Start: 2024-08-22 20:14:53 GMT [bookworm] Package: augur Version: 20.0.0-1 Installed-Size: 829 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-bcbio-gff, python3-biopython, python3-cvxopt, python3-isodate, python3-jsonschema, python3-networkx, python3-numpy, python3-packaging, python3-pandas, python3-pyfastx, python3-scipy, python3-treetime (>= 0.9.4), python3-xopen (>= 1.7.0-1~), python3:any (>= 3.11~), python3-boto3, python3-dendropy, python3-matplotlib, python3-schedule, python3-seaborn, python3-zstandard, seqmagick, python3-ipdb, mafft, raxml, fasttree, vcftools Recommends: iqtree Description: pipeline components for real-time virus analysis Homepage: https://github.com/nextstrain/augur Description-md5: e2aaa44840d7b632d0e95700bc100196 Section: science Priority: optional Filename: pool/main/a/augur/augur_20.0.0-1_all.deb Size: 187288 MD5sum: e3fe15acc709cc259fd3c65e7ae307be SHA256: af76cecb21ea71f78e4fbce03feac9056af9cfde8b4f9d20aeaf229fe38d000f [bookworm-next] Package: augur Version: 20.0.0-1 Installed-Size: 829 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-bcbio-gff, python3-biopython, python3-cvxopt, python3-isodate, python3-jsonschema, python3-networkx, python3-numpy, python3-packaging, python3-pandas, python3-pyfastx, python3-scipy, python3-treetime (>= 0.9.4), python3-xopen (>= 1.7.0-1~), python3:any (>= 3.11~), python3-boto3, python3-dendropy, python3-matplotlib, python3-schedule, python3-seaborn, python3-zstandard, seqmagick, python3-ipdb, mafft, raxml, fasttree, vcftools Recommends: iqtree Description: pipeline components for real-time virus analysis Homepage: https://github.com/nextstrain/augur Description-md5: e2aaa44840d7b632d0e95700bc100196 Section: science Priority: optional Filename: pool/main/a/augur/augur_20.0.0-1_all.deb Size: 187288 MD5sum: e3fe15acc709cc259fd3c65e7ae307be SHA256: af76cecb21ea71f78e4fbce03feac9056af9cfde8b4f9d20aeaf229fe38d000f 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 --warn-on-usr-move fail --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 bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt augur=20.0.0-1 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 1.4.4~202408201642~1.4.3-11-g36a88c35 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 --warn-on-usr-move fail --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 bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt augur=20.0.0-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp5515yq17 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp5515yq17 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5515yq17', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5515yq17', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5515yq17/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5515yq17/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp5515yq17/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', 'update'] 0m1.1s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', 'update'] 0m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-yf', 'dist-upgrade'] 0m1.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-yf', 'dist-upgrade'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.9s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.9s INFO: Running scripts post_setup 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s 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 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.0s 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' 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_minimize'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_minimize'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_zz_backports'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_setup_zz_backports'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.0s 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+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 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+deb12u1 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+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 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+deb12u3 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+deb12u1 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+deb12u1 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+deb12u1 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 252.26-1~deb12u2 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 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 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+deb12u1 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+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m3.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 0m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 0m3.5s INFO: Running scripts is_testable 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s INFO: Running scripts pre_test 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_test_root_password'] 0m3.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'show', '--no-all-versions', 'augur'] 0m3.8s DUMP: Package: augur Version: 20.0.0-1 Installed-Size: 829 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-bcbio-gff, python3-biopython, python3-cvxopt, python3-isodate, python3-jsonschema, python3-networkx, python3-numpy, python3-packaging, python3-pandas, python3-pyfastx, python3-scipy, python3-treetime (>= 0.9.4), python3-xopen (>= 1.7.0-1~), python3:any (>= 3.11~), python3-boto3, python3-dendropy, python3-matplotlib, python3-schedule, python3-seaborn, python3-zstandard, seqmagick, python3-ipdb, mafft, raxml, fasttree, vcftools Recommends: iqtree Description-en: pipeline components for real-time virus analysis The nextstrain project is an attempt to make flexible informatic pipelines and visualization tools to track ongoing pathogen evolution as sequence data emerges. The nextstrain project derives from nextflu, which was specific to influenza evolution. . nextstrain is comprised of three components: . * fauna: database and IO scripts for sequence and serological data * augur: informatic pipelines to conduct inferences from raw data * auspice: web app to visualize resulting inferences Description-md5: e2aaa44840d7b632d0e95700bc100196 Homepage: https://github.com/nextstrain/augur Section: science Priority: optional Filename: pool/main/a/augur/augur_20.0.0-1_all.deb Size: 187288 MD5sum: e3fe15acc709cc259fd3c65e7ae307be SHA256: af76cecb21ea71f78e4fbce03feac9056af9cfde8b4f9d20aeaf229fe38d000f 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'show', '--no-all-versions', 'augur'] 0m3.8s INFO: apt-cache knows about the following packages: augur 0m3.8s INFO: Running scripts pre_install 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_database-server'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_database-server'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_exceptions'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_exceptions'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_extras'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_extras'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy'] 0m3.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy', 'augur'] 0m3.9s DUMP: augur: Installed: (none) Candidate: 20.0.0-1 Version table: 20.0.0-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy', 'augur'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-y', 'install', 'augur'] 1m54.4s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-12 fasttree fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 g++ g++-12 gcc gcc-12 ipython3 libamd2 libasan8 libatomic1 libbinutils libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcamd2 libcc1-0 libccolamd2 libcholmod3 libcolamd2 libcrypt-dev libctf-nobfd0 libctf0 libdeflate0 libdsdp-5.8gf libexpat1 libexpat1-dev libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libglpk40 libgomp1 libgprofng0 libgraphite2-3 libgsl27 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libltdl7 libmetis5 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libperl5.36 libpng16-16 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libstdc++-12-dev libsuitesparseconfig5 libtcl8.6 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libumfpack5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 linux-libc-dev mafft mailcap media-types mime-support openssl perl perl-modules-5.36 pigz python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-asttokens python3-attr python3-backcall python3-bcbio-gff python3-beniget python3-biopython python3-boto3 python3-botocore python3-brotli python3-certifi python3-cffi-backend python3-chardet python3-charset-normalizer python3-contourpy python3-cvxopt python3-cycler python3-dateutil python3-decorator python3-dendropy python3-dev python3-distutils python3-executing python3-fonttools python3-fs python3-gast python3-idna python3-ipdb python3-ipython python3-isodate python3-jedi python3-jmespath python3-jsonschema python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-mpmath python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pickleshare python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pyfaidx python3-pyfastx python3-pygments python3-pygtrie python3-pyparsing python3-pyrsistent python3-pythran python3-renderpm python3-reportlab python3-reportlab-accel python3-requests python3-s3transfer python3-schedule python3-scipy python3-seaborn python3-setuptools python3-six python3-stack-data python3-sympy python3-tk python3-toml python3-traitlets python3-treetime python3-tz python3-ufolib2 python3-urllib3 python3-wcwidth python3-xopen python3-zstandard python3.11 python3.11-dev python3.11-minimal raxml readline-common rpcsvc-proto seqmagick sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core zlib1g-dev Suggested packages: binutils-doc blt-demo cpp-doc gcc-12-locales cpp-12-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre g++-multilib g++-12-multilib gcc-12-doc gcc-multilib make manpages-dev autoconf automake libtool flex bison gdb gcc-doc gcc-12-multilib libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev glibc-doc libfftw3-bin libfftw3-dev gdbm-l10n low-memory-monitor libiodbc2-dev default-libmysqlclient-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils sensible-utils libstdc++-12-doc tcl8.6 tk8.6 libxsimd-doc perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 samtools t-coffee wise python-cvxopt-doc python-cycler-doc python-ipython-doc python-jsonschema-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape librsvg2-common python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gfortran python3-pytest python-pandas-doc python3-statsmodels python-pexpect-doc python-pil-doc python-ply-doc python-pygments-doc ttf-bitstream-vera python-pygtrie-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python-zstandard-doc python3.11-venv python3.11-doc binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: iqtree manpages manpages-dev libc-devtools libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libgpm2 blast2 libwww-perl lynx ruby bzip2 file xz-utils netbase python-biopython-doc ncbi-blast+ python3-json-pointer python3-rfc3987 python3-uritemplate python3-webcolors python3-bs4 python3-html5lib python3-gdal python3-pydot python3-pygraphviz python3-yaml python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-tables python3-jinja2 python3-numba python3-olefile python3-patsy isympy-common tabix The following NEW packages will be installed: augur binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-12 fasttree fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 g++ g++-12 gcc gcc-12 ipython3 libamd2 libasan8 libatomic1 libbinutils libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcamd2 libcc1-0 libccolamd2 libcholmod3 libcolamd2 libcrypt-dev libctf-nobfd0 libctf0 libdeflate0 libdsdp-5.8gf libexpat1 libexpat1-dev libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libglpk40 libgomp1 libgprofng0 libgraphite2-3 libgsl27 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libltdl7 libmetis5 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libperl5.36 libpng16-16 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libstdc++-12-dev libsuitesparseconfig5 libtcl8.6 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libumfpack5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 linux-libc-dev mafft mailcap media-types mime-support openssl perl perl-modules-5.36 pigz python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-asttokens python3-attr python3-backcall python3-bcbio-gff python3-beniget python3-biopython python3-boto3 python3-botocore python3-brotli python3-certifi python3-cffi-backend python3-chardet python3-charset-normalizer python3-contourpy python3-cvxopt python3-cycler python3-dateutil python3-decorator python3-dendropy python3-dev python3-distutils python3-executing python3-fonttools python3-fs python3-gast python3-idna python3-ipdb python3-ipython python3-isodate python3-jedi python3-jmespath python3-jsonschema python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-mpmath python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pickleshare python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pyfaidx python3-pyfastx python3-pygments python3-pygtrie python3-pyparsing python3-pyrsistent python3-pythran python3-renderpm python3-reportlab python3-reportlab-accel python3-requests python3-s3transfer python3-schedule python3-scipy python3-seaborn python3-setuptools python3-six python3-stack-data python3-sympy python3-tk python3-toml python3-traitlets python3-treetime python3-tz python3-ufolib2 python3-urllib3 python3-wcwidth python3-xopen python3-zstandard python3.11 python3.11-dev python3.11-minimal raxml readline-common rpcsvc-proto seqmagick sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core zlib1g-dev 0 upgraded, 247 newly installed, 0 to remove and 0 not upgraded. Need to get 227 MB of archives. After this operation, 1159 MB of additional disk space will be used. 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1.3.3+ds-1 [14.0 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u2 [1799 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u2 [573 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:30 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5+deb12u3 [398 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get:49 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+deb12u1 [74.2 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+deb12u1 [472 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 python3-bcbio-gff all 0.6.9-1 [33.5 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libsuitesparseconfig5 amd64 1:5.12.0+dfsg-2 [23.9 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libamd2 amd64 1:5.12.0+dfsg-2 [36.2 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libcamd2 amd64 1:5.12.0+dfsg-2 [37.8 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libccolamd2 amd64 1:5.12.0+dfsg-2 [39.7 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 libcolamd2 amd64 1:5.12.0+dfsg-2 [32.9 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 libmetis5 amd64 5.1.0.dfsg-7 [171 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libcholmod3 amd64 1:5.12.0+dfsg-2 [335 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 libdsdp-5.8gf amd64 5.8-10 [182 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libfftw3-double3 amd64 3.3.10-1 [776 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-7~deb12u1 [393 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libglpk40 amd64 5.0-1 [400 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-5 [108 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-5 [941 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 libumfpack5 amd64 1:5.12.0+dfsg-2 [245 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 python3-cvxopt amd64 1.3.0+dfsg-1+b1 [262 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 python3-isodate all 0.6.1-1 [25.3 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 python3-pyrsistent amd64 0.18.1-1+b3 [60.0 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 python3-jsonschema all 4.10.3-1 [67.9 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.8.8-1 [1425 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 python3-pyfaidx all 0.7.1-2 [28.0 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 python3-pyfastx amd64 0.8.4-2 [52.0 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libisl23 amd64 0.25-1.1 [683 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libmpfr6 amd64 4.2.0-1 [701 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 libmpc3 amd64 1.3.1-1 [51.5 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 cpp-12 amd64 12.2.0-14 [9764 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 cpp amd64 4:12.2.0-3 [6836 B] Get:127 http://deb.debian.org/debian bookworm/main amd64 libcc1-0 amd64 12.2.0-14 [41.7 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 binutils-common amd64 2.40-2 [2487 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 libbinutils amd64 2.40-2 [572 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 libctf-nobfd0 amd64 2.40-2 [153 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libctf0 amd64 2.40-2 [89.8 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libgprofng0 amd64 2.40-2 [812 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libjansson4 amd64 2.14-2 [40.8 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2 [2246 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 binutils amd64 2.40-2 [65.0 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:138 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 gcc-12 amd64 12.2.0-14 [19.3 MB] Get:144 http://deb.debian.org/debian bookworm/main amd64 gcc amd64 4:12.2.0-3 [5216 B] Get:145 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u7 [45.8 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.94-1 [1994 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u7 [1899 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 g++-12 amd64 12.2.0-14 [10.7 MB] Get:154 http://deb.debian.org/debian bookworm/main amd64 g++ amd64 4:12.2.0-3 [1356 B] Get:155 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:160 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6+deb12u2 [1987 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6+deb12u2 [4742 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get:165 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get:166 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get:169 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6+deb12u2 [615 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get:175 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get:177 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get:178 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get:182 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get:188 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 python3-treetime all 0.9.4-1 [921 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 python3-xopen all 1.7.0-2 [16.9 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 python3-jmespath all 1.0.1-1 [21.1 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1+deb12u1 [41.0 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 python3-botocore all 1.29.27+repack-1 [5502 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 python3-s3transfer all 0.6.0-1 [53.0 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 python3-boto3 all 1.26.27+dfsg-1 [187 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 python3-dendropy all 4.5.2-1 [275 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 python3-schedule all 1.1.0-0.2 [12.9 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 python3-seaborn all 0.12.2-1 [215 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 python3-cffi-backend amd64 1.15.1-5+b1 [84.6 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 python3-zstandard amd64 0.20.0-3 [324 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 python3-pygtrie all 2.2-2 [16.8 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 seqmagick all 0.8.4-3 [42.6 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 python3-backcall all 0.2.0-4 [12.1 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 python3-parso all 0.8.3-1 [67.4 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 python3-jedi all 0.18.2-1 [689 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 python3-traitlets all 5.5.0-1 [92.4 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib-inline all 0.1.6-2 [8652 B] Get:228 http://deb.debian.org/debian bookworm/main amd64 python3-ptyprocess all 0.7.0-5 [14.7 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 python3-pexpect all 4.8.0-4 [52.9 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 python3-pickleshare all 0.7.5-5 [7600 B] Get:231 http://deb.debian.org/debian bookworm/main amd64 python3-wcwidth all 0.2.5+dfsg1-1.1 [21.4 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 python3-prompt-toolkit all 3.0.36-2 [276 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get:234 http://deb.debian.org/debian bookworm/main amd64 python3-asttokens all 2.2.1-1 [19.8 kB] Get:235 http://deb.debian.org/debian bookworm/main amd64 python3-executing all 1.2.0-2 [22.6 kB] Get:236 http://deb.debian.org/debian bookworm/main amd64 python3-pure-eval all 0.2.2-1 [11.2 kB] Get:237 http://deb.debian.org/debian bookworm/main amd64 python3-stack-data all 0.6.2-3 [21.8 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get:239 http://deb.debian.org/debian bookworm/main amd64 python3-ipython all 8.5.0-4 [517 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 ipython3 all 8.5.0-4 [22.7 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get:242 http://deb.debian.org/debian bookworm/main amd64 python3-ipdb all 0.13.9-1 [17.1 kB] Get:243 http://deb.debian.org/debian bookworm/main amd64 mafft amd64 7.505-1 [1078 kB] Get:244 http://deb.debian.org/debian bookworm/main amd64 raxml amd64 8.2.12+dfsg-8+b2 [1481 kB] Get:245 http://deb.debian.org/debian bookworm/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get:246 http://deb.debian.org/debian bookworm/main amd64 vcftools amd64 0.1.16-3+b1 [431 kB] Get:247 http://deb.debian.org/debian bookworm/main amd64 augur all 20.0.0-1 [187 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 227 MB in 6s (35.1 MB/s) Selecting previously unselected package perl-modules-5.36. 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Selecting previously unselected package python3-parso. Preparing to unpack .../194-python3-parso_0.8.3-1_all.deb ... Unpacking python3-parso (0.8.3-1) ... Selecting previously unselected package python3-jedi. Preparing to unpack .../195-python3-jedi_0.18.2-1_all.deb ... Unpacking python3-jedi (0.18.2-1) ... Selecting previously unselected package python3-traitlets. Preparing to unpack .../196-python3-traitlets_5.5.0-1_all.deb ... Unpacking python3-traitlets (5.5.0-1) ... Selecting previously unselected package python3-matplotlib-inline. Preparing to unpack .../197-python3-matplotlib-inline_0.1.6-2_all.deb ... Unpacking python3-matplotlib-inline (0.1.6-2) ... Selecting previously unselected package python3-ptyprocess. Preparing to unpack .../198-python3-ptyprocess_0.7.0-5_all.deb ... Unpacking python3-ptyprocess (0.7.0-5) ... Selecting previously unselected package python3-pexpect. Preparing to unpack .../199-python3-pexpect_4.8.0-4_all.deb ... Unpacking python3-pexpect (4.8.0-4) ... Selecting previously unselected package python3-pickleshare. Preparing to unpack .../200-python3-pickleshare_0.7.5-5_all.deb ... Unpacking python3-pickleshare (0.7.5-5) ... Selecting previously unselected package python3-wcwidth. Preparing to unpack .../201-python3-wcwidth_0.2.5+dfsg1-1.1_all.deb ... Unpacking python3-wcwidth (0.2.5+dfsg1-1.1) ... Selecting previously unselected package python3-prompt-toolkit. Preparing to unpack .../202-python3-prompt-toolkit_3.0.36-2_all.deb ... Unpacking python3-prompt-toolkit (3.0.36-2) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../203-python3-pygments_2.14.0+dfsg-1_all.deb ... Unpacking python3-pygments (2.14.0+dfsg-1) ... Selecting previously unselected package python3-asttokens. Preparing to unpack .../204-python3-asttokens_2.2.1-1_all.deb ... Unpacking python3-asttokens (2.2.1-1) ... Selecting previously unselected package python3-executing. Preparing to unpack .../205-python3-executing_1.2.0-2_all.deb ... Unpacking python3-executing (1.2.0-2) ... Selecting previously unselected package python3-pure-eval. Preparing to unpack .../206-python3-pure-eval_0.2.2-1_all.deb ... Unpacking python3-pure-eval (0.2.2-1) ... Selecting previously unselected package python3-stack-data. Preparing to unpack .../207-python3-stack-data_0.6.2-3_all.deb ... Unpacking python3-stack-data (0.6.2-3) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../208-python3-setuptools_66.1.1-1_all.deb ... Unpacking python3-setuptools (66.1.1-1) ... Selecting previously unselected package python3-ipython. Preparing to unpack .../209-python3-ipython_8.5.0-4_all.deb ... Unpacking python3-ipython (8.5.0-4) ... Selecting previously unselected package ipython3. Preparing to unpack .../210-ipython3_8.5.0-4_all.deb ... Unpacking ipython3 (8.5.0-4) ... Selecting previously unselected package python3-toml. Preparing to unpack .../211-python3-toml_0.10.2-1_all.deb ... Unpacking python3-toml (0.10.2-1) ... Selecting previously unselected package python3-ipdb. Preparing to unpack .../212-python3-ipdb_0.13.9-1_all.deb ... Unpacking python3-ipdb (0.13.9-1) ... Selecting previously unselected package mafft. Preparing to unpack .../213-mafft_7.505-1_amd64.deb ... Unpacking mafft (7.505-1) ... Selecting previously unselected package raxml. Preparing to unpack .../214-raxml_8.2.12+dfsg-8+b2_amd64.deb ... Unpacking raxml (8.2.12+dfsg-8+b2) ... Selecting previously unselected package fasttree. Preparing to unpack .../215-fasttree_2.1.11-2_amd64.deb ... Unpacking fasttree (2.1.11-2) ... Selecting previously unselected package vcftools. Preparing to unpack .../216-vcftools_0.1.16-3+b1_amd64.deb ... Unpacking vcftools (0.1.16-3+b1) ... Selecting previously unselected package augur. Preparing to unpack .../217-augur_20.0.0-1_all.deb ... Unpacking augur (20.0.0-1) ... Setting up media-types (10.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-5) ... Setting up libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... No schema files found: doing nothing. Setting up libtirpc-common (1.3.3+ds-1) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up binutils-common:amd64 (2.40-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libdeflate0:amd64 (1.14-1) ... Setting up linux-libc-dev:amd64 (6.1.94-1) ... Setting up libctf-nobfd0:amd64 (2.40-2) ... Setting up libgsl27:amd64 (2.7.1+dfsg-5) ... Setting up libqhull-r8.0:amd64 (2020.2-5) ... Setting up libmetis5:amd64 (5.1.0.dfsg-7) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libjansson4:amd64 (2.14-2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up rpcsvc-proto (1.4.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libmpfr6:amd64 (4.2.0-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libmpc3:amd64 (1.3.1-1) ... Setting up libatomic1:amd64 (12.2.0-14) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libltdl7:amd64 (2.4.7-7~deb12u1) ... Setting up libfftw3-double3:amd64 (3.3.10-1) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libubsan1:amd64 (12.2.0-14) ... Setting up pigz (2.6-1) ... Setting up libcrypt-dev:amd64 (1:4.4.33-2) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libasan8:amd64 (12.2.0-14) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up fasttree (2.1.11-2) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libtsan2:amd64 (12.2.0-14) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbinutils:amd64 (2.40-2) ... Setting up libisl23:amd64 (0.25-1.1) ... Setting up libc-dev-bin (2.36-9+deb12u7) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.13-1~deb12u1) ... Setting up libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up libsuitesparseconfig5:amd64 (1:5.12.0+dfsg-2) ... Setting up libcc1-0:amd64 (12.2.0-14) ... Setting up liblsan0:amd64 (12.2.0-14) ... Setting up libitm1:amd64 (12.2.0-14) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up raxml (8.2.12+dfsg-8+b2) ... Setting up libctf0:amd64 (2.40-2) ... Setting up libamd2:amd64 (1:5.12.0+dfsg-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up cpp-12 (12.2.0-14) ... Setting up libxcb1:amd64 (1.15-1) ... 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 libcolamd2:amd64 (1:5.12.0+dfsg-2) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libcamd2:amd64 (1:5.12.0+dfsg-2) ... Setting up libgprofng0:amd64 (2.40-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Setting up libdsdp-5.8gf (5.8-10) ... Setting up libglpk40:amd64 (5.0-1) ... Setting up libgcc-12-dev:amd64 (12.2.0-14) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up libccolamd2:amd64 (1:5.12.0+dfsg-2) ... Setting up cpp (4:12.2.0-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libcholmod3:amd64 (1:5.12.0+dfsg-2) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up binutils-x86-64-linux-gnu (2.40-2) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up binutils (2.40-2) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ... Setting up libumfpack5:amd64 (1:5.12.0+dfsg-2) ... Setting up gcc-12 (12.2.0-14) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up mailcap (3.70+nmu1) ... Setting up vcftools (0.1.16-3+b1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up mime-support (3.66) ... Setting up mafft (7.505-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up gcc (4:12.2.0-3) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.36-9+deb12u7) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6+deb12u2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up libpython3.11:amd64 (3.11.2-6+deb12u2) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-isodate (0.6.1-1) ... Setting up python3-pil:amd64 (9.4.0-1.1+deb12u1) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-pygtrie (2.2-2) ... Setting up python3-packaging (23.0-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up python3-wcwidth (0.2.5+dfsg1-1.1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-jmespath (1.0.1-1) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-idna (3.3-1+deb12u1) ... Setting up python3-pickleshare (0.7.5-5) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up python3-pyrsistent:amd64 (0.18.1-1+b3) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up python3-traitlets (5.5.0-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-cffi-backend:amd64 (1.15.1-5+b1) ... Setting up python3-ptyprocess (0.7.0-5) ... Setting up g++-12 (12.2.0-14) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-prompt-toolkit (3.0.36-2) ... Setting up python3-distutils (3.11.2-3) ... Setting up python3-schedule (1.1.0-0.2) ... Setting up python3-pyfaidx (0.7.1-2) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-pure-eval (0.2.2-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-backcall (0.2.0-4) ... Setting up python3-parso (0.8.3-1) ... Setting up python3-cvxopt (1.3.0+dfsg-1+b1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3-asttokens (2.2.1-1) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-ply (3.11-5) ... Setting up python3-pyfastx (0.8.4-2) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-tk:amd64 (3.11.2-3) ... Setting up python3-networkx (2.8.8-1) ... Setting up python3-matplotlib-inline (0.1.6-2) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-xopen (1.7.0-2) ... Setting up python3-zstandard (0.20.0-3) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+deb12u1) ... Setting up python3-jsonschema (4.10.3-1) ... Setting up python3-executing (1.2.0-2) ... Setting up libpython3.11-dev:amd64 (3.11.2-6+deb12u2) ... Setting up python3-pexpect (4.8.0-4) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up g++ (4:12.2.0-3) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up python3-contourpy (1.0.7-1+b1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up python3-dendropy (4.5.2-1) ... Setting up python3-stack-data (0.6.2-3) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3-jedi (0.18.2-1) ... Setting up python3.11-dev (3.11.2-6+deb12u2) ... Setting up python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-ipython (8.5.0-4) ... Setting up python3-botocore (1.29.27+repack-1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up ipython3 (8.5.0-4) ... Setting up python3-ipdb (0.13.9-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-s3transfer (0.6.0-1) ... Setting up python3-boto3 (1.26.27+dfsg-1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-scipy (1.10.1-2) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Setting up python3-seaborn (0.12.2-1) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Setting up python3-treetime (0.9.4-1) ... Setting up seqmagick (0.8.4-3) ... Setting up python3-bcbio-gff (0.6.9-1) ... Setting up augur (20.0.0-1) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-y', 'install', 'augur'] 1m54.4s INFO: Running scripts post_install 1m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_install_exceptions'] 1m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_install_exceptions'] 1m54.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 1m57.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 1m57.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp5515yq17 to bookworm-next 1m57.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 1m57.5s INFO: Running scripts pre_distupgrade 1m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m57.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_exceptions'] 1m57.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_exceptions'] 1m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m57.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m57.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', 'update'] 1m59.2s DUMP: Get:1 http://security.debian.org bookworm-security InRelease [48.0 kB] Hit:2 http://deb.debian.org/debian bookworm InRelease Get:3 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [176 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [106 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [109 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [62.8 kB] Fetched 647 kB in 1s (1072 kB/s) Reading package lists... 1m59.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', 'update'] 1m59.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-yf', 'dist-upgrade'] 2m4.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc-dev-bin libc6 libc6-dev libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libssl3 libsystemd0 libudev1 linux-libc-dev openssl python3-numpy 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 16.8 MB of archives. After this operation, 1607 kB disk space will be freed. Get:1 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6-dev amd64 2.36-9+deb12u8 [1900 kB] Get:2 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:3 http://security.debian.org bookworm-security/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-dev-bin amd64 2.36-9+deb12u8 [46.3 kB] Get:5 http://security.debian.org bookworm-security/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB] Get:6 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 linux-libc-dev amd64 6.1.106-2 [2027 kB] Get:7 http://security.debian.org bookworm-security/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB] Get:8 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:11 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] Get:12 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl3 amd64 3.0.13-1~deb12u2 [2023 kB] Get:13 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 openssl amd64 3.0.13-1~deb12u2 [1421 kB] Get:14 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 python3-numpy amd64 1:1.24.2-1+deb12u1 [4960 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.8 MB in 0s (54.3 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 ... 49473 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.36-9+deb12u8_amd64.deb ... Unpacking libc6-dev:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Preparing to unpack .../libc-dev-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-dev-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Preparing to unpack .../linux-libc-dev_6.1.106-2_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.1.106-2) over (6.1.94-1) ... Preparing to unpack .../libc6_2.36-9+deb12u8_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc6:amd64 (2.36-9+deb12u8) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49473 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc-bin (2.36-9+deb12u8) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49473 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.29-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libsystemd0:amd64 (252.29-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49473 files and directories currently installed.) Preparing to unpack .../libudev1_252.29-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (252.29-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49473 files and directories currently installed.) Preparing to unpack .../0-libgssapi-krb5-2_1.20.1-2+deb12u2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../1-libkrb5-3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../2-libkrb5support0_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../4-libssl3_3.0.13-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../5-openssl_3.0.13-1~deb12u2_amd64.deb ... Unpacking openssl (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../6-python3-numpy_1%3a1.24.2-1+deb12u1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1+deb12u1) over (1:1.24.2-1) ... Setting up libssl3:amd64 (3.0.13-1~deb12u2) ... Setting up linux-libc-dev:amd64 (6.1.106-2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up python3-numpy (1:1.24.2-1+deb12u1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Setting up libc-dev-bin (2.36-9+deb12u8) ... Setting up openssl (3.0.13-1~deb12u2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Setting up libc6-dev:amd64 (2.36-9+deb12u8) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 2m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-yf', 'dist-upgrade'] 2m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m5.0s DUMP: 0bdc56bc83ae6d8c6f994c42aef2be7c - 2m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'show', '--no-all-versions', 'augur'] 2m5.2s DUMP: Package: augur Version: 20.0.0-1 Installed-Size: 829 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-bcbio-gff, python3-biopython, python3-cvxopt, python3-isodate, python3-jsonschema, python3-networkx, python3-numpy, python3-packaging, python3-pandas, python3-pyfastx, python3-scipy, python3-treetime (>= 0.9.4), python3-xopen (>= 1.7.0-1~), python3:any (>= 3.11~), python3-boto3, python3-dendropy, python3-matplotlib, python3-schedule, python3-seaborn, python3-zstandard, seqmagick, python3-ipdb, mafft, raxml, fasttree, vcftools Recommends: iqtree Description-en: pipeline components for real-time virus analysis The nextstrain project is an attempt to make flexible informatic pipelines and visualization tools to track ongoing pathogen evolution as sequence data emerges. The nextstrain project derives from nextflu, which was specific to influenza evolution. . nextstrain is comprised of three components: . * fauna: database and IO scripts for sequence and serological data * augur: informatic pipelines to conduct inferences from raw data * auspice: web app to visualize resulting inferences Description-md5: e2aaa44840d7b632d0e95700bc100196 Homepage: https://github.com/nextstrain/augur Section: science Priority: optional Filename: pool/main/a/augur/augur_20.0.0-1_all.deb Size: 187288 MD5sum: e3fe15acc709cc259fd3c65e7ae307be SHA256: af76cecb21ea71f78e4fbce03feac9056af9cfde8b4f9d20aeaf229fe38d000f 2m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'show', '--no-all-versions', 'augur'] 2m5.2s INFO: apt-cache knows about the following packages: augur 2m5.2s INFO: Running scripts pre_install 2m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_database-server'] 2m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_database-server'] 2m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_exceptions'] 2m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_exceptions'] 2m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_extras'] 2m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_extras'] 2m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture'] 2m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture'] 2m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy'] 2m5.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy'] 2m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy', 'augur'] 2m5.4s DUMP: augur: Installed: 20.0.0-1 Candidate: 20.0.0-1 Version table: *** 20.0.0-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 2m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy', 'augur'] 2m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-y', 'install', 'augur'] 2m5.7s DUMP: Reading package lists... Building dependency tree... Reading state information... augur is already the newest version (20.0.0-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-y', 'install', 'augur'] 2m5.7s INFO: Running scripts post_install 2m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_install_exceptions'] 2m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_install_exceptions'] 2m5.7s INFO: Running scripts post_distupgrade 2m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_exceptions'] 2m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_exceptions'] 2m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_zz_backports'] 2m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_distupgrade_zz_backports'] 2m5.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 2m8.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 2m8.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 2m10.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 2m10.8s INFO: Running scripts pre_install 2m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_database-server'] 2m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_database-server'] 2m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_exceptions'] 2m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_exceptions'] 2m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_extras'] 2m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_extras'] 2m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture'] 2m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture'] 2m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy'] 2m11.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy'] 2m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy', 'augur'] 2m11.0s DUMP: augur: Installed: 20.0.0-1 Candidate: 20.0.0-1 Version table: *** 20.0.0-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 2m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-cache', 'policy', 'augur'] 2m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-y', 'install', 'augur=20.0.0-1'] 2m11.4s DUMP: Reading package lists... Building dependency tree... Reading state information... augur is already the newest version (20.0.0-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', '-y', 'install', 'augur=20.0.0-1'] 2m11.4s INFO: Running scripts post_install 2m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_install_exceptions'] 2m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_install_exceptions'] 2m11.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 2m14.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 2m14.6s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 2m14.6s INFO: /bin converted to /usr/bin by /usr merge 2m14.6s INFO: /lib converted to /usr/lib by /usr merge 2m14.6s INFO: /lib/init converted to /usr/lib/init by /usr merge 2m14.6s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 2m14.6s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 2m14.6s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 2m14.6s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 2m14.6s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 2m14.6s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 2m14.6s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 2m14.6s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 2m14.6s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 2m14.6s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 2m14.6s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 2m14.6s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 2m14.6s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 2m14.6s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 2m14.6s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 2m14.6s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 2m14.6s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 2m14.6s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 2m14.6s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 2m14.6s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 2m14.6s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 2m14.6s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 2m14.6s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 2m14.6s INFO: /lib64 converted to /usr/lib64 by /usr merge 2m14.6s INFO: /sbin converted to /usr/sbin by /usr merge 2m17.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5515yq17', '-ac', '--ignore-obsolete'] 2m23.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5515yq17', '-ac', '--ignore-obsolete'] 2m23.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m23.5s DUMP: 0.15.6 2m23.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m23.5s INFO: Running adequate version 0.15.6 now. 2m23.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'augur'] 2m23.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'augur'] 2m23.6s INFO: Running scripts pre_remove 2m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_exceptions'] 2m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/pre_remove_exceptions'] 2m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m31.3s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed augur augur 20.0.0-1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed binutils binutils 2.40-2 install ok installed binutils-common:amd64 binutils-common 2.40-2 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.40-2 install ok installed blt blt 2.5.3+dfsg-4.1 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed ca-certificates ca-certificates 20230311 install ok installed coreutils coreutils 9.1-1 install ok installed cpp cpp 4:12.2.0-3 install ok installed cpp-12 cpp-12 12.2.0-14 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 fasttree fasttree 2.1.11-2 install ok installed findutils findutils 4.9.0-4 install ok installed fontconfig-config fontconfig-config 2.14.1-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-6 install ok installed fonts-lyx fonts-lyx 2.3.7-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-7 install ok installed g++ g++ 4:12.2.0-3 install ok installed g++-12 g++-12 12.2.0-14 install ok installed gcc gcc 4:12.2.0-3 install ok installed gcc-12 gcc-12 12.2.0-14 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 ipython3 ipython3 8.5.0-4 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libamd2:amd64 libamd2 1:5.12.0+dfsg-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libasan8:amd64 libasan8 12.2.0-14 install ok installed libatomic1:amd64 libatomic1 12.2.0-14 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 libbinutils:amd64 libbinutils 2.40-2 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libboost-dev:amd64 libboost-dev 1.74.0.3 install ok installed libboost1.74-dev:amd64 libboost1.74-dev 1.74.0+ds1-21 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 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+deb12u8 install ok installed libc-dev-bin libc-dev-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 install ok installed libc6-dev:amd64 libc6-dev 2.36-9+deb12u8 install ok installed libcamd2:amd64 libcamd2 1:5.12.0+dfsg-2 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 libcc1-0:amd64 libcc1-0 12.2.0-14 install ok installed libccolamd2:amd64 libccolamd2 1:5.12.0+dfsg-2 install ok installed libcholmod3:amd64 libcholmod3 1:5.12.0+dfsg-2 install ok installed libcolamd2:amd64 libcolamd2 1:5.12.0+dfsg-2 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.33-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.40-2 install ok installed libctf0:amd64 libctf0 2.40-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libdsdp-5.8gf libdsdp-5.8gf 5.8-10 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libexpat1-dev:amd64 libexpat1-dev 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfftw3-double3:amd64 libfftw3-double3 3.3.10-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.1-4 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.4-1 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5+deb12u3 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.2.0-14 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 libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-14 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u3 install ok installed libglpk40:amd64 libglpk40 5.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgomp1:amd64 libgomp1 12.2.0-14 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgprofng0:amd64 libgprofng0 2.40-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgsl27:amd64 libgsl27 2.7.1+dfsg-5 install ok installed libgslcblas0:amd64 libgslcblas0 2.7.1+dfsg-5 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 6.0.0+dfsg-3 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libicu72:amd64 libicu72 72.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libimagequant0:amd64 libimagequant0 2.17.0-1 install ok installed libisl23:amd64 libisl23 0.25-1.1 install ok installed libitm1:amd64 libitm1 12.2.0-14 install ok installed libjansson4:amd64 libjansson4 2.14-2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 5.3.0-4 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u2 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed liblsan0:amd64 liblsan0 12.2.0-14 install ok installed libltdl7:amd64 libltdl7 2.4.7-7~deb12u1 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 libmetis5:amd64 libmetis5 5.1.0.dfsg-7 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libmpc3:amd64 libmpc3 1.3.1-1 install ok installed libmpfr6:amd64 libmpfr6 4.2.0-1 install ok installed libncursesw6:amd64 libncursesw6 6.4-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.21+ds-4 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.21+ds-4 install ok installed libopenblas0:amd64 libopenblas0 0.3.21+ds-4 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.21+ds-4 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2 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 libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 install ok installed libpython3-all-dev:amd64 libpython3-all-dev 3.11.2-1+b1 install ok installed libpython3-dev:amd64 libpython3-dev 3.11.2-1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.2-1+b1 install ok installed libpython3.11:amd64 libpython3.11 3.11.2-6+deb12u2 install ok installed libpython3.11-dev:amd64 libpython3.11-dev 3.11.2-6+deb12u2 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.2-6+deb12u2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6+deb12u2 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-5 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-14 install ok installed libraqm0:amd64 libraqm0 0.7.0-4.1 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 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+deb12u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.1-2 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssl3:amd64 libssl3 3.0.13-1~deb12u2 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.2.0-14 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsuitesparseconfig5:amd64 libsuitesparseconfig5 1:5.12.0+dfsg-2 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2 install ok installed libtiff6:amd64 libtiff6 4.5.0-6+deb12u1 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2 install ok installed libtsan2:amd64 libtsan2 12.2.0-14 install ok installed libubsan1:amd64 libubsan1 12.2.0-14 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libumfpack5:amd64 libumfpack5 1:5.12.0+dfsg-2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2+deb12u1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.2.4-0.2+deb12u1 install ok installed libwebpmux3:amd64 libwebpmux3 1.2.4-0.2+deb12u1 install ok installed libx11-6:amd64 libx11-6 2:1.8.4-2+deb12u2 install ok installed libx11-data libx11-data 2:1.8.4-2+deb12u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3~deb12u1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxsimd-dev:amd64 libxsimd-dev 8.1.0-7 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed linux-libc-dev:amd64 linux-libc-dev 6.1.106-2 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mafft mafft 7.505-1 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 10.0.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed openssl openssl 3.0.13-1~deb12u2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7+deb12u1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed pigz pigz 2.6-1 install ok installed python-matplotlib-data python-matplotlib-data 3.6.3-1 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-all python3-all 3.11.2-1+b1 install ok installed python3-all-dev python3-all-dev 3.11.2-1+b1 install ok installed python3-appdirs python3-appdirs 1.4.4-3 install ok installed python3-asttokens python3-asttokens 2.2.1-1 install ok installed python3-attr python3-attr 22.2.0-1 install ok installed python3-backcall python3-backcall 0.2.0-4 install ok installed python3-bcbio-gff python3-bcbio-gff 0.6.9-1 install ok installed python3-beniget python3-beniget 0.4.1-3 install ok installed python3-biopython python3-biopython 1.80+dfsg-4+b1 install ok installed python3-boto3 python3-boto3 1.26.27+dfsg-1 install ok installed python3-botocore python3-botocore 1.29.27+repack-1 install ok installed python3-brotli python3-brotli 1.0.9-2+b6 install ok installed python3-certifi python3-certifi 2022.9.24-1 install ok installed python3-cffi-backend:amd64 python3-cffi-backend 1.15.1-5+b1 install ok installed python3-chardet python3-chardet 5.1.0+dfsg-2 install ok installed python3-charset-normalizer python3-charset-normalizer 3.0.1-2 install ok installed python3-contourpy python3-contourpy 1.0.7-1+b1 install ok installed python3-cvxopt python3-cvxopt 1.3.0+dfsg-1+b1 install ok installed python3-cycler python3-cycler 0.11.0-1 install ok installed python3-dateutil python3-dateutil 2.8.2-2 install ok installed python3-decorator python3-decorator 5.1.1-3 install ok installed python3-dendropy python3-dendropy 4.5.2-1 install ok installed python3-dev python3-dev 3.11.2-1+b1 install ok installed python3-distutils python3-distutils 3.11.2-3 install ok installed python3-executing python3-executing 1.2.0-2 install ok installed python3-fonttools python3-fonttools 4.38.0-1+b1 install ok installed python3-fs python3-fs 2.4.16-2 install ok installed python3-gast python3-gast 0.5.2-2 install ok installed python3-idna python3-idna 3.3-1+deb12u1 install ok installed python3-ipdb python3-ipdb 0.13.9-1 install ok installed python3-ipython python3-ipython 8.5.0-4 install ok installed python3-isodate python3-isodate 0.6.1-1 install ok installed python3-jedi python3-jedi 0.18.2-1 install ok installed python3-jmespath python3-jmespath 1.0.1-1 install ok installed python3-jsonschema python3-jsonschema 4.10.3-1 install ok installed python3-kiwisolver python3-kiwisolver 1.4.4-1+b1 install ok installed python3-lib2to3 python3-lib2to3 3.11.2-3 install ok installed python3-lxml:amd64 python3-lxml 4.9.2-1+b1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b2 install ok installed python3-matplotlib python3-matplotlib 3.6.3-1+b1 install ok installed python3-matplotlib-inline python3-matplotlib-inline 0.1.6-2 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3-mpmath python3-mpmath 1.2.1-2 install ok installed python3-networkx python3-networkx 2.8.8-1 install ok installed python3-numpy python3-numpy 1:1.24.2-1+deb12u1 install ok installed python3-packaging python3-packaging 23.0-1 install ok installed python3-pandas python3-pandas 1.5.3+dfsg-2 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 1.5.3+dfsg-2 install ok installed python3-parso python3-parso 0.8.3-1 install ok installed python3-pexpect python3-pexpect 4.8.0-4 install ok installed python3-pickleshare python3-pickleshare 0.7.5-5 install ok installed python3-pil:amd64 python3-pil 9.4.0-1.1+deb12u1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 9.4.0-1.1+deb12u1 install ok installed python3-pkg-resources python3-pkg-resources 66.1.1-1 install ok installed python3-ply python3-ply 3.11-5 install ok installed python3-prompt-toolkit python3-prompt-toolkit 3.0.36-2 install ok installed python3-ptyprocess python3-ptyprocess 0.7.0-5 install ok installed python3-pure-eval python3-pure-eval 0.2.2-1 install ok installed python3-pyfaidx python3-pyfaidx 0.7.1-2 install ok installed python3-pyfastx python3-pyfastx 0.8.4-2 install ok installed python3-pygments python3-pygments 2.14.0+dfsg-1 install ok installed python3-pygtrie python3-pygtrie 2.2-2 install ok installed python3-pyparsing python3-pyparsing 3.0.9-1 install ok installed python3-pyrsistent:amd64 python3-pyrsistent 0.18.1-1+b3 install ok installed python3-pythran python3-pythran 0.11.0+ds-7 install ok installed python3-renderpm:amd64 python3-renderpm 3.6.12-1+b1 install ok installed python3-reportlab python3-reportlab 3.6.12-1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.6.12-1+b1 install ok installed python3-requests python3-requests 2.28.1+dfsg-1 install ok installed python3-s3transfer python3-s3transfer 0.6.0-1 install ok installed python3-schedule python3-schedule 1.1.0-0.2 install ok installed python3-scipy python3-scipy 1.10.1-2 install ok installed python3-seaborn python3-seaborn 0.12.2-1 install ok installed python3-setuptools python3-setuptools 66.1.1-1 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3-stack-data python3-stack-data 0.6.2-3 install ok installed python3-sympy python3-sympy 1.11.1-1 install ok installed python3-tk:amd64 python3-tk 3.11.2-3 install ok installed python3-toml python3-toml 0.10.2-1 install ok installed python3-traitlets python3-traitlets 5.5.0-1 install ok installed python3-treetime python3-treetime 0.9.4-1 install ok installed python3-tz python3-tz 2022.7.1-4 install ok installed python3-ufolib2 python3-ufolib2 0.14.0+dfsg1-1 install ok installed python3-urllib3 python3-urllib3 1.26.12-1 install ok installed python3-wcwidth python3-wcwidth 0.2.5+dfsg1-1.1 install ok installed python3-xopen python3-xopen 1.7.0-2 install ok installed python3-zstandard python3-zstandard 0.20.0-3 install ok installed python3.11 python3.11 3.11.2-6+deb12u2 install ok installed python3.11-dev python3.11-dev 3.11.2-6+deb12u2 install ok installed python3.11-minimal python3.11-minimal 3.11.2-6+deb12u2 install ok installed raxml raxml 8.2.12+dfsg-8+b2 install ok installed readline-common readline-common 8.2-1.3 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-1 install ok installed seqmagick seqmagick 0.8.4-3 install ok installed sgml-base sgml-base 1.31 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-4.1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed unicode-data unicode-data 15.0.0-1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed vcftools vcftools 0.1.16-3+b1 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+6 install ok installed xml-core xml-core 0.18+nmu1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.2.13.dfsg-1 2m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-lyx', 'fonts-urw-base35', 'g++-', 'g++-12', 'gcc', 'gcc-12', 'ipython3', 'libamd2:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcamd2:amd64', 'libcc1-0:amd64', 'libccolamd2:amd64', 'libcholmod3:amd64', 'libcolamd2:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libdeflate0:amd64', 'libdsdp-5.8gf', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libltdl7:amd64', 'libmetis5:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libsuitesparseconfig5:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libumfpack5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev:amd64', 'mafft', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.36', 'pigz', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-asttokens', 'python3-attr', 'python3-backcall', 'python3-bcbio-gff', 'python3-beniget', 'python3-biopython', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-certifi', 'python3-cffi-backend:amd64', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cvxopt', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-dev', 'python3-distutils', 'python3-executing', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-idna', 'python3-ipdb', 'python3-ipython', 'python3-isodate', 'python3-jedi', 'python3-jmespath', 'python3-jsonschema', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-matplotlib-inline', 'python3-minimal', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-parso', 'python3-pexpect', 'python3-pickleshare', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-prompt-toolkit', 'python3-ptyprocess', 'python3-pure-eval', 'python3-pyfaidx', 'python3-pyfastx', 'python3-pygments', 'python3-pygtrie', 'python3-pyparsing', 'python3-pyrsistent:amd64', 'python3-pythran', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-requests', 'python3-s3transfer', 'python3-schedule', 'python3-scipy', 'python3-seaborn', 'python3-setuptools', 'python3-six', 'python3-stack-data', 'python3-sympy', 'python3-tk:amd64', 'python3-toml', 'python3-traitlets', 'python3-treetime', 'python3-tz', 'python3-ufolib2', 'python3-urllib3', 'python3-wcwidth', 'python3-xopen', 'python3-zstandard', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'raxml', 'readline-common', 'rpcsvc-proto', 'seqmagick', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'vcftools', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zlib1g-dev:amd64', 'augur'] 3m15.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: augur binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-12 fasttree fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 g++ g++-12 gcc gcc-12 ipython3 libamd2 libasan8 libatomic1 libbinutils libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcamd2 libcc1-0 libccolamd2 libcholmod3 libcolamd2 libcrypt-dev libctf-nobfd0 libctf0 libdeflate0 libdsdp-5.8gf libexpat1 libexpat1-dev libfftw3-double3 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libglpk40 libgomp1 libgprofng0 libgraphite2-3 libgsl27 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libltdl7 libmetis5 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libperl5.36 libpng16-16 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libstdc++-12-dev libsuitesparseconfig5 libtcl8.6 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libumfpack5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 linux-libc-dev mafft mailcap media-types mime-support openssl perl perl-modules-5.36 pigz python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-asttokens python3-attr python3-backcall python3-bcbio-gff python3-beniget python3-biopython python3-boto3 python3-botocore python3-brotli python3-certifi python3-cffi-backend python3-chardet python3-charset-normalizer python3-contourpy python3-cvxopt python3-cycler python3-dateutil python3-decorator python3-dendropy python3-dev python3-distutils python3-executing python3-fonttools python3-fs python3-gast python3-idna python3-ipdb python3-ipython python3-isodate python3-jedi python3-jmespath python3-jsonschema python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline python3-minimal python3-mpmath python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pickleshare python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pyfaidx python3-pyfastx python3-pygments python3-pygtrie python3-pyparsing python3-pyrsistent python3-pythran python3-renderpm python3-reportlab python3-reportlab-accel python3-requests python3-s3transfer python3-schedule python3-scipy python3-seaborn python3-setuptools python3-six python3-stack-data python3-sympy python3-tk python3-toml python3-traitlets python3-treetime python3-tz python3-ufolib2 python3-urllib3 python3-wcwidth python3-xopen python3-zstandard python3.11 python3.11-dev python3.11-minimal raxml readline-common rpcsvc-proto seqmagick sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core zlib1g-dev 0 upgraded, 0 newly installed, 247 to remove and 0 not upgraded. After this operation, 1157 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49473 files and directories currently installed.) Removing augur (20.0.0-1) ... Removing python3-seaborn (0.12.2-1) ... Removing python3-treetime (0.9.4-1) ... Removing g++ (4:12.2.0-3) ... Removing gcc (4:12.2.0-3) ... Removing seqmagick (0.8.4-3) ... Removing python3-bcbio-gff (0.6.9-1) ... Removing python3-biopython (1.80+dfsg-4+b1) ... Removing python3-reportlab (3.6.12-1) ... Removing python3-matplotlib (3.6.3-1+b1) ... Removing python3-pil.imagetk:amd64 (9.4.0-1.1+deb12u1) ... Removing python3-pil:amd64 (9.4.0-1.1+deb12u1) ... Removing python3-tk:amd64 (3.11.2-3) ... Removing blt (2.5.3+dfsg-4.1) ... Removing python3-boto3 (1.26.27+dfsg-1) ... Removing python3-s3transfer (0.6.0-1) ... Removing python3-botocore (1.29.27+repack-1) ... Removing python3-requests (2.28.1+dfsg-1) ... Removing python3-certifi (2022.9.24-1) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing cpp (4:12.2.0-3) ... Removing fasttree (2.1.11-2) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Removing libtk8.6:amd64 (8.6.13-2) ... Removing libxft2:amd64 (2.3.6-1) ... Removing libfontconfig1:amd64 (2.14.1-4) ... Removing fontconfig-config (2.14.1-4) ... Removing python-matplotlib-data (3.6.3-1) ... Removing fonts-dejavu-core (2.37-6) ... Removing fonts-lyx (2.3.7-1) ... Removing python3-renderpm:amd64 (3.6.12-1+b1) ... Removing fonts-urw-base35 (20200910-7) ... Removing python3-ipdb (0.13.9-1) ... Removing ipython3 (8.5.0-4) ... Removing python3-cvxopt (1.3.0+dfsg-1+b1) ... Removing libumfpack5:amd64 (1:5.12.0+dfsg-2) ... Removing libcholmod3:amd64 (1:5.12.0+dfsg-2) ... Removing python3-pandas (1.5.3+dfsg-2) ... Removing python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Removing python3-contourpy (1.0.7-1+b1) ... Removing libdsdp-5.8gf (5.8-10) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing xfonts-utils (1:7.7+6) ... Removing libraqm0:amd64 (0.7.0-4.1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing libcamd2:amd64 (1:5.12.0+dfsg-2) ... Removing libccolamd2:amd64 (1:5.12.0+dfsg-2) ... Removing libglpk40:amd64 (5.0-1) ... Removing libcolamd2:amd64 (1:5.12.0+dfsg-2) ... Removing libtiff6:amd64 (4.5.0-6+deb12u1) ... Removing libdeflate0:amd64 (1.14-1) ... Removing python3-ipython (8.5.0-4) ... Removing python3-setuptools (66.1.1-1) ... Removing python3-zstandard (0.20.0-3) ... Removing python3-prompt-toolkit (3.0.36-2) ... Removing python3-wcwidth (0.2.5+dfsg1-1.1) ... Removing libfftw3-double3:amd64 (3.3.10-1) ... Removing libfontenc1:amd64 (1:1.1.4-1) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing vcftools (0.1.16-3+b1) ... Removing mafft (7.505-1) ... Removing perl (5.36.0-7+deb12u1) ... Removing libperl5.36:amd64 (5.36.0-7+deb12u1) ... Removing libgdbm-compat4:amd64 (1.23-3) ... Removing libgdbm6:amd64 (1.23-3) ... Removing libopenblas-dev:amd64 (0.3.21+ds-4) ... Removing libopenblas0:amd64 (0.3.21+ds-4) ... Removing libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Removing libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... Removing libimagequant0:amd64 (2.17.0-1) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libgsl27:amd64 (2.7.1+dfsg-5) ... Removing libgslcblas0:amd64 (2.7.1+dfsg-5) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing libltdl7:amd64 (2.4.7-7~deb12u1) ... Removing libmetis5:amd64 (5.1.0.dfsg-7) ... Removing libopenjp2-7:amd64 (2.5.0-2) ... Removing libqhull-r8.0:amd64 (2020.2-5) ... Removing python3-pyfastx (0.8.4-2) ... Removing openssl (3.0.13-1~deb12u2) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2) ... Removing libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Removing libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Removing libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Removing python3-xopen (1.7.0-2) ... Removing pigz (2.6-1) ... Removing python3-stack-data (0.6.2-3) ... Removing python3-executing (1.2.0-2) ... Removing python3-asttokens (2.2.1-1) ... Removing python3-jsonschema (4.10.3-1) ... Removing python3-backcall (0.2.0-4) ... Removing python3-cffi-backend:amd64 (1.15.1-5+b1) ... Removing python3-chardet (5.1.0+dfsg-2) ... Removing python3-charset-normalizer (3.0.1-2) ... Removing python3-cycler (0.11.0-1) ... Removing python3-dateutil (2.8.2-2) ... Removing python3-dendropy (4.5.2-1) ... Removing python3-idna (3.3-1+deb12u1) ... Removing python3-isodate (0.6.1-1) ... Removing python3-jedi (0.18.2-1) ... Removing python3-jmespath (1.0.1-1) ... Removing python3-kiwisolver (1.4.4-1+b1) ... Removing python3-matplotlib-inline (0.1.6-2) ... Removing python3-networkx (2.8.8-1) ... Removing python3-packaging (23.0-1) ... Removing python3-parso (0.8.3-1) ... Removing python3-pexpect (4.8.0-4) ... Removing python3-pickleshare (0.7.5-5) ... Removing python3-pyfaidx (0.7.1-2) ... Removing python3-ptyprocess (0.7.0-5) ... Removing python3-pure-eval (0.2.2-1) ... Removing python3-pygments (2.14.0+dfsg-1) ... Removing python3-pygtrie (2.2-2) ... Removing python3-pyparsing (3.0.9-1) ... Removing python3-pyrsistent:amd64 (0.18.1-1+b3) ... Removing python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Removing python3-schedule (1.1.0-0.2) ... Removing python3-urllib3 (1.26.12-1) ... Removing python3-toml (0.10.2-1) ... Removing python3-traitlets (5.5.0-1) ... Removing raxml (8.2.12+dfsg-8+b2) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.18+nmu1) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libamd2:amd64 (1:5.12.0+dfsg-2) ... Removing libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libpng16-16:amd64 (1.6.39-2) ... Removing libsuitesparseconfig5:amd64 (1:5.12.0+dfsg-2) ... Removing libx11-data (2:1.8.4-2+deb12u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing python3-fonttools (4.38.0-1+b1) ... Removing python3-lxml:amd64 (4.9.2-1+b1) ... Removing libxslt1.1:amd64 (1.1.35-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Removing libicu72:amd64 (72.1-3) ... Removing python3-fs (2.4.16-2) ... Removing python3-appdirs (1.4.4-3) ... Removing python3-brotli (1.0.9-2+b6) ... Removing python3-lz4 (4.0.2+dfsg-1+b2) ... Removing python3-sympy (1.11.1-1) ... Removing python3-mpmath (1.2.1-2) ... Removing python3-six (1.16.0-4) ... Removing python3-tz (2022.7.1-4) ... Removing unicode-data (15.0.0-1) ... Removing python3-scipy (1.10.1-2) ... Removing python3-pythran (0.11.0+ds-7) ... Removing g++-12 (12.2.0-14) ... Removing libboost-dev:amd64 (1.74.0.3) ... Removing libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Removing libstdc++-12-dev:amd64 (12.2.0-14) ... Removing python3-numpy (1:1.24.2-1+deb12u1) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Removing python3-all-dev (3.11.2-1+b1) ... Removing python3-dev (3.11.2-1+b1) ... Removing python3.11-dev (3.11.2-6+deb12u2) ... Removing libpython3-all-dev:amd64 (3.11.2-1+b1) ... Removing libpython3-dev:amd64 (3.11.2-1+b1) ... Removing libpython3.11-dev:amd64 (3.11.2-6+deb12u2) ... Removing zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Removing libexpat1-dev:amd64 (2.5.0-1) ... Removing libc6-dev:amd64 (2.36-9+deb12u8) ... Removing libc-dev-bin (2.36-9+deb12u8) ... Removing libcrypt-dev:amd64 (1:4.4.33-2) ... Removing python3-ufolib2 (0.14.0+dfsg1-1) ... Removing python3-all (3.11.2-1+b1) ... Removing python3-distutils (3.11.2-3) ... Removing libpython3.11:amd64 (3.11.2-6+deb12u2) ... Removing libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... Removing libopenblas0-pthread:amd64 (0.3.21+ds-4) ... Removing libgfortran5:amd64 (12.2.0-14) ... Removing libnsl-dev:amd64 (1.3.0-2) ... Removing libtirpc-dev:amd64 (1.3.3+ds-1) ... Removing libjs-sphinxdoc (5.3.0-4) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing libxsimd-dev:amd64 (8.1.0-7) ... Removing linux-libc-dev:amd64 (6.1.106-2) ... Removing python3-attr (22.2.0-1) ... Removing python3-beniget (0.4.1-3) ... Removing python3-decorator (5.1.1-3) ... Removing python3-gast (0.5.2-2) ... Removing python3-lib2to3 (3.11.2-3) ... Removing python3-pkg-resources (66.1.1-1) ... Removing python3-ply (3.11-5) ... Removing rpcsvc-proto (1.4.3-1) ... Removing gcc-12 (12.2.0-14) ... Removing binutils (2.40-2) ... Removing binutils-x86-64-linux-gnu (2.40-2) ... Removing libgprofng0:amd64 (2.40-2) ... Removing libctf0:amd64 (2.40-2) ... Removing libbinutils:amd64 (2.40-2) ... Removing binutils-common:amd64 (2.40-2) ... Removing cpp-12 (12.2.0-14) ... Removing libgcc-12-dev:amd64 (12.2.0-14) ... Removing libasan8:amd64 (12.2.0-14) ... Removing libatomic1:amd64 (12.2.0-14) ... Removing libcc1-0:amd64 (12.2.0-14) ... Removing libctf-nobfd0:amd64 (2.40-2) ... Removing python3 (3.11.2-1+b1) ... Removing python3.11 (3.11.2-6+deb12u2) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.2-6+deb12u2) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libpython3-stdlib:amd64 (3.11.2-1+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libgomp1:amd64 (12.2.0-14) ... Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Removing libisl23:amd64 (0.25-1.1) ... Removing libitm1:amd64 (12.2.0-14) ... Removing libjansson4:amd64 (2.14-2) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Removing liblsan0:amd64 (12.2.0-14) ... Removing libmpc3:amd64 (1.3.1-1) ... Removing libmpfr6:amd64 (4.2.0-1) ... Removing libncursesw6:amd64 (6.4-4) ... Removing libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (12.2.0-14) ... Removing libreadline8:amd64 (8.2-1.3) ... Removing libsqlite3-0:amd64 (3.40.1-2) ... Removing libssl3:amd64 (3.0.13-1~deb12u2) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing libtsan2:amd64 (12.2.0-14) ... Removing libubsan1:amd64 (12.2.0-14) ... Removing media-types (10.0.0) ... Removing readline-common (8.2-1.3) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 3m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-lyx', 'fonts-urw-base35', 'g++-', 'g++-12', 'gcc', 'gcc-12', 'ipython3', 'libamd2:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcamd2:amd64', 'libcc1-0:amd64', 'libccolamd2:amd64', 'libcholmod3:amd64', 'libcolamd2:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libdeflate0:amd64', 'libdsdp-5.8gf', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libltdl7:amd64', 'libmetis5:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libsuitesparseconfig5:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libumfpack5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev:amd64', 'mafft', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.36', 'pigz', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-asttokens', 'python3-attr', 'python3-backcall', 'python3-bcbio-gff', 'python3-beniget', 'python3-biopython', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-certifi', 'python3-cffi-backend:amd64', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cvxopt', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-dev', 'python3-distutils', 'python3-executing', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-idna', 'python3-ipdb', 'python3-ipython', 'python3-isodate', 'python3-jedi', 'python3-jmespath', 'python3-jsonschema', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-matplotlib-inline', 'python3-minimal', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-parso', 'python3-pexpect', 'python3-pickleshare', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-prompt-toolkit', 'python3-ptyprocess', 'python3-pure-eval', 'python3-pyfaidx', 'python3-pyfastx', 'python3-pygments', 'python3-pygtrie', 'python3-pyparsing', 'python3-pyrsistent:amd64', 'python3-pythran', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-requests', 'python3-s3transfer', 'python3-schedule', 'python3-scipy', 'python3-seaborn', 'python3-setuptools', 'python3-six', 'python3-stack-data', 'python3-sympy', 'python3-tk:amd64', 'python3-toml', 'python3-traitlets', 'python3-treetime', 'python3-tz', 'python3-ufolib2', 'python3-urllib3', 'python3-wcwidth', 'python3-xopen', 'python3-zstandard', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'raxml', 'readline-common', 'rpcsvc-proto', 'seqmagick', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'vcftools', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zlib1g-dev:amd64', 'augur'] 3m15.1s INFO: Running scripts post_remove 3m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_remove_exceptions'] 3m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_remove_exceptions'] 3m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-12', 'gcc', 'gcc-12', 'ipython3', 'libamd2:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcamd2:amd64', 'libcc1-0:amd64', 'libccolamd2:amd64', 'libcholmod3:amd64', 'libcolamd2:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libdeflate0:amd64', 'libdsdp-5.8gf', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libltdl7:amd64', 'libmetis5:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libsuitesparseconfig5:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libumfpack5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev:amd64', 'mafft', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.36', 'pigz', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-asttokens', 'python3-attr', 'python3-backcall', 'python3-bcbio-gff', 'python3-beniget', 'python3-biopython', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-certifi', 'python3-cffi-backend:amd64', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cvxopt', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-dev', 'python3-distutils', 'python3-executing', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-idna', 'python3-ipdb', 'python3-ipython', 'python3-isodate', 'python3-jedi', 'python3-jmespath', 'python3-jsonschema', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-matplotlib-inline', 'python3-minimal', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-parso', 'python3-pexpect', 'python3-pickleshare', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-prompt-toolkit', 'python3-ptyprocess', 'python3-pure-eval', 'python3-pyfaidx', 'python3-pyfastx', 'python3-pygments', 'python3-pygtrie', 'python3-pyparsing', 'python3-pyrsistent:amd64', 'python3-pythran', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-requests', 'python3-s3transfer', 'python3-schedule', 'python3-scipy', 'python3-seaborn', 'python3-setuptools', 'python3-six', 'python3-stack-data', 'python3-sympy', 'python3-tk:amd64', 'python3-toml', 'python3-traitlets', 'python3-treetime', 'python3-tz', 'python3-ufolib2', 'python3-urllib3', 'python3-wcwidth', 'python3-xopen', 'python3-zstandard', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'raxml', 'readline-common', 'rpcsvc-proto', 'seqmagick', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'vcftools', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zlib1g-dev:amd64'] 3m15.9s DUMP: dpkg: warning: ignoring request to remove binutils which isn't installed (Reading database ... 6155 files and directories currently installed.) Purging configuration files for binutils-common:amd64 (2.40-2) ... dpkg: warning: ignoring request to remove binutils-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove blt which isn't installed Purging configuration files for ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove cpp which isn't installed dpkg: warning: ignoring request to remove cpp-12 which isn't installed dpkg: warning: ignoring request to remove fasttree which isn't installed Purging configuration files for fontconfig-config (2.14.1-4) ... Purging configuration files for fonts-dejavu-core (2.37-6) ... dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-7) ... dpkg: warning: ignoring request to remove g++ which isn't installed dpkg: warning: ignoring request to remove g++-12 which isn't installed dpkg: warning: ignoring request to remove gcc which isn't installed dpkg: warning: ignoring request to remove gcc-12 which isn't installed dpkg: warning: ignoring request to remove ipython3 which isn't installed dpkg: warning: ignoring request to remove libamd2 which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbinutils which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost1.74-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcamd2 which isn't installed dpkg: warning: ignoring request to remove libcc1-0 which isn't installed dpkg: warning: ignoring request to remove libccolamd2 which isn't installed dpkg: warning: ignoring request to remove libcholmod3 which isn't installed dpkg: warning: ignoring request to remove libcolamd2 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.33-2) ... dpkg: warning: ignoring request to remove libctf-nobfd0 which isn't installed dpkg: warning: ignoring request to remove libctf0 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdsdp-5.8gf which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libexpat1-dev which isn't installed dpkg: warning: ignoring request to remove libfftw3-double3 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-12-dev which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... dpkg: warning: ignoring request to remove libglpk40 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgprofng0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libgsl27 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libisl23 which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjansson4 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore 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 liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove libltdl7 which isn't installed dpkg: warning: ignoring request to remove libmetis5 which isn't installed dpkg: warning: ignoring request to remove libmpc3 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenblas-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas-pthread-dev 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 libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpython3-all-dev which isn't installed dpkg: warning: ignoring request to remove libpython3-dev which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.11 which isn't installed dpkg: warning: ignoring request to remove libpython3.11-dev which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed dpkg: warning: ignoring request to remove libstdc++-12-dev which isn't installed dpkg: warning: ignoring request to remove libsuitesparseconfig5 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libumfpack5 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxsimd-dev which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove mafft which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for media-types (10.0.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed Purging configuration files for openssl (3.0.13-1~deb12u2) ... Purging configuration files for perl (5.36.0-7+deb12u1) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed dpkg: warning: ignoring request to remove pigz which isn't installed Purging configuration files for python-matplotlib-data (3.6.3-1) ... Purging configuration files for python3 (3.11.2-1+b1) ... dpkg: warning: ignoring request to remove python3-all which isn't installed dpkg: warning: ignoring request to remove python3-all-dev which isn't installed dpkg: warning: ignoring request to remove python3-appdirs which isn't installed dpkg: warning: ignoring request to remove python3-asttokens which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-backcall which isn't installed dpkg: warning: ignoring request to remove python3-bcbio-gff which isn't installed dpkg: warning: ignoring request to remove python3-beniget which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-boto3 which isn't installed dpkg: warning: ignoring request to remove python3-botocore which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-cffi-backend which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cvxopt which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-dendropy which isn't installed dpkg: warning: ignoring request to remove python3-dev which isn't installed dpkg: warning: ignoring request to remove python3-distutils which isn't installed dpkg: warning: ignoring request to remove python3-executing which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-gast which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-ipdb which isn't installed dpkg: warning: ignoring request to remove python3-ipython which isn't installed dpkg: warning: ignoring request to remove python3-isodate which isn't installed dpkg: warning: ignoring request to remove python3-jedi which isn't installed dpkg: warning: ignoring request to remove python3-jmespath which isn't installed Purging configuration files for python3-jsonschema (4.10.3-1) ... dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib-inline which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pandas which isn't installed dpkg: warning: ignoring request to remove python3-pandas-lib which isn't installed dpkg: warning: ignoring request to remove python3-parso which isn't installed dpkg: warning: ignoring request to remove python3-pexpect which isn't installed dpkg: warning: ignoring request to remove python3-pickleshare which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-ply which isn't installed dpkg: warning: ignoring request to remove python3-prompt-toolkit which isn't installed dpkg: warning: ignoring request to remove python3-ptyprocess which isn't installed dpkg: warning: ignoring request to remove python3-pure-eval which isn't installed dpkg: warning: ignoring request to remove python3-pyfaidx which isn't installed dpkg: warning: ignoring request to remove python3-pyfastx which isn't installed dpkg: warning: ignoring request to remove python3-pygments which isn't installed dpkg: warning: ignoring request to remove python3-pygtrie which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pyrsistent which isn't installed dpkg: warning: ignoring request to remove python3-pythran which isn't installed dpkg: warning: ignoring request to remove python3-renderpm which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-s3transfer which isn't installed dpkg: warning: ignoring request to remove python3-schedule which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-seaborn which isn't installed dpkg: warning: ignoring request to remove python3-setuptools which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-stack-data which isn't installed Purging configuration files for python3-sympy (1.11.1-1) ... dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-toml which isn't installed dpkg: warning: ignoring request to remove python3-traitlets which isn't installed dpkg: warning: ignoring request to remove python3-treetime which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3-wcwidth which isn't installed dpkg: warning: ignoring request to remove python3-xopen which isn't installed dpkg: warning: ignoring request to remove python3-zstandard which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed dpkg: warning: ignoring request to remove python3.11-dev which isn't installed Purging configuration files for python3.11-minimal (3.11.2-6+deb12u2) ... dpkg: warning: ignoring request to remove raxml which isn't installed Purging configuration files for readline-common (8.2-1.3) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove seqmagick which isn't installed Purging configuration files for sgml-base (1.31) ... dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove unicode-data which isn't installed dpkg: warning: ignoring request to remove vcftools which isn't installed Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+6) ... Purging configuration files for xml-core (0.18+nmu1) ... dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 3m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-12', 'gcc', 'gcc-12', 'ipython3', 'libamd2:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcamd2:amd64', 'libcc1-0:amd64', 'libccolamd2:amd64', 'libcholmod3:amd64', 'libcolamd2:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libdeflate0:amd64', 'libdsdp-5.8gf', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfftw3-double3:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libltdl7:amd64', 'libmetis5:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libsuitesparseconfig5:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libumfpack5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev:amd64', 'mafft', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.36', 'pigz', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-asttokens', 'python3-attr', 'python3-backcall', 'python3-bcbio-gff', 'python3-beniget', 'python3-biopython', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-certifi', 'python3-cffi-backend:amd64', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cvxopt', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-dev', 'python3-distutils', 'python3-executing', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-idna', 'python3-ipdb', 'python3-ipython', 'python3-isodate', 'python3-jedi', 'python3-jmespath', 'python3-jsonschema', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-matplotlib-inline', 'python3-minimal', 'python3-mpmath', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-parso', 'python3-pexpect', 'python3-pickleshare', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-prompt-toolkit', 'python3-ptyprocess', 'python3-pure-eval', 'python3-pyfaidx', 'python3-pyfastx', 'python3-pygments', 'python3-pygtrie', 'python3-pyparsing', 'python3-pyrsistent:amd64', 'python3-pythran', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-requests', 'python3-s3transfer', 'python3-schedule', 'python3-scipy', 'python3-seaborn', 'python3-setuptools', 'python3-six', 'python3-stack-data', 'python3-sympy', 'python3-tk:amd64', 'python3-toml', 'python3-traitlets', 'python3-treetime', 'python3-tz', 'python3-ufolib2', 'python3-urllib3', 'python3-wcwidth', 'python3-xopen', 'python3-zstandard', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'raxml', 'readline-common', 'rpcsvc-proto', 'seqmagick', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'vcftools', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zlib1g-dev:amd64'] 3m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg', '--purge', 'augur'] 3m15.9s DUMP: dpkg: warning: ignoring request to remove augur which isn't installed 3m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg', '--purge', 'augur'] 3m15.9s INFO: Running scripts post_purge 3m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_purge_exceptions'] 3m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_purge_exceptions'] 3m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg', '--purge', '--pending'] 3m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg', '--purge', '--pending'] 3m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg', '--remove', '--pending'] 3m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg', '--remove', '--pending'] 3m15.9s INFO: Running scripts post_test 3m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_test_exceptions'] 3m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'tmp/scripts/post_test_exceptions'] 3m15.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 3m16.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 3m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg-divert', '--list'] 3m16.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 3m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'dpkg-divert', '--list'] 3m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', 'clean'] 3m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5515yq17', 'apt-get', 'clean'] 3m16.3s DEBUG: Recording chroot state 3m17.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/shm'] 3m17.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/shm'] 3m17.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/console'] 3m17.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/console'] 3m17.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/ptmx'] 3m17.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/ptmx'] 3m17.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/pts'] 3m17.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/dev/pts'] 3m17.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/proc'] 3m17.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5515yq17/proc'] 3m17.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 3m17.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5515yq17'] 3m17.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp5515yq17 3m17.6s INFO: PASS: Upgrading between Debian distributions. 3m17.6s INFO: PASS: All tests. 3m17.6s INFO: piuparts run ends. ret=0 End: 2024-08-22 20:18:11 GMT