Start: 2025-02-22 03:15:42 GMT [testing] Package: deblur Version: 1.1.1-4 Installed-Size: 17262 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biom-format, python3-click, python3-h5py (>= 2.2.0), python3-numpy, python3-scipy, python3-skbio, python3:any Description: deconvolution for Illumina amplicon sequencing Homepage: https://github.com/biocore/deblur Description-md5: 4921fec74cbf30ee8bccd475c9017e08 Section: science Priority: optional Filename: pool/main/d/deblur/deblur_1.1.1-4_all.deb Size: 1970592 MD5sum: eb2aecb3d1f994222ef1ada843b80c71 SHA256: f672c1dea09876aacaadd0c4cdbc1bc4b4efc46793e0ffdbf3f0dba9820073b0 [sid] Package: deblur Version: 1.1.1-4 Installed-Size: 17262 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biom-format, python3-click, python3-h5py (>= 2.2.0), python3-numpy, python3-scipy, python3-skbio, python3:any Description: deconvolution for Illumina amplicon sequencing Homepage: https://github.com/biocore/deblur Description-md5: 4921fec74cbf30ee8bccd475c9017e08 Section: science Priority: optional Filename: pool/main/d/deblur/deblur_1.1.1-4_all.deb Size: 1970592 MD5sum: eb2aecb3d1f994222ef1ada843b80c71 SHA256: f672c1dea09876aacaadd0c4cdbc1bc4b4efc46793e0ffdbf3f0dba9820073b0 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt deblur=1.1.1-4 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 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt deblur=1.1.1-4 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmprg_bq8ky 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmprg_bq8ky 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/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/tmprg_bq8ky/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/tmprg_bq8ky/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie 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/tmprg_bq8ky/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', 'update'] 0m2.3s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9482 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6358 kB] Fetched 16.0 MB in 1s (13.9 MB/s) Reading package lists... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', 'update'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-yf', 'dist-upgrade'] 0m5.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following NEW packages will be installed: libapt-pkg7.0 The following packages will be upgraded: apt libc-bin libc6 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 5990 kB of archives. After this operation, 3898 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.40-7 [2815 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libapt-pkg7.0 amd64 2.9.30 [1104 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.30 [1440 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.40-7 [631 kB] Preconfiguring packages ... Fetched 5990 kB in 0s (72.1 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 ... 5026 files and directories currently installed.) Preparing to unpack .../libc6_2.40-7_amd64.deb ... Unpacking libc6:amd64 (2.40-7) over (2.40-6) ... Setting up libc6:amd64 (2.40-7) ... Selecting previously unselected package libapt-pkg7.0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5026 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_2.9.30_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (2.9.30) ... Setting up libapt-pkg7.0:amd64 (2.9.30) ... (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 ... 5075 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.30_amd64.deb ... Unpacking apt (2.9.30) over (2.9.29) ... Setting up apt (2.9.30) ... (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 ... 5075 files and directories currently installed.) Preparing to unpack .../libc-bin_2.40-7_amd64.deb ... Unpacking libc-bin (2.40-7) over (2.40-6) ... Setting up libc-bin (2.40-7) ... 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-yf', 'dist-upgrade'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.4s DUMP: 61226e1bdd6e39e450effa7a573c5392 - 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.4s INFO: Running scripts post_setup 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_dummy_users'] 0m7.2s 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 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_dummy_users'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_forbid_home'] 0m7.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_forbid_home'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.2s 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' 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_minimize'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_minimize'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_zz_backports'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_setup_zz_backports'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.2s DUMP: install ok installed apt apt 2.9.30 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.4-3 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.15 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-16 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.29 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.30 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b1 install ok installed libblkid1:amd64 libblkid1 2.40.4-3 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-7 install ok installed libc6:amd64 libc6 2.40-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-16 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.4-3 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3.1 install ok installed libsemanage-common libsemanage-common 3.7-2.1 install ok installed libsemanage2:amd64 libsemanage2 3.7-2.1+b1 install ok installed libsepol2:amd64 libsepol2 3.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-3 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-16 install ok installed libsystemd0:amd64 libsystemd0 257.3-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250125-2 install ok installed libudev1:amd64 libudev1 257.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.4-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-3 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.40.4-3 install ok installed ncurses-base ncurses-base 6.5+20250125-2 install ok installed ncurses-bin ncurses-bin 6.5+20250125-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.1-2 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.2.1-6+b1 install ok installed sysvinit-utils sysvinit-utils 3.14-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025a-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m7.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m7.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m7.8s INFO: Running scripts is_testable 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/is_testable_uninstallable'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/is_testable_uninstallable'] 0m7.8s INFO: Running scripts pre_test 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_test_exceptions'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_test_exceptions'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_test_root_password'] 0m7.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_test_root_password'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'show', '--no-all-versions', 'deblur'] 0m8.6s DUMP: Package: deblur Version: 1.1.1-4 Installed-Size: 17262 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biom-format, python3-click, python3-h5py (>= 2.2.0), python3-numpy, python3-scipy, python3-skbio, python3:any Description-en: deconvolution for Illumina amplicon sequencing Deblur is a greedy deconvolution algorithm for amplicon sequencing based on Illumina Miseq/Hiseq error profiles. The authors recommend using Deblur via the QIIME2 plugin q2-deblur. Examples of its use can be found within the plugin itself. However, Deblur itself does not depend on QIIME2. . The input to Deblur workflow is a directory of FASTA or FASTQ files (1 per sample) or a single demultiplexed FASTA or FASTQ file. These files can be gzip'd. The output directory will contain three BIOM tables in which the observation IDs are the Deblurred sequences. The outputs are contingent on the reference databases used and a more focused discussion on them is in the subsequent README section titled "Positive and Negative Filtering." The output files are as follows: . * reference-hit.biom : contains only Deblurred reads matching the positive filtering database. By default, a reference composed of 16S sequences is used, and this resulting table will contain only those reads which recruit at a coarse level to it will be retained. Reads are also filtered against the negative reference, which by default will remove any read which appears to be PhiX or adapter. . * reference-hit.seqs.fa : a fasta file containing all the sequences in reference-hit.biom . * reference-non-hit.biom : contains only Deblurred reads that did not align to the positive filtering database. Negative filtering is also appied to this table, so by default, PhiX and adapter are removed. . * reference-non-hit.seqs.fa : a fasta file containing all the sequences in reference-non-hit.biom . * all.biom : contains all Deblurred reads. This file represents the union of the "reference-hit.biom" and "reference-non-hit.biom" tables. . * all.seqs.fa : a fasta file containing all the sequences in all.biom . Deblur uses two types of filtering on the sequences: . * Negative mode - removes known artifact sequences (i.e. sequences aligning to PhiX or Adapter with >=95% identity and coverage). . * Positive mode - keeps only sequences similar to a reference database (by default known 16S sequences). SortMeRNA is used, and any sequence with an e-value <= 10 is retained. Deblur also outputs a BIOM table without this positive filtering step (named all.biom). . The FASTA files for both of these filtering steps can be supplied via the --neg-ref-fp and --pos-ref-fp options. By default, the negative database is composed of PhiX and adapter sequence and the positive database of known 16S sequences. . Deblur uses negative mode filtering to remove known artifact (i.e. PhiX and Adapter sequences) prior to denoising. The output of Deblur contains three files: all.biom, which includes all sOTUs, reference-hit.biom, which contains the output of positive filtering of the sOTUs (default only sOTUs similar to 16S sequences), and reference-non-hit.biom, which contains only sOTUs failing the positive filtering (default only non-16S sOTUs). Description-md5: 4921fec74cbf30ee8bccd475c9017e08 Homepage: https://github.com/biocore/deblur Section: science Priority: optional Filename: pool/main/d/deblur/deblur_1.1.1-4_all.deb Size: 1970592 MD5sum: eb2aecb3d1f994222ef1ada843b80c71 SHA256: f672c1dea09876aacaadd0c4cdbc1bc4b4efc46793e0ffdbf3f0dba9820073b0 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'show', '--no-all-versions', 'deblur'] 0m8.6s INFO: apt-cache knows about the following packages: deblur 0m8.6s INFO: Running scripts pre_install 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_database-server'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_database-server'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_exceptions'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_exceptions'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_extras'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_extras'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy'] 0m8.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy', 'deblur'] 0m8.8s DUMP: deblur: Installed: (none) Candidate: 1.1.1-4 Version table: 1.1.1-4 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy', 'deblur'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-y', 'install', 'deblur'] 0m34.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates libaec0 libblas3 libbrotli1 libcurl4t64 libexpat1 libffi8 libgfortran5 libgnutls30t64 libgomp1 libgssapi-krb5-2 libhdf5-310 libhdf5-hl-310 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 libldap2 liblzf1 libncursesw6 libnghttp2-14 libnghttp3-9 libp11-kit0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libssw0 libsz2 libtasn1-6 libunistring5 media-types netbase openssl python3 python3-biom-format python3-certifi python3-chardet python3-charset-normalizer python3-click python3-dateutil python3-decorator python3-h5py python3-h5py-serial python3-hdmedians python3-idna python3-minimal python3-natsort python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-patsy python3-pytz python3-requests python3-scipy python3-skbio python3-statsmodels python3-statsmodels-lib python3-tz python3-urllib3 python3.13 python3.13-minimal readline-common Suggested packages: gnutls-bin krb5-doc krb5-user python3-doc python3-tk python3-venv python-biom-format-doc python-charset-normalizer-doc python-h5py-doc python-natsort-doc gcc gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc python-patsy-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-skbio-doc python-statsmodels-doc python3-brotli python3.13-venv python3.13-doc binutils binfmt-support readline-doc Recommended packages: krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules python3-matplotlib python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-numba g++ | c++-compiler python3-pil python3-pooch python3-joblib python3-colorama python3-cvxopt The following NEW packages will be installed: ca-certificates deblur libaec0 libblas3 libbrotli1 libcurl4t64 libexpat1 libffi8 libgfortran5 libgnutls30t64 libgomp1 libgssapi-krb5-2 libhdf5-310 libhdf5-hl-310 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 libldap2 liblzf1 libncursesw6 libnghttp2-14 libnghttp3-9 libp11-kit0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libssw0 libsz2 libtasn1-6 libunistring5 media-types netbase openssl python3 python3-biom-format python3-certifi python3-chardet python3-charset-normalizer python3-click python3-dateutil python3-decorator python3-h5py python3-h5py-serial python3-hdmedians python3-idna python3-minimal python3-natsort python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-patsy python3-pytz python3-requests python3-scipy python3-skbio python3-statsmodels python3-statsmodels-lib python3-tz python3-urllib3 python3.13 python3.13-minimal readline-common 0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded. 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python3-urllib3 all 2.3.0-1 [114 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 python3-patsy all 1.0.1-1 [172 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 python3-statsmodels-lib amd64 0.14.4+dfsg-1+b2 [2498 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 python3-statsmodels all 0.14.4+dfsg-1 [4825 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 python3-hdmedians amd64 0.14.2-6 [177 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 python3-skbio amd64 0.6.2-4+b1 [1506 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 deblur all 1.1.1-4 [1971 kB] Preconfiguring packages ... Fetched 68.0 MB in 1s (115 MB/s) Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5079 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... 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Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../15-libsasl2-modules-db_2.1.28+dfsg1-8+b1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../16-libsasl2-2_2.1.28+dfsg1-8+b1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../17-libldap2_2.6.9+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../18-libnghttp2-14_1.64.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../19-libnghttp3-9_1.6.0-2_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.6.0-2) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../20-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../21-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../22-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../23-libgnutls30t64_3.8.9-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.9-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../24-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../25-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../26-libcurl4t64_8.12.1-2_amd64.deb ... Unpacking libcurl4t64:amd64 (8.12.1-2) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../27-libaec0_1.1.3-1+b1_amd64.deb ... Unpacking libaec0:amd64 (1.1.3-1+b1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../28-libsz2_1.1.3-1+b1_amd64.deb ... Unpacking libsz2:amd64 (1.1.3-1+b1) ... Selecting previously unselected package libhdf5-310:amd64. Preparing to unpack .../29-libhdf5-310_1.14.5+repack-3_amd64.deb ... Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-310:amd64. Preparing to unpack .../30-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Selecting previously unselected package liblzf1:amd64. Preparing to unpack .../31-liblzf1_3.6-4+b3_amd64.deb ... Unpacking liblzf1:amd64 (3.6-4+b3) ... Selecting previously unselected package python3-h5py-serial. Preparing to unpack .../32-python3-h5py-serial_3.12.1-1+b2_amd64.deb ... Unpacking python3-h5py-serial (3.12.1-1+b2) ... Selecting previously unselected package python3-h5py. Preparing to unpack .../33-python3-h5py_3.12.1-1_all.deb ... Unpacking python3-h5py (3.12.1-1) ... Selecting previously unselected package python3-click. Preparing to unpack .../34-python3-click_8.1.8-1_all.deb ... Unpacking python3-click (8.1.8-1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../35-python3-dateutil_2.9.0-3_all.deb ... Unpacking python3-dateutil (2.9.0-3) ... Selecting previously unselected package python3-pytz. Preparing to unpack .../36-python3-pytz_2025.1-3_all.deb ... Unpacking python3-pytz (2025.1-3) ... Selecting previously unselected package python3-tz. Preparing to unpack .../37-python3-tz_2025.1-3_all.deb ... Unpacking python3-tz (2025.1-3) ... Selecting previously unselected package python3-pandas-lib:amd64. Preparing to unpack .../38-python3-pandas-lib_2.2.3+dfsg-8_amd64.deb ... Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../39-python3-pandas_2.2.3+dfsg-8_all.deb ... Unpacking python3-pandas (2.2.3+dfsg-8) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../40-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) ... Selecting previously unselected package liblbfgsb0:amd64. Preparing to unpack .../41-liblbfgsb0_3.0+dfsg.4-1+b2_amd64.deb ... Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../42-python3-scipy_1.14.1-4_amd64.deb ... Unpacking python3-scipy (1.14.1-4) ... Selecting previously unselected package python3-biom-format. Preparing to unpack .../43-python3-biom-format_2.1.16-1+b4_amd64.deb ... Unpacking python3-biom-format (2.1.16-1+b4) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../44-libgomp1_14.2.0-16_amd64.deb ... Unpacking libgomp1:amd64 (14.2.0-16) ... Selecting previously unselected package libssw0:amd64. Preparing to unpack .../45-libssw0_1.1-15+b2_amd64.deb ... Unpacking libssw0:amd64 (1.1-15+b2) ... Selecting previously unselected package python3-natsort. Preparing to unpack .../46-python3-natsort_8.0.2-2_all.deb ... Unpacking python3-natsort (8.0.2-2) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../47-python3-certifi_2025.1.31+ds-1_all.deb ... Unpacking python3-certifi (2025.1.31+ds-1) ... Selecting previously unselected package python3-charset-normalizer. Preparing to unpack .../48-python3-charset-normalizer_3.4.1-1_amd64.deb ... Unpacking python3-charset-normalizer (3.4.1-1) ... Selecting previously unselected package python3-idna. Preparing to unpack .../49-python3-idna_3.10-1_all.deb ... Unpacking python3-idna (3.10-1) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../50-python3-urllib3_2.3.0-1_all.deb ... Unpacking python3-urllib3 (2.3.0-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../51-python3-chardet_5.2.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-2) ... Selecting previously unselected package python3-requests. Preparing to unpack .../52-python3-requests_2.32.3+dfsg-1_all.deb ... Unpacking python3-requests (2.32.3+dfsg-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../53-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-patsy. Preparing to unpack .../54-python3-patsy_1.0.1-1_all.deb ... Unpacking python3-patsy (1.0.1-1) ... Selecting previously unselected package python3-statsmodels-lib:amd64. Preparing to unpack .../55-python3-statsmodels-lib_0.14.4+dfsg-1+b2_amd64.deb ... Unpacking python3-statsmodels-lib:amd64 (0.14.4+dfsg-1+b2) ... Selecting previously unselected package python3-statsmodels. Preparing to unpack .../56-python3-statsmodels_0.14.4+dfsg-1_all.deb ... Unpacking python3-statsmodels (0.14.4+dfsg-1) ... Selecting previously unselected package python3-hdmedians. Preparing to unpack .../57-python3-hdmedians_0.14.2-6_amd64.deb ... Unpacking python3-hdmedians (0.14.2-6) ... Selecting previously unselected package python3-skbio. Preparing to unpack .../58-python3-skbio_0.6.2-4+b1_amd64.deb ... Unpacking python3-skbio (0.6.2-4+b1) ... Selecting previously unselected package deblur. Preparing to unpack .../59-deblur_1.1.1-4_all.deb ... Unpacking deblur (1.1.1-4) ... Setting up media-types (10.1.0) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libgomp1:amd64 (14.2.0-16) ... Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libblas3:amd64 (3.12.1-2) ... 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 liblzf1:amd64 (3.6-4+b3) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up libncursesw6:amd64 (6.5+20250125-2) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:amd64 (14.2.0-16) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up openssl (3.4.1-1) ... Setting up libssw0:amd64 (1.1-15+b2) ... Setting up readline-common (8.2-6) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up liblapack3:amd64 (3.12.1-2) ... 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 libidn2-0:amd64 (2.3.7-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up python3.13 (3.13.2-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-2) ... Setting up python3-click (8.1.8-1) ... Setting up python3-natsort (8.0.2-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-idna (3.10-1) ... Setting up python3-numpy (1:1.26.4+ds-13) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-hdmedians (0.14.2-6) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-statsmodels-lib:amd64 (0.14.4+dfsg-1+b2) ... Setting up python3-scipy (1.14.1-4) ... Setting up libcurl4t64:amd64 (8.12.1-2) ... Setting up python3-charset-normalizer (3.4.1-1) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... Setting up python3-pytz (2025.1-3) ... Setting up python3-tz (2025.1-3) ... Setting up python3-patsy (1.0.1-1) ... Setting up python3-pandas (2.2.3+dfsg-8) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... Setting up python3-statsmodels (0.14.4+dfsg-1) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Setting up python3-h5py-serial (3.12.1-1+b2) ... Setting up python3-h5py (3.12.1-1) ... Setting up python3-biom-format (2.1.16-1+b4) ... Setting up python3-skbio (0.6.2-4+b1) ... Setting up deblur (1.1.1-4) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-y', 'install', 'deblur'] 0m34.2s INFO: Running scripts post_install 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_install_exceptions'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_install_exceptions'] 0m34.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m35.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m35.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmprg_bq8ky to sid 0m35.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m35.0s INFO: Running scripts pre_distupgrade 0m35.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m35.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m35.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_exceptions'] 0m35.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_exceptions'] 0m35.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m35.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m35.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m35.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m35.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m35.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m35.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', 'update'] 0m37.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7379 kB] Fetched 17.7 MB in 2s (8954 kB/s) Reading package lists... 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', 'update'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-yf', 'dist-upgrade'] 0m43.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: python3-numpy-dev The following packages will be upgraded: bash bsdutils gcc-14-base libattr1 libblkid1 libcap2 libgcc-s1 libgfortran5 libgomp1 libhogweed6t64 libmount1 libncursesw6 libnettle8t64 libpcre2-8-0 libselinux1 libsemanage-common libsemanage2 libsmartcols1 libstdc++6 libtinfo6 libuuid1 login login.defs media-types mount ncurses-base ncurses-bin passwd python3-click python3-numpy python3-requests util-linux 32 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 17.1 MB of archives. After this operation, 7658 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.37-1.1 [1500 kB] Get:2 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.4-4 [106 kB] Get:3 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.5+20250216-1 [439 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.4-4 [36.5 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.4-4 [169 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.4-4 [200 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.4-4 [140 kB] Get:8 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.4-4 [1206 kB] Get:9 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.4-4 [156 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.8-3 [84.6 kB] Get:12 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.5+20250216-1 [273 kB] Get:13 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.4-4 [88.7 kB] Get:14 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.3+ds-2 [7517 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2 [138 kB] Get:16 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-17 [49.1 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-17 [72.7 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-17 [137 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-17 [713 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-3 [22.9 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.73-4 [27.3 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.10.1-1 [305 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.10.1-1 [335 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250216-1 [136 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.5+20250216-1 [348 kB] Get:27 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.17.2-5 [186 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.8-1 [7720 B] Get:29 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.8-1 [94.4 kB] Get:30 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.17.2-5 [1234 kB] Get:31 http://deb.debian.org/debian sid/main amd64 media-types all 11.0.0 [27.6 kB] Get:32 http://deb.debian.org/debian sid/main amd64 python3-click all 8.2.0-1 [98.7 kB] Get:33 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Fetched 17.1 MB in 0s (139 MB/s) (Reading database ... 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Processing triggers for debianutils (5.21) ... 0m43.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-yf', 'dist-upgrade'] 0m43.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m44.4s DUMP: 2a0a29f7feef3f9d8287fb8dcd7189c7 - 0m44.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'show', '--no-all-versions', 'deblur'] 0m44.6s DUMP: Package: deblur Version: 1.1.1-4 Installed-Size: 17262 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biom-format, python3-click, python3-h5py (>= 2.2.0), python3-numpy, python3-scipy, python3-skbio, python3:any Description-en: deconvolution for Illumina amplicon sequencing Deblur is a greedy deconvolution algorithm for amplicon sequencing based on Illumina Miseq/Hiseq error profiles. The authors recommend using Deblur via the QIIME2 plugin q2-deblur. Examples of its use can be found within the plugin itself. However, Deblur itself does not depend on QIIME2. . The input to Deblur workflow is a directory of FASTA or FASTQ files (1 per sample) or a single demultiplexed FASTA or FASTQ file. These files can be gzip'd. The output directory will contain three BIOM tables in which the observation IDs are the Deblurred sequences. The outputs are contingent on the reference databases used and a more focused discussion on them is in the subsequent README section titled "Positive and Negative Filtering." The output files are as follows: . * reference-hit.biom : contains only Deblurred reads matching the positive filtering database. By default, a reference composed of 16S sequences is used, and this resulting table will contain only those reads which recruit at a coarse level to it will be retained. Reads are also filtered against the negative reference, which by default will remove any read which appears to be PhiX or adapter. . * reference-hit.seqs.fa : a fasta file containing all the sequences in reference-hit.biom . * reference-non-hit.biom : contains only Deblurred reads that did not align to the positive filtering database. Negative filtering is also appied to this table, so by default, PhiX and adapter are removed. . * reference-non-hit.seqs.fa : a fasta file containing all the sequences in reference-non-hit.biom . * all.biom : contains all Deblurred reads. This file represents the union of the "reference-hit.biom" and "reference-non-hit.biom" tables. . * all.seqs.fa : a fasta file containing all the sequences in all.biom . Deblur uses two types of filtering on the sequences: . * Negative mode - removes known artifact sequences (i.e. sequences aligning to PhiX or Adapter with >=95% identity and coverage). . * Positive mode - keeps only sequences similar to a reference database (by default known 16S sequences). SortMeRNA is used, and any sequence with an e-value <= 10 is retained. Deblur also outputs a BIOM table without this positive filtering step (named all.biom). . The FASTA files for both of these filtering steps can be supplied via the --neg-ref-fp and --pos-ref-fp options. By default, the negative database is composed of PhiX and adapter sequence and the positive database of known 16S sequences. . Deblur uses negative mode filtering to remove known artifact (i.e. PhiX and Adapter sequences) prior to denoising. The output of Deblur contains three files: all.biom, which includes all sOTUs, reference-hit.biom, which contains the output of positive filtering of the sOTUs (default only sOTUs similar to 16S sequences), and reference-non-hit.biom, which contains only sOTUs failing the positive filtering (default only non-16S sOTUs). Description-md5: 4921fec74cbf30ee8bccd475c9017e08 Homepage: https://github.com/biocore/deblur Section: science Priority: optional Filename: pool/main/d/deblur/deblur_1.1.1-4_all.deb Size: 1970592 MD5sum: eb2aecb3d1f994222ef1ada843b80c71 SHA256: f672c1dea09876aacaadd0c4cdbc1bc4b4efc46793e0ffdbf3f0dba9820073b0 0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'show', '--no-all-versions', 'deblur'] 0m44.6s INFO: apt-cache knows about the following packages: deblur 0m44.6s INFO: Running scripts pre_install 0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_database-server'] 0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_database-server'] 0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_exceptions'] 0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_exceptions'] 0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_extras'] 0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_extras'] 0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture'] 0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture'] 0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy'] 0m44.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy'] 0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy', 'deblur'] 0m44.8s DUMP: deblur: Installed: 1.1.1-4 Candidate: 1.1.1-4 Version table: *** 1.1.1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy', 'deblur'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-y', 'install', 'deblur'] 0m45.3s DUMP: Reading package lists... Building dependency tree... Reading state information... deblur is already the newest version (1.1.1-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-y', 'install', 'deblur'] 0m45.3s INFO: Running scripts post_install 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_install_exceptions'] 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_install_exceptions'] 0m45.3s INFO: Running scripts post_distupgrade 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_exceptions'] 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_exceptions'] 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_zz_backports'] 0m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_distupgrade_zz_backports'] 0m45.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m46.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m46.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m47.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m47.1s INFO: Running scripts pre_install 0m47.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_database-server'] 0m47.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_database-server'] 0m47.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_exceptions'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_exceptions'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_extras'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_extras'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy'] 0m47.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy', 'deblur'] 0m47.3s DUMP: deblur: Installed: 1.1.1-4 Candidate: 1.1.1-4 Version table: *** 1.1.1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-cache', 'policy', 'deblur'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-y', 'install', 'deblur=1.1.1-4'] 0m47.9s DUMP: Reading package lists... Building dependency tree... Reading state information... deblur is already the newest version (1.1.1-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', '-y', 'install', 'deblur=1.1.1-4'] 0m47.9s INFO: Running scripts post_install 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_install_exceptions'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_install_exceptions'] 0m48.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m48.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m49.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', '-ac', '--ignore-obsolete'] 0m51.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', '-ac', '--ignore-obsolete'] 0m51.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m51.5s DUMP: 0.15.6 0m51.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m51.5s INFO: Running adequate version 0.15.6 now. 0m51.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'deblur'] 0m51.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'deblur'] 0m51.6s INFO: Running scripts pre_remove 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m53.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m53.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_exceptions'] 0m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/pre_remove_exceptions'] 0m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m53.1s DUMP: install ok installed apt apt 2.9.30 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1.1 install ok installed bsdutils bsdutils 1:2.40.4-4 install ok installed ca-certificates ca-certificates 20241223 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed deblur deblur 1.1.1-4 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.15 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-17 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libaec0:amd64 libaec0 1.1.3-1+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.29 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.30 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b1 install ok installed libblas3:amd64 libblas3 3.12.1-2 install ok installed libblkid1:amd64 libblkid1 2.40.4-4 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-7 install ok installed libc6:amd64 libc6 2.40-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.73-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcurl4t64:amd64 libcurl4t64 8.12.1-2 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libffi8:amd64 libffi8 3.4.7-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-17 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-17 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-17 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-4 install ok installed libhdf5-310:amd64 libhdf5-310 1.14.5+repack-3 install ok installed libhdf5-hl-310:amd64 libhdf5-hl-310 1.14.5+repack-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-4 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-4 install ok installed liblapack3:amd64 liblapack3 3.12.1-2 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b2 install ok installed libldap2:amd64 libldap2 2.6.9+dfsg-1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 install ok installed liblzf1:amd64 liblzf1 3.6-4+b3 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.4-4 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.6.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.1-2 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.2-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.2-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.8-3 install ok installed libsemanage-common libsemanage-common 3.8-1 install ok installed libsemanage2:amd64 libsemanage2 3.8-1 install ok installed libsepol2:amd64 libsepol2 3.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1 install ok installed libssw0:amd64 libssw0 1.1-15+b2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-17 install ok installed libsystemd0:amd64 libsystemd0 257.3-1 install ok installed libsz2:amd64 libsz2 1.1.3-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-1 install ok installed libudev1:amd64 libudev1 257.3-1 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.4-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-4 install ok installed login.defs login.defs 1:4.17.2-5 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 11.0.0 install ok installed mount mount 2.40.4-4 install ok installed ncurses-base ncurses-base 6.5+20250216-1 install ok installed ncurses-bin ncurses-bin 6.5+20250216-1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.4.1-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1 install ok installed passwd passwd 1:4.17.2-5 install ok installed perl-base perl-base 5.40.1-2 install ok installed python3 python3 3.13.1-2 install ok installed python3-biom-format python3-biom-format 2.1.16-1+b4 install ok installed python3-certifi python3-certifi 2025.1.31+ds-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.1-1 install ok installed python3-click python3-click 8.2.0-1 install ok installed python3-dateutil python3-dateutil 2.9.0-3 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-h5py python3-h5py 3.12.1-1 install ok installed python3-h5py-serial python3-h5py-serial 3.12.1-1+b2 install ok installed python3-hdmedians python3-hdmedians 0.14.2-6 install ok installed python3-idna python3-idna 3.10-1 install ok installed python3-minimal python3-minimal 3.13.1-2 install ok installed python3-natsort python3-natsort 8.0.2-2 install ok installed python3-numpy python3-numpy 1:2.2.3+ds-2 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.3+ds-2 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pandas python3-pandas 2.2.3+dfsg-8 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.2.3+dfsg-8 install ok installed python3-patsy python3-patsy 1.0.1-1 install ok installed python3-pytz python3-pytz 2025.1-3 install ok installed python3-requests python3-requests 2.32.3+dfsg-4 install ok installed python3-scipy python3-scipy 1.14.1-4 install ok installed python3-skbio python3-skbio 0.6.2-4+b1 install ok installed python3-statsmodels python3-statsmodels 0.14.4+dfsg-1 install ok installed python3-statsmodels-lib:amd64 python3-statsmodels-lib 0.14.4+dfsg-1+b2 install ok installed python3-tz python3-tz 2025.1-3 install ok installed python3-urllib3 python3-urllib3 2.3.0-1 install ok installed python3.13 python3.13 3.13.2-1 install ok installed python3.13-minimal python3.13-minimal 3.13.2-1 install ok installed readline-common readline-common 8.2-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.2.1-6+b1 install ok installed sysvinit-utils sysvinit-utils 3.14-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025a-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', 'remove', 'ca-certificates', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl4t64:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-310:amd64', 'libhdf5-hl-310:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'libldap2:amd64', 'liblzf1:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libssw0:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-biom-format', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-dateutil', 'python3-decorator', 'python3-h5py', 'python3-h5py-serial', 'python3-hdmedians', 'python3-idna', 'python3-minimal', 'python3-natsort', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-patsy', 'python3-pytz', 'python3-requests', 'python3-scipy', 'python3-skbio', 'python3-statsmodels', 'python3-statsmodels-lib:amd64', 'python3-tz', 'python3-urllib3', 'python3.13', 'python3.13-minimal', 'readline-common', 'deblur'] 0m57.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates deblur libaec0 libblas3 libbrotli1 libcurl4t64 libexpat1 libffi8 libgfortran5 libgnutls30t64 libgomp1 libgssapi-krb5-2 libhdf5-310 libhdf5-hl-310 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 libldap2 liblzf1 libncursesw6 libnghttp2-14 libnghttp3-9 libp11-kit0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libssw0 libsz2 libtasn1-6 libunistring5 media-types netbase openssl python3 python3-biom-format python3-certifi python3-chardet python3-charset-normalizer python3-click python3-dateutil python3-decorator python3-h5py python3-h5py-serial python3-hdmedians python3-idna python3-minimal python3-natsort python3-numpy python3-numpy-dev python3-packaging python3-pandas python3-pandas-lib python3-patsy python3-pytz python3-requests python3-scipy python3-skbio python3-statsmodels python3-statsmodels-lib python3-tz python3-urllib3 python3.13 python3.13-minimal readline-common 0 upgraded, 0 newly installed, 75 to remove and 0 not upgraded. After this operation, 381 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 ... 14689 files and directories currently installed.) Removing deblur (1.1.1-4) ... Removing python3-skbio (0.6.2-4+b1) ... Removing python3-requests (2.32.3+dfsg-4) ... Removing python3-certifi (2025.1.31+ds-1) ... Removing ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing python3-biom-format (2.1.16-1+b4) ... Removing python3-h5py (3.12.1-1) ... Removing python3-h5py-serial (3.12.1-1+b2) ... Removing libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Removing libhdf5-310:amd64 (1.14.5+repack-3) ... Removing libsz2:amd64 (1.1.3-1+b1) ... Removing libaec0:amd64 (1.1.3-1+b1) ... Removing python3-statsmodels (0.14.4+dfsg-1) ... Removing python3-scipy (1.14.1-4) ... Removing python3-statsmodels-lib:amd64 (0.14.4+dfsg-1+b2) ... Removing python3-hdmedians (0.14.2-6) ... Removing python3-pandas (2.2.3+dfsg-8) ... Removing python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing libcurl4t64:amd64 (8.12.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing python3-charset-normalizer (3.4.1-1) ... Removing python3-urllib3 (2.3.0-1) ... Removing python3-tz (2025.1-3) ... Removing python3-pytz (2025.1-3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libgnutls30t64:amd64 (3.8.9-2) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libgomp1:amd64 (14.2.0-17) ... Removing libgssapi-krb5-2:amd64 (1.21.3-4) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libidn2-0:amd64 (2.3.7-2+b1) ... Removing libkrb5-3:amd64 (1.21.3-4) ... Removing libk5crypto3:amd64 (1.21.3-4) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-4) ... Removing libldap2:amd64 (2.6.9+dfsg-1) ... Removing liblzf1:amd64 (3.6-4+b3) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.6.0-2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libssw0:amd64 (1.1-15+b2) ... Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libunistring5:amd64 (1.3-1) ... Removing openssl (3.4.1-1) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3-click (8.2.0-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-decorator (5.1.1-5) ... Removing python3-idna (3.10-1) ... Removing python3-natsort (8.0.2-2) ... Removing python3-packaging (24.2-1) ... Removing python3-patsy (1.0.1-1) ... Removing python3-numpy (1:2.2.3+ds-2) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing python3 (3.13.1-2) ... Removing python3.13 (3.13.2-1) ... Removing python3-minimal (3.13.1-2) ... Removing python3.13-minimal (3.13.2-1) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.13.1-2) ... Removing libpython3.13-stdlib:amd64 (3.13.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.4.7-1) ... Removing libgfortran5:amd64 (14.2.0-17) ... Removing libncursesw6:amd64 (6.5+20250216-1) ... Removing libpython3.13-minimal:amd64 (3.13.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing media-types (11.0.0) ... Removing netbase (6.4) ... Removing python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.40-7) ... 0m57.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', 'remove', 'ca-certificates', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl4t64:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-310:amd64', 'libhdf5-hl-310:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'libldap2:amd64', 'liblzf1:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libssw0:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-biom-format', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-dateutil', 'python3-decorator', 'python3-h5py', 'python3-h5py-serial', 'python3-hdmedians', 'python3-idna', 'python3-minimal', 'python3-natsort', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-patsy', 'python3-pytz', 'python3-requests', 'python3-scipy', 'python3-skbio', 'python3-statsmodels', 'python3-statsmodels-lib:amd64', 'python3-tz', 'python3-urllib3', 'python3.13', 'python3.13-minimal', 'readline-common', 'deblur'] 0m57.1s INFO: Running scripts post_remove 0m57.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_remove_exceptions'] 0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_remove_exceptions'] 0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg', '--purge', 'ca-certificates', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl4t64:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-310:amd64', 'libhdf5-hl-310:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'libldap2:amd64', 'liblzf1:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libssw0:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-biom-format', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-dateutil', 'python3-decorator', 'python3-h5py', 'python3-h5py-serial', 'python3-hdmedians', 'python3-idna', 'python3-minimal', 'python3-natsort', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-patsy', 'python3-pytz', 'python3-requests', 'python3-scipy', 'python3-skbio', 'python3-statsmodels', 'python3-statsmodels-lib:amd64', 'python3-tz', 'python3-urllib3', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m57.3s DUMP: (Reading database ... 5079 files and directories currently installed.) Purging configuration files for ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. 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 libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi8 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-4) ... dpkg: warning: ignoring request to remove libhdf5-310 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-310 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 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 libldap2 which isn't installed dpkg: warning: ignoring request to remove liblzf1 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.2-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libssw0 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libunistring5 which isn't installed Purging configuration files for media-types (11.0.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.4.1-1) ... Purging configuration files for python3 (3.13.1-2) ... dpkg: warning: ignoring request to remove python3-biom-format which isn't installed dpkg: warning: ignoring request to remove python3-certifi 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-click 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-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-hdmedians which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-natsort which isn't installed Purging configuration files for python3-numpy (1:2.2.3+ds-2) ... dpkg: warning: ignoring request to remove python3-numpy-dev 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-patsy which isn't installed dpkg: warning: ignoring request to remove python3-pytz which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-skbio which isn't installed dpkg: warning: ignoring request to remove python3-statsmodels which isn't installed dpkg: warning: ignoring request to remove python3-statsmodels-lib which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.2-1) ... Purging configuration files for readline-common (8.2-6) ... 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg', '--purge', 'ca-certificates', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl4t64:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-310:amd64', 'libhdf5-hl-310:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'libldap2:amd64', 'liblzf1:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libssw0:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-biom-format', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-dateutil', 'python3-decorator', 'python3-h5py', 'python3-h5py-serial', 'python3-hdmedians', 'python3-idna', 'python3-minimal', 'python3-natsort', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-patsy', 'python3-pytz', 'python3-requests', 'python3-scipy', 'python3-skbio', 'python3-statsmodels', 'python3-statsmodels-lib:amd64', 'python3-tz', 'python3-urllib3', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg', '--purge', 'deblur'] 0m57.3s DUMP: dpkg: warning: ignoring request to remove deblur which isn't installed 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg', '--purge', 'deblur'] 0m57.3s INFO: Running scripts post_purge 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_purge_exceptions'] 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_purge_exceptions'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg', '--purge', '--pending'] 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg', '--purge', '--pending'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg', '--remove', '--pending'] 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg', '--remove', '--pending'] 0m57.3s INFO: Running scripts post_test 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_test_exceptions'] 0m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'tmp/scripts/post_test_exceptions'] 0m57.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m57.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m57.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg-divert', '--list'] 0m57.8s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m57.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'dpkg-divert', '--list'] 0m57.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', 'clean'] 0m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky', 'apt-get', 'clean'] 0m57.9s DEBUG: Recording chroot state 0m58.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/shm'] 0m58.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/shm'] 0m58.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/console'] 0m58.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/console'] 0m58.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/ptmx'] 0m58.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/ptmx'] 0m58.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/pts'] 0m58.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/dev/pts'] 0m58.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/proc'] 0m58.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky/proc'] 0m58.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m58.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprg_bq8ky'] 0m58.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmprg_bq8ky 0m58.8s INFO: PASS: Upgrading between Debian distributions. 0m58.8s INFO: PASS: All tests. 0m58.8s INFO: piuparts run ends. ret=0 End: 2025-02-22 03:16:41 GMT