5support0:amd64-', 'libldap-2.5-0:amd64-', 'libnghttp2-14:amd64-', 'libopenblas0:amd64-', 'libopenblas0-pthread:amd64-', 'libpsl5t64:amd64-', 'libquadmath0:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libssh2-1t64:amd64-', 'bio-eagle-'] 0m39.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bio-eagle libboost-iostreams1.74.0 libboost-iostreams1.83.0 libboost-program-options1.74.0 libboost-program-options1.83.0 libbrotli1 libcurl3t64-gnutls libdb5.3t64 libdeflate0 libgfortran5 libgomp1 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libnghttp2-14 libopenblas0 libopenblas0-pthread libpsl5t64 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1t64 The following NEW packages will be installed: libdb5.3 0 upgraded, 1 newly installed, 28 to remove and 0 not upgraded. Need to get 697 kB of archives. After this operation, 67.4 MB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 697 kB in 0s (9990 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5539 files and directories currently installed.) Removing bio-eagle (2.4.1-3+b3) ... Removing libboost-iostreams1.74.0:amd64 (1.74.0+ds1-23.1) ... Removing libboost-iostreams1.83.0:amd64 (1.83.0-2.1) ... Removing libboost-program-options1.74.0:amd64 (1.74.0+ds1-23.1) ... Removing libboost-program-options1.83.0:amd64 (1.83.0-2.1) ... Removing libhts3t64:amd64 (1.19+ds-1.1+b1) ... Removing libcurl3t64-gnutls:amd64 (8.6.0-4) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Removing libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Removing libdeflate0:amd64 (1.20-1) ... Removing libopenblas0:amd64 (0.3.26+ds-1) ... Removing libopenblas0-pthread:amd64 (0.3.26+ds-1) ... Removing libgfortran5:amd64 (14-20240315-1) ... Removing libgomp1:amd64 (14-20240315-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-6) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libkrb5-3:amd64 (1.20.1-6) ... Removing libk5crypto3:amd64 (1.20.1-6) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.20.1-6) ... Removing libnghttp2-14:amd64 (1.59.0-1+b1) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libquadmath0:amd64 (14-20240315-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) ... Removing libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Selecting previously unselected package libdb5.3:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5333 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15.1) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libboost-iostreams1.74.0:amd64-', 'libboost-iostreams1.83.0:amd64-', 'libboost-program-options1.74.0:amd64-', 'libboost-program-options1.83.0:amd64-', 'libbrotli1:amd64-', 'libcurl3t64-gnutls:amd64-', 'libdb5.3t64:amd64-', 'libdeflate0:amd64-', 'libgfortran5:amd64-', 'libgomp1:amd64-', 'libgssapi-krb5-2:amd64-', 'libhts3t64:amd64-', 'libhtscodecs2:amd64-', 'libk5crypto3:amd64-', 'libkeyutils1:amd64-', 'libkrb5-3:amd64-', 'libkrb5support0:amd64-', 'libldap-2.5-0:amd64-', 'libnghttp2-14:amd64-', 'libopenblas0:amd64-', 'libopenblas0-pthread:amd64-', 'libpsl5t64:amd64-', 'libquadmath0:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libssh2-1t64:amd64-', 'bio-eagle-'] 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1'] 0m40.8s DUMP: Reading package lists... Building dependency tree... Reading state information... debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/697 kB of archives. After this operation, 0 B of additional disk space will be used. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5340 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) over (5.3.28+dfsg2-4+b1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15.1) ... 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1'] 0m40.8s INFO: Running scripts post_remove 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_remove_exceptions'] 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_remove_exceptions'] 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg', '--purge', 'libboost-iostreams1.74.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost-program-options1.83.0:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libnghttp2-14:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64'] 0m40.9s DUMP: dpkg: warning: ignoring request to remove libboost-iostreams1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-iostreams1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.83.0 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libdb5.3t64 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed (Reading database ... 5340 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-6) ... dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libopenblas0 which isn't installed dpkg: warning: ignoring request to remove libopenblas0-pthread which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg', '--purge', 'libboost-iostreams1.74.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost-program-options1.83.0:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libnghttp2-14:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64'] 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg', '--purge', 'bio-eagle'] 0m40.9s DUMP: dpkg: warning: ignoring request to remove bio-eagle which isn't installed 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg', '--purge', 'bio-eagle'] 0m40.9s INFO: Running scripts post_purge 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_purge_exceptions'] 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_purge_exceptions'] 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg', '--purge', '--pending'] 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg', '--purge', '--pending'] 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg', '--remove', '--pending'] 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg', '--remove', '--pending'] 0m40.9s INFO: Running scripts post_test 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_test_exceptions'] 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'tmp/scripts/post_test_exceptions'] 0m40.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m41.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg-divert', '--list'] 0m41.2s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'dpkg-divert', '--list'] 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', 'clean'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdwsnhara', 'apt-get', 'clean'] 0m41.3s DEBUG: Recording chroot state 0m42.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/shm'] 0m42.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/shm'] 0m42.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/console'] 0m42.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/console'] 0m42.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/ptmx'] 0m42.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/ptmx'] 0m42.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/pts'] 0m42.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/dev/pts'] 0m42.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/proc'] 0m42.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdwsnhara/proc'] 0m42.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m42.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpdwsnhara'] 0m42.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpdwsnhara 0m42.4s INFO: PASS: Upgrading between Debian distributions. 0m42.4s INFO: PASS: All tests. 0m42.4s INFO: piuparts run ends. ret=0 End: 2024-03-24 16:01:30 GMT