Start: 2024-03-19 11:33:00 GMT [bullseye] Package: python3-biom-format Source: python-biom-format (2.1.10-1) Version: 2.1.10-1+b1 Installed-Size: 737 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: biom-format-tools (<< 2.1.7+dfsg-3) Provides: biom-format-tools Depends: python3-h5py, python3-numpy (>= 1:1.16.0~rc1), python3-numpy-abi9, cython3, python3 (<< 3.10), python3 (>= 3.9~), python3-click, python3-future, python3-h5py-serial, python3-pandas, python3-scipy, python3-six (>= 1.10.0), python3:any, libc6 (>= 2.4) Suggests: python-biom-format-doc Breaks: biom-format-tools (<< 2.1.7+dfsg-3) Description: Biological Observation Matrix (BIOM) format (Python 3) Homepage: https://biom-format.org/ Description-md5: a8e1165fb97cc05bc8c23295225341cd Section: python Priority: optional Filename: pool/main/p/python-biom-format/python3-biom-format_2.1.10-1+b1_amd64.deb Size: 131572 MD5sum: 03cee6a83ffa0564bd0cb56e1b608638 SHA256: fd922d8dd525a5ffd6889c206da7390af4ed478eb42dcc74610b4219a2891242 [bullseye-next] Package: python3-biom-format Source: python-biom-format (2.1.10-1) Version: 2.1.10-1+b1 Installed-Size: 737 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: biom-format-tools (<< 2.1.7+dfsg-3) Provides: biom-format-tools Depends: python3-h5py, python3-numpy (>= 1:1.16.0~rc1), python3-numpy-abi9, cython3, python3 (<< 3.10), python3 (>= 3.9~), python3-click, python3-future, python3-h5py-serial, python3-pandas, python3-scipy, python3-six (>= 1.10.0), python3:any, libc6 (>= 2.4) Suggests: python-biom-format-doc Breaks: biom-format-tools (<< 2.1.7+dfsg-3) Description: Biological Observation Matrix (BIOM) format (Python 3) Homepage: https://biom-format.org/ Description-md5: a8e1165fb97cc05bc8c23295225341cd Section: python Priority: optional Filename: pool/main/p/python-biom-format/python3-biom-format_2.1.10-1+b1_amd64.deb Size: 131572 MD5sum: 03cee6a83ffa0564bd0cb56e1b608638 SHA256: fd922d8dd525a5ffd6889c206da7390af4ed478eb42dcc74610b4219a2891242 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/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt python3-biom-format=2.1.10-1+b1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --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/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt python3-biom-format=2.1.10-1+b1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpniwlb4rx 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpniwlb4rx 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpniwlb4rx/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s 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' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m4.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m4.1s INFO: Running scripts is_testable 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_test_root_password'] 0m4.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_test_root_password'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'show', '--no-all-versions', 'python3-biom-format'] 0m4.4s DUMP: Package: python3-biom-format Source: python-biom-format (2.1.10-1) Version: 2.1.10-1+b1 Installed-Size: 737 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: biom-format-tools (<< 2.1.7+dfsg-3) Provides: biom-format-tools Depends: python3-h5py, python3-numpy (>= 1:1.16.0~rc1), python3-numpy-abi9, cython3, python3 (<< 3.10), python3 (>= 3.9~), python3-click, python3-future, python3-h5py-serial, python3-pandas, python3-scipy, python3-six (>= 1.10.0), python3:any, libc6 (>= 2.4) Suggests: python-biom-format-doc Breaks: biom-format-tools (<< 2.1.7+dfsg-3) Description-en: Biological Observation Matrix (BIOM) format (Python 3) The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project. . The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. . This package provides the BIOM format library for the Python 3 interpreter. Description-md5: a8e1165fb97cc05bc8c23295225341cd Homepage: https://biom-format.org/ Section: python Priority: optional Filename: pool/main/p/python-biom-format/python3-biom-format_2.1.10-1+b1_amd64.deb Size: 131572 MD5sum: 03cee6a83ffa0564bd0cb56e1b608638 SHA256: fd922d8dd525a5ffd6889c206da7390af4ed478eb42dcc74610b4219a2891242 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'show', '--no-all-versions', 'python3-biom-format'] 0m4.4s INFO: apt-cache knows about the following packages: python3-biom-format 0m4.4s INFO: Running scripts pre_install 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy'] 0m4.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy', 'python3-biom-format'] 0m4.6s DUMP: python3-biom-format: Installed: (none) Candidate: 2.1.10-1+b1 Version table: 2.1.10-1+b1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy', 'python3-biom-format'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-y', 'install', 'python3-biom-format'] 0m24.4s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: cython3 libaec0 libblas3 libexpat1 libgfortran5 libhdf5-103-1 libhdf5-hl-100 liblapack3 liblbfgsb0 liblzf1 libmpdec3 libncursesw6 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 libsqlite3-0 libsz2 media-types python3 python3-click python3-colorama python3-dateutil python3-decorator python3-future python3-h5py python3-h5py-serial python3-lib2to3 python3-minimal python3-numpy python3-pandas python3-pandas-lib python3-pkg-resources python3-scipy python3-six python3-tz python3.9 python3.9-minimal readline-common Suggested packages: cython-doc python3-doc python3-tk python3-venv python-biom-format-doc python-future-doc python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-numpy-dbg python3-pytest python-pandas-doc python3-statsmodels python3-setuptools python-scipy-doc python3.9-venv python3.9-doc binutils binfmt-support readline-doc Recommended packages: python3-dev gcc libgpm2 ca-certificates python3-matplotlib python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlwt python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-numba g++ | c++-compiler python3-pil The following NEW packages will be installed: cython3 libaec0 libblas3 libexpat1 libgfortran5 libhdf5-103-1 libhdf5-hl-100 liblapack3 liblbfgsb0 liblzf1 libmpdec3 libncursesw6 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 libsqlite3-0 libsz2 media-types python3 python3-biom-format python3-click python3-colorama python3-dateutil python3-decorator python3-future python3-h5py python3-h5py-serial python3-lib2to3 python3-minimal python3-numpy python3-pandas python3-pandas-lib python3-pkg-resources python3-scipy python3-six python3-tz python3.9 python3.9-minimal readline-common 0 upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 34.3 MB of archives. After this operation, 150 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 cython3 amd64 0.29.21-3+b1 [1312 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get:21 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-100 amd64 1.10.6+repack-4+deb11u1 [81.8 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 liblbfgsb0 amd64 3.0+dfsg.3-9 [28.5 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 liblzf1 amd64 3.6-3 [10.2 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 python3-h5py-serial amd64 2.10.0-9+b2 [655 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 python3-h5py all 2.10.0-9 [11.4 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 python3-colorama all 0.4.4-1 [28.5 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 python3-click all 7.1.2-1 [75.7 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 python3-future all 0.18.2-5 [349 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 python3-pandas-lib amd64 1.1.5+dfsg-2 [3287 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 python3-scipy amd64 1.6.0-2 [12.3 MB] Get:41 http://deb.debian.org/debian bullseye/main amd64 python3-biom-format amd64 2.1.10-1+b1 [132 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.3 MB in 0s (95.1 MB/s) Selecting previously unselected package libpython3.9-minimal:amd64. 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Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... 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 libreadline8:amd64 (8.1-1) ... Setting up libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-9) ... Setting up libhdf5-hl-100:amd64 (1.10.6+repack-4+deb11u1) ... Setting up python3.9 (3.9.2-1) ... Setting up python3 (3.9.2-3) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-decorator (4.4.2-2) ... Setting up cython3 (0.29.21-3+b1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-colorama (0.4.4-1) ... Setting up python3-click (7.1.2-1) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-future (0.18.2-5) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-scipy (1.6.0-2) ... Setting up python3-pandas-lib:amd64 (1.1.5+dfsg-2) ... Setting up python3-h5py-serial (2.10.0-9+b2) ... Setting up python3-pandas (1.1.5+dfsg-2) ... Setting up python3-h5py (2.10.0-9) ... Setting up python3-biom-format (2.1.10-1+b1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-y', 'install', 'python3-biom-format'] 0m24.4s INFO: Running scripts post_install 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_install_exceptions'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_install_exceptions'] 0m24.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m25.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m25.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpniwlb4rx to bullseye-next 0m25.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 0m25.5s INFO: Running scripts pre_distupgrade 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', 'update'] 0m27.1s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Get:2 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:3 http://security.debian.org bullseye-security InRelease [48.4 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:5 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:6 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Get:7 http://security.debian.org bullseye-security/main amd64 Packages [269 kB] Get:8 http://security.debian.org bullseye-security/main Translation-en [174 kB] Get:9 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages [18.9 kB] Get:10 http://deb.debian.org/debian bullseye-proposed-updates/main Translation-en [13.8 kB] Fetched 652 kB in 1s (875 kB/s) Reading package lists... 0m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', 'update'] 0m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-yf', 'dist-upgrade'] 0m27.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-yf', 'dist-upgrade'] 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m28.1s DUMP: 1c19f1dfe717069730438cc10cd7db43 - 0m28.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m28.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'show', '--no-all-versions', 'python3-biom-format'] 0m28.3s DUMP: Package: python3-biom-format Source: python-biom-format (2.1.10-1) Version: 2.1.10-1+b1 Installed-Size: 737 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: biom-format-tools (<< 2.1.7+dfsg-3) Provides: biom-format-tools Depends: python3-h5py, python3-numpy (>= 1:1.16.0~rc1), python3-numpy-abi9, cython3, python3 (<< 3.10), python3 (>= 3.9~), python3-click, python3-future, python3-h5py-serial, python3-pandas, python3-scipy, python3-six (>= 1.10.0), python3:any, libc6 (>= 2.4) Suggests: python-biom-format-doc Breaks: biom-format-tools (<< 2.1.7+dfsg-3) Description-en: Biological Observation Matrix (BIOM) format (Python 3) The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project. . The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. . This package provides the BIOM format library for the Python 3 interpreter. Description-md5: a8e1165fb97cc05bc8c23295225341cd Homepage: https://biom-format.org/ Section: python Priority: optional Filename: pool/main/p/python-biom-format/python3-biom-format_2.1.10-1+b1_amd64.deb Size: 131572 MD5sum: 03cee6a83ffa0564bd0cb56e1b608638 SHA256: fd922d8dd525a5ffd6889c206da7390af4ed478eb42dcc74610b4219a2891242 0m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'show', '--no-all-versions', 'python3-biom-format'] 0m28.3s INFO: apt-cache knows about the following packages: python3-biom-format 0m28.3s INFO: Running scripts pre_install 0m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_database-server'] 0m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_database-server'] 0m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_exceptions'] 0m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_exceptions'] 0m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_extras'] 0m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_extras'] 0m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy'] 0m28.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy', 'python3-biom-format'] 0m28.5s DUMP: python3-biom-format: Installed: 2.1.10-1+b1 Candidate: 2.1.10-1+b1 Version table: *** 2.1.10-1+b1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy', 'python3-biom-format'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-y', 'install', 'python3-biom-format'] 0m28.9s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-biom-format is already the newest version (2.1.10-1+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-y', 'install', 'python3-biom-format'] 0m28.9s INFO: Running scripts post_install 0m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_install_exceptions'] 0m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_install_exceptions'] 0m28.9s INFO: Running scripts post_distupgrade 0m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_exceptions'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_exceptions'] 0m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_zz_backports'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_distupgrade_zz_backports'] 0m29.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m29.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m29.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m30.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m30.8s INFO: Running scripts pre_install 0m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_database-server'] 0m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_database-server'] 0m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_exceptions'] 0m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_exceptions'] 0m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_extras'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_extras'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy'] 0m30.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy', 'python3-biom-format'] 0m31.0s DUMP: python3-biom-format: Installed: 2.1.10-1+b1 Candidate: 2.1.10-1+b1 Version table: *** 2.1.10-1+b1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-cache', 'policy', 'python3-biom-format'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-y', 'install', 'python3-biom-format=2.1.10-1+b1'] 0m31.3s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-biom-format is already the newest version (2.1.10-1+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', '-y', 'install', 'python3-biom-format=2.1.10-1+b1'] 0m31.3s INFO: Running scripts post_install 0m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_install_exceptions'] 0m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_install_exceptions'] 0m31.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m32.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m32.4s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m32.4s INFO: /bin converted to /usr/bin by /usr merge 0m32.5s INFO: /lib converted to /usr/lib by /usr merge 0m32.5s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m32.5s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m32.5s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m32.5s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m32.5s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m32.5s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m32.5s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m32.5s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m32.5s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m32.5s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m32.5s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m32.5s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m32.5s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m32.5s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m32.5s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m32.5s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m32.5s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m32.5s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m32.5s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m32.5s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m32.5s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m32.5s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m32.5s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m32.5s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m32.5s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m32.5s INFO: /sbin converted to /usr/sbin by /usr merge 0m33.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', '-ac', '--ignore-obsolete'] 0m35.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', '-ac', '--ignore-obsolete'] 0m35.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m35.5s DUMP: 0.15.6 0m35.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m35.5s INFO: Running adequate version 0.15.6 now. 0m35.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'python3-biom-format'] 0m35.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'python3-biom-format'] 0m35.6s INFO: Running scripts pre_remove 0m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m37.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m37.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_exceptions'] 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/pre_remove_exceptions'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.9s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed cython3 cython3 0.29.21-3+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libaec0:amd64 libaec0 1.0.4-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblas3:amd64 libblas3 3.9.0-3+deb11u1 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libexpat1:amd64 libexpat1 2.2.10-2+deb11u5 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgfortran5:amd64 libgfortran5 10.2.1-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.6+repack-4+deb11u1 install ok installed libhdf5-hl-100:amd64 libhdf5-hl-100 1.10.6+repack-4+deb11u1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblapack3:amd64 liblapack3 3.9.0-3+deb11u1 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.3-9 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzf1:amd64 liblzf1 3.6-3 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-2+deb11u2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.2-3 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libquadmath0:amd64 libquadmath0 10.2.1-6 install ok installed libreadline8:amd64 libreadline8 8.1-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.1-3 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libsz2:amd64 libsz2 1.0.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed media-types media-types 4.0.0 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed python3 python3 3.9.2-3 install ok installed python3-biom-format python3-biom-format 2.1.10-1+b1 install ok installed python3-click python3-click 7.1.2-1 install ok installed python3-colorama python3-colorama 0.4.4-1 install ok installed python3-dateutil python3-dateutil 2.8.1-6 install ok installed python3-decorator python3-decorator 4.4.2-2 install ok installed python3-future python3-future 0.18.2-5 install ok installed python3-h5py python3-h5py 2.10.0-9 install ok installed python3-h5py-serial python3-h5py-serial 2.10.0-9+b2 install ok installed python3-lib2to3 python3-lib2to3 3.9.2-1 install ok installed python3-minimal python3-minimal 3.9.2-3 install ok installed python3-numpy python3-numpy 1:1.19.5-1 install ok installed python3-pandas python3-pandas 1.1.5+dfsg-2 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 1.1.5+dfsg-2 install ok installed python3-pkg-resources python3-pkg-resources 52.0.0-4 install ok installed python3-scipy python3-scipy 1.6.0-2 install ok installed python3-six python3-six 1.16.0-2 install ok installed python3-tz python3-tz 2021.1-1 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.1-1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', 'remove', 'cython3', 'libaec0:amd64', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libhdf5-103-1:amd64', 'libhdf5-hl-100:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblzf1:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libsz2:amd64', 'media-types', 'python3', 'python3-click', 'python3-colorama', 'python3-dateutil', 'python3-decorator', 'python3-future', 'python3-h5py', 'python3-h5py-serial', 'python3-lib2to3', 'python3-minimal', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-scipy', 'python3-six', 'python3-tz', 'python3.9', 'python3.9-minimal', 'readline-common', 'python3-biom-format'] 0m41.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: cython3 libaec0 libblas3 libexpat1 libgfortran5 libhdf5-103-1 libhdf5-hl-100 liblapack3 liblbfgsb0 liblzf1 libmpdec3 libncursesw6 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 libsqlite3-0 libsz2 media-types python3 python3-biom-format python3-click python3-colorama python3-dateutil python3-decorator python3-future python3-h5py python3-h5py-serial python3-lib2to3 python3-minimal python3-numpy python3-pandas python3-pandas-lib python3-pkg-resources python3-scipy python3-six python3-tz python3.9 python3.9-minimal readline-common 0 upgraded, 0 newly installed, 41 to remove and 0 not upgraded. After this operation, 150 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 ... 11290 files and directories currently installed.) Removing python3-biom-format (2.1.10-1+b1) ... Removing cython3 (0.29.21-3+b1) ... Removing python3-h5py (2.10.0-9) ... Removing python3-h5py-serial (2.10.0-9+b2) ... Removing libhdf5-hl-100:amd64 (1.10.6+repack-4+deb11u1) ... Removing libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Removing libsz2:amd64 (1.0.4-1) ... Removing libaec0:amd64 (1.0.4-1) ... Removing python3-scipy (1.6.0-2) ... Removing python3-pandas (1.1.5+dfsg-2) ... Removing python3-pandas-lib:amd64 (1.1.5+dfsg-2) ... Removing python3-numpy (1:1.19.5-1) ... Removing liblbfgsb0:amd64 (3.0+dfsg.3-9) ... Removing liblapack3:amd64 (3.9.0-3+deb11u1) ... Removing libblas3:amd64 (3.9.0-3+deb11u1) ... Removing python3-dateutil (2.8.1-6) ... Removing python3-six (1.16.0-2) ... Removing python3-pkg-resources (52.0.0-4) ... Removing libgfortran5:amd64 (10.2.1-6) ... Removing liblzf1:amd64 (3.6-3) ... Removing libquadmath0:amd64 (10.2.1-6) ... Removing python3-click (7.1.2-1) ... Removing python3-colorama (0.4.4-1) ... Removing python3-decorator (4.4.2-2) ... Removing python3-future (0.18.2-5) ... Removing python3-lib2to3 (3.9.2-1) ... Removing python3-tz (2021.1-1) ... Removing python3 (3.9.2-3) ... Removing python3-minimal (3.9.2-3) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing libexpat1:amd64 (2.2.10-2+deb11u5) ... Removing libpython3-stdlib:amd64 (3.9.2-3) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-1) ... Removing libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.1-1) ... Removing libsqlite3-0:amd64 (3.34.1-3) ... Removing media-types (4.0.0) ... Removing readline-common (8.1-1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', 'remove', 'cython3', 'libaec0:amd64', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libhdf5-103-1:amd64', 'libhdf5-hl-100:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblzf1:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libsz2:amd64', 'media-types', 'python3', 'python3-click', 'python3-colorama', 'python3-dateutil', 'python3-decorator', 'python3-future', 'python3-h5py', 'python3-h5py-serial', 'python3-lib2to3', 'python3-minimal', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-scipy', 'python3-six', 'python3-tz', 'python3.9', 'python3.9-minimal', 'readline-common', 'python3-biom-format'] 0m41.4s INFO: Running scripts post_remove 0m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_remove_exceptions'] 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_remove_exceptions'] 0m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg', '--purge', 'cython3', 'libaec0:amd64', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libhdf5-103-1:amd64', 'libhdf5-hl-100:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblzf1:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libsz2:amd64', 'media-types', 'python3', 'python3-click', 'python3-colorama', 'python3-dateutil', 'python3-decorator', 'python3-future', 'python3-h5py', 'python3-h5py-serial', 'python3-lib2to3', 'python3-minimal', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-scipy', 'python3-six', 'python3-tz', 'python3.9', 'python3.9-minimal', 'readline-common'] 0m41.5s DUMP: dpkg: warning: ignoring request to remove cython3 which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libhdf5-103-1 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-100 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 liblzf1 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed (Reading database ... 6677 files and directories currently installed.) Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 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 libsz2 which isn't installed Purging configuration files for media-types (4.0.0) ... Purging configuration files for python3 (3.9.2-3) ... dpkg: warning: ignoring request to remove python3-click which isn't installed dpkg: warning: ignoring request to remove python3-colorama 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-future which isn't installed dpkg: warning: ignoring request to remove python3-h5py which isn't installed dpkg: warning: ignoring request to remove python3-h5py-serial which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy 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-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.1-1) ... 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg', '--purge', 'cython3', 'libaec0:amd64', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libhdf5-103-1:amd64', 'libhdf5-hl-100:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblzf1:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libsz2:amd64', 'media-types', 'python3', 'python3-click', 'python3-colorama', 'python3-dateutil', 'python3-decorator', 'python3-future', 'python3-h5py', 'python3-h5py-serial', 'python3-lib2to3', 'python3-minimal', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-scipy', 'python3-six', 'python3-tz', 'python3.9', 'python3.9-minimal', 'readline-common'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg', '--purge', 'python3-biom-format'] 0m41.5s DUMP: dpkg: warning: ignoring request to remove python3-biom-format which isn't installed 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg', '--purge', 'python3-biom-format'] 0m41.5s INFO: Running scripts post_purge 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_purge_exceptions'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_purge_exceptions'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg', '--purge', '--pending'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg', '--purge', '--pending'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg', '--remove', '--pending'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg', '--remove', '--pending'] 0m41.5s INFO: Running scripts post_test 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_test_exceptions'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'tmp/scripts/post_test_exceptions'] 0m41.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m42.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg-divert', '--list'] 0m42.0s 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 0m42.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'dpkg-divert', '--list'] 0m42.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', 'clean'] 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx', 'apt-get', 'clean'] 0m42.1s DEBUG: Recording chroot state 0m43.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/shm'] 0m43.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/shm'] 0m43.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/console'] 0m43.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/console'] 0m43.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/ptmx'] 0m43.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/ptmx'] 0m43.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/pts'] 0m43.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/dev/pts'] 0m43.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/proc'] 0m43.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx/proc'] 0m43.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m43.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpniwlb4rx'] 0m43.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpniwlb4rx 0m43.6s INFO: PASS: Upgrading between Debian distributions. 0m43.6s INFO: PASS: All tests. 0m43.6s INFO: piuparts run ends. ret=0 End: 2024-03-19 11:33:44 GMT