Start: 2025-02-26 22:35:21 GMT
[testing]
Package: python3-bx
Source: python-bx (0.13.0-1)
Version: 0.13.0-1+b2
Installed-Size: 5754
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Provides: python3-bx-tools
Depends: python3-lzo, libc6 (>= 2.14), zlib1g (>= 1:1.1.4), python3 (<< 3.14), python3 (>= 3.12~), python3-numpy, python3-numpy2-abi0 | python3-numpy-abi9, python3-pyparsing, python3:any
Description: library to manage genomic data and its alignment
Homepage: https://github.com/bxlab/bx-python
Description-md5: 67d503eba4b89cb2b658656d4c7560a1
Section: python
Priority: optional
Filename: pool/main/p/python-bx/python3-bx_0.13.0-1+b2_amd64.deb
Size: 941944
MD5sum: 194cf869744873aeff171c880dffc5bb
SHA256: 1a6dc179451367894c0e8981d85a67342d1f1402e5d26e4a35d069ec06a0e991
[sid]
Package: python3-bx
Source: python-bx (0.13.0-1)
Version: 0.13.0-1+b3
Installed-Size: 3485
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Provides: python3-bx-tools
Depends: python3-lzo, libc6 (>= 2.14), zlib1g (>= 1:1.1.4), python3 (<< 3.14), python3 (>= 3.13~), python3-numpy, python3-numpy2-abi0 | python3-numpy-abi9, python3-pyparsing, python3:any
Description: library to manage genomic data and its alignment
Homepage: https://github.com/bxlab/bx-python
Description-md5: 67d503eba4b89cb2b658656d4c7560a1
Section: python
Priority: optional
Filename: pool/main/p/python-bx/python3-bx_0.13.0-1+b3_amd64.deb
Size: 711784
MD5sum: 284408d35921b0c2c9f1aab85db3b857
SHA256: 071ef6247463988193bfc5b46e0eb342d2bf142bccba902d07926960df429444
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 python3-bx=0.13.0-1+b3
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile.
0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ
0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong.
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-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 python3-bx=0.13.0-1+b3
0m0.0s INFO: Running on: Linux piu-slave-ubc-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/tmpvbvq_vp_
0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpvbvq_vp_
0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz']
0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz']
0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/proc']
0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/proc']
0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/pts']
0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/pts']
0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/ptmx']
0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/ptmx']
0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/console']
0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/console']
0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/shm']
0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/shm']
0m0.3s DEBUG: sources.list:
deb http://deb.debian.org/debian/ trixie main
0m0.3s DEBUG: Created policy-rc.d and chmodded it.
0m0.3s DEBUG: Created resolv.conf.
0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpvbvq_vp_/tmp/scripts/
0m0.3s INFO: Running scripts post_chroot_unpack
0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', 'update']
0m1.5s DUMP:
Get:1 http://deb.debian.org/debian trixie InRelease [175 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9490 kB]
Get:3 http://deb.debian.org/debian trixie/main Translation-en [6365 kB]
Fetched 16.0 MB in 1s (19.3 MB/s)
Reading package lists...
0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', 'update']
0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-yf', 'dist-upgrade']
0m3.4s 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 bash bsdutils libattr1 libblkid1 libc-bin libc6 libhogweed6t64 libmount1
libnettle8t64 libpcre2-8-0 libselinux1 libsemanage-common libsemanage2
libsmartcols1 libtinfo6 libuuid1 login login.defs mount ncurses-base
ncurses-bin passwd util-linux
24 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 13.2 MB of archives.
After this operation, 3980 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.37-1.1 [1500 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.4-4 [106 kB]
Get:3 http://deb.debian.org/debian trixie/main amd64 ncurses-bin amd64 6.5+20250216-1 [439 kB]
Get:4 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.40-7 [2815 kB]
Get:5 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.4-4 [36.5 kB]
Get:6 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.4-4 [169 kB]
Get:7 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.4-4 [200 kB]
Get:8 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.4-4 [140 kB]
Get:9 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.4-4 [1206 kB]
Get:10 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.4-4 [156 kB]
Get:11 http://deb.debian.org/debian trixie/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB]
Get:12 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.8-3 [84.6 kB]
Get:13 http://deb.debian.org/debian trixie/main amd64 libapt-pkg7.0 amd64 2.9.30 [1104 kB]
Get:14 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.30 [1440 kB]
Get:15 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.40-7 [631 kB]
Get:16 http://deb.debian.org/debian trixie/main amd64 ncurses-base all 6.5+20250216-1 [273 kB]
Get:17 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.4-4 [88.7 kB]
Get:18 http://deb.debian.org/debian trixie/main amd64 libattr1 amd64 1:2.5.2-3 [22.9 kB]
Get:19 http://deb.debian.org/debian trixie/main amd64 libnettle8t64 amd64 3.10.1-1 [305 kB]
Get:20 http://deb.debian.org/debian trixie/main amd64 libhogweed6t64 amd64 3.10.1-1 [335 kB]
Get:21 http://deb.debian.org/debian trixie/main amd64 libtinfo6 amd64 6.5+20250216-1 [348 kB]
Get:22 http://deb.debian.org/debian trixie/main amd64 login.defs all 1:4.17.2-5 [186 kB]
Get:23 http://deb.debian.org/debian trixie/main amd64 libsemanage-common all 3.8-1 [7720 B]
Get:24 http://deb.debian.org/debian trixie/main amd64 libsemanage2 amd64 3.8-1 [94.4 kB]
Get:25 http://deb.debian.org/debian trixie/main amd64 passwd amd64 1:4.17.2-5 [1234 kB]
Preconfiguring packages ...
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update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode
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Preparing to unpack .../login_1%3a4.16.0-2+really2.40.4-4_amd64.deb ...
Unpacking login (1:4.16.0-2+really2.40.4-4) over (1:4.16.0-2+really2.40.4-3) ...
Preparing to unpack .../libattr1_1%3a2.5.2-3_amd64.deb ...
Unpacking libattr1:amd64 (1:2.5.2-3) over (1:2.5.2-2) ...
Setting up libattr1:amd64 (1:2.5.2-3) ...
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Preparing to unpack .../libnettle8t64_3.10.1-1_amd64.deb ...
Unpacking libnettle8t64:amd64 (3.10.1-1) over (3.10-1+b1) ...
Setting up libnettle8t64:amd64 (3.10.1-1) ...
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(Reading database ... 5071 files and directories currently installed.)
Preparing to unpack .../libhogweed6t64_3.10.1-1_amd64.deb ...
Unpacking libhogweed6t64:amd64 (3.10.1-1) over (3.10-1+b1) ...
Setting up libhogweed6t64:amd64 (3.10.1-1) ...
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(Reading database ... 5070 files and directories currently installed.)
Preparing to unpack .../libtinfo6_6.5+20250216-1_amd64.deb ...
Unpacking libtinfo6:amd64 (6.5+20250216-1) over (6.5+20250125-2) ...
Setting up libtinfo6:amd64 (6.5+20250216-1) ...
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Preparing to unpack .../login.defs_1%3a4.17.2-5_all.deb ...
Unpacking login.defs (1:4.17.2-5) over (1:4.16.0-7) ...
Preparing to unpack .../libsemanage-common_3.8-1_all.deb ...
Unpacking libsemanage-common (3.8-1) over (3.7-2.1) ...
Preparing to unpack .../libsemanage2_3.8-1_amd64.deb ...
Unpacking libsemanage2:amd64 (3.8-1) over (3.7-2.1+b1) ...
Preparing to unpack .../passwd_1%3a4.17.2-5_amd64.deb ...
Unpacking passwd (1:4.17.2-5) over (1:4.16.0-7) ...
Setting up login.defs (1:4.17.2-5) ...
Setting up libsemanage-common (3.8-1) ...
Setting up mount (2.40.4-4) ...
Setting up libsemanage2:amd64 (3.8-1) ...
Setting up login (1:4.16.0-2+really2.40.4-4) ...
Setting up passwd (1:4.17.2-5) ...
Processing triggers for libc-bin (2.40-7) ...
Processing triggers for debianutils (5.21) ...
0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-yf', 'dist-upgrade']
0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m4.0s DUMP:
2b7c68ddae4fd6c8a28e24dcbff5cf5f -
0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m4.0s INFO: Running scripts post_setup
0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_dummy_users']
0m4.4s DUMP:
useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999
useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999
useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999
useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999
useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999
useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999
useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999
useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999
useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999
useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999
useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999
0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_dummy_users']
0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_forbid_home']
0m4.4s DUMP:
Disabling /home
Adding 'local diversion of /home to /home.distrib'
0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_forbid_home']
0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_force-unsafe-io']
0m4.4s DUMP:
Enabling dpkg --force-unsafe-io.
Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib'
Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged'
'/bin/sync' -> 'true'
0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_force-unsafe-io']
0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_minimize']
0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_minimize']
0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_squeeze-backports']
0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_squeeze-backports']
0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_zz_backports']
0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_setup_zz_backports']
0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m4.4s 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 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 1:2.5.2-3
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 libblkid1:amd64 libblkid1 2.40.4-4
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 3.10.1-1
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 2.40.4-4
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
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 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 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+20250216-1
install ok installed libudev1:amd64 libudev1 257.3-1
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 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 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 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
0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m4.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat
0m4.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m4.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m4.7s INFO: Running scripts is_testable
0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/is_testable_uninstallable']
0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/is_testable_uninstallable']
0m4.7s INFO: Running scripts pre_test
0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_test_exceptions']
0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_test_exceptions']
0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_test_root_password']
0m4.7s DUMP:
New password: Retype new password: passwd: password updated successfully
0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_test_root_password']
0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'show', '--no-all-versions', 'python3-bx']
0m4.8s DUMP:
Package: python3-bx
Source: python-bx (0.13.0-1)
Version: 0.13.0-1+b2
Installed-Size: 5754
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Provides: python3-bx-tools
Depends: python3-lzo, libc6 (>= 2.14), zlib1g (>= 1:1.1.4), python3 (<< 3.14), python3 (>= 3.12~), python3-numpy, python3-numpy2-abi0 | python3-numpy-abi9, python3-pyparsing, python3:any
Description-en: library to manage genomic data and its alignment
The bx-python project is a Python3 library and associated set of scripts to
allow for rapid implementation of genome scale analyses. The library contains
a variety of useful modules, but the particular strengths are:
* Classes for reading and working with genome-scale multiple local
alignments (in MAF, AXT, and LAV formats)
* Generic data structure for indexing on disk files that contain blocks of
data associated with intervals on various sequences (used, for example, to
provide random access to individual alignments in huge files; optimized
for use over network filesystems)
* Data structures for working with intervals on sequences
* "Binned bitsets" which act just like chromosome sized bit arrays, but
lazily allocate regions and allow large blocks of all set or all unset
bits to be stored compactly
* "Intersecter" for performing fast intersection tests that preserve both
query and target intervals and associated annotation
Description-md5: 67d503eba4b89cb2b658656d4c7560a1
Homepage: https://github.com/bxlab/bx-python
Section: python
Priority: optional
Filename: pool/main/p/python-bx/python3-bx_0.13.0-1+b2_amd64.deb
Size: 941944
MD5sum: 194cf869744873aeff171c880dffc5bb
SHA256: 1a6dc179451367894c0e8981d85a67342d1f1402e5d26e4a35d069ec06a0e991
0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'show', '--no-all-versions', 'python3-bx']
0m4.8s INFO: apt-cache knows about the following packages: python3-bx
0m4.8s INFO: Running scripts pre_install
0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_database-server']
0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_database-server']
0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_exceptions']
0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_exceptions']
0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_extras']
0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_extras']
0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture']
0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture']
0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy']
0m4.8s 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:
0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy']
0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy', 'python3-bx']
0m4.9s DUMP:
python3-bx:
Installed: (none)
Candidate: 0.13.0-1+b2
Version table:
0.13.0-1+b2 500
500 http://deb.debian.org/debian trixie/main amd64 Packages
0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy', 'python3-bx']
0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-y', 'install', 'python3-bx']
0m8.9s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
libblas3 libexpat1 libffi8 libgfortran5 liblapack3 liblzo2-2 libncursesw6
libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64
libsqlite3-0 media-types netbase python3 python3-lzo python3-minimal
python3-numpy python3-numpy-dev python3-pyparsing python3.13
python3.13-minimal readline-common
Suggested packages:
python3-doc python3-tk python3-venv gcc gfortran python-numpy-doc
python3-dev python3-pytest python-pyparsing-doc python3.13-venv
python3.13-doc binutils binfmt-support readline-doc
Recommended packages:
libgpm2 ca-certificates
The following NEW packages will be installed:
libblas3 libexpat1 libffi8 libgfortran5 liblapack3 liblzo2-2 libncursesw6
libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64
libsqlite3-0 media-types netbase python3 python3-bx python3-lzo
python3-minimal python3-numpy python3-numpy-dev python3-pyparsing python3.13
python3.13-minimal readline-common
0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.6 MB of archives.
After this operation, 90.2 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get:3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-1 [27.1 kB]
Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB]
Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get:7 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get:8 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-1 [136 kB]
Get:9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB]
Get:10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get:11 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB]
Get:12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get:13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get:14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB]
Get:15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-1 [28.1 kB]
Get:16 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2 [138 kB]
Get:17 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get:18 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB]
Get:19 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get:20 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.3+ds-2 [7517 kB]
Get:21 http://deb.debian.org/debian trixie/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB]
Get:22 http://deb.debian.org/debian trixie/main amd64 python3-lzo amd64 1.15-2+b1 [9276 B]
Get:23 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:24 http://deb.debian.org/debian trixie/main amd64 python3-bx amd64 0.13.0-1+b2 [942 kB]
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Adding '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'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding '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'
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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
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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
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Processing triggers for libc-bin (2.40-7) ...
0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-y', 'install', 'python3-bx']
0m8.9s INFO: Running scripts post_install
0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_install_exceptions']
0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_install_exceptions']
0m8.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m9.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m9.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpvbvq_vp_ to sid
0m9.2s DEBUG: sources.list:
deb http://deb.debian.org/debian/ sid main
0m9.2s INFO: Running scripts pre_distupgrade
0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_exceptions']
0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_exceptions']
0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', 'update']
0m11.1s 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 [7380 kB]
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Reading package lists...
0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', 'update']
0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-yf', 'dist-upgrade']
0m12.9s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
bsdutils gcc-14-base libblkid1 libcap2 libgcc-s1 libgfortran5 libmount1
libseccomp2 libselinux1 libsemanage2 libsmartcols1 libstdc++6 libuuid1 login
login.defs media-types mount passwd python3-bx sysvinit-utils util-linux
21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 6214 kB of archives.
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Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.4-5 [106 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.4-5 [36.5 kB]
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Get:5 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.4-5 [140 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.4-5 [1205 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.4-5 [156 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.8-4 [84.8 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.14-3 [34.0 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.4-5 [88.7 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-17 [49.1 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-17 [713 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
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Get:15 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.73-4 [27.3 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-2+b1 [48.1 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.17.3-1 [186 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.8-1+b1 [94.7 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.17.3-1 [1227 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 media-types all 12.0.0 [28.9 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 python3-bx amd64 0.13.0-1+b3 [712 kB]
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Preparing to unpack .../libstdc++6_14.2.0-17_amd64.deb ...
Unpacking libstdc++6:amd64 (14.2.0-17) over (14.2.0-16) ...
Setting up libstdc++6:amd64 (14.2.0-17) ...
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Preparing to unpack .../libgfortran5_14.2.0-17_amd64.deb ...
Unpacking libgfortran5:amd64 (14.2.0-17) over (14.2.0-16) ...
Preparing to unpack .../libgcc-s1_14.2.0-17_amd64.deb ...
Unpacking libgcc-s1:amd64 (14.2.0-17) over (14.2.0-16) ...
Setting up libgcc-s1:amd64 (14.2.0-17) ...
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Preparing to unpack .../libcap2_1%3a2.73-4_amd64.deb ...
Unpacking libcap2:amd64 (1:2.73-4) over (1:2.66-5+b1) ...
Setting up libcap2:amd64 (1:2.73-4) ...
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Unpacking libseccomp2:amd64 (2.5.5-2+b1) over (2.5.5-2) ...
Setting up libseccomp2:amd64 (2.5.5-2+b1) ...
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Preparing to unpack .../login.defs_1%3a4.17.3-1_all.deb ...
Unpacking login.defs (1:4.17.3-1) over (1:4.17.2-5) ...
Preparing to unpack .../libsemanage2_3.8-1+b1_amd64.deb ...
Unpacking libsemanage2:amd64 (3.8-1+b1) over (3.8-1) ...
Preparing to unpack .../passwd_1%3a4.17.3-1_amd64.deb ...
Unpacking passwd (1:4.17.3-1) over (1:4.17.2-5) ...
Preparing to unpack .../media-types_12.0.0_all.deb ...
Unpacking media-types (12.0.0) over (10.1.0) ...
Preparing to unpack .../python3-bx_0.13.0-1+b3_amd64.deb ...
Unpacking python3-bx (0.13.0-1+b3) over (0.13.0-1+b2) ...
Setting up media-types (12.0.0) ...
Installing new version of config file /etc/mime.types ...
Setting up python3-bx (0.13.0-1+b3) ...
Setting up login.defs (1:4.17.3-1) ...
Setting up libgfortran5:amd64 (14.2.0-17) ...
Setting up mount (2.40.4-5) ...
Setting up libsemanage2:amd64 (3.8-1+b1) ...
Setting up login (1:4.16.0-2+really2.40.4-5) ...
Setting up passwd (1:4.17.3-1) ...
Processing triggers for libc-bin (2.40-7) ...
0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-yf', 'dist-upgrade']
0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m13.1s DUMP:
af70a70f294ee3f13d7d41368ee5bbaf -
0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'show', '--no-all-versions', 'python3-bx']
0m13.2s DUMP:
Package: python3-bx
Source: python-bx (0.13.0-1)
Version: 0.13.0-1+b3
Installed-Size: 3485
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Provides: python3-bx-tools
Depends: python3-lzo, libc6 (>= 2.14), zlib1g (>= 1:1.1.4), python3 (<< 3.14), python3 (>= 3.13~), python3-numpy, python3-numpy2-abi0 | python3-numpy-abi9, python3-pyparsing, python3:any
Description-en: library to manage genomic data and its alignment
The bx-python project is a Python3 library and associated set of scripts to
allow for rapid implementation of genome scale analyses. The library contains
a variety of useful modules, but the particular strengths are:
* Classes for reading and working with genome-scale multiple local
alignments (in MAF, AXT, and LAV formats)
* Generic data structure for indexing on disk files that contain blocks of
data associated with intervals on various sequences (used, for example, to
provide random access to individual alignments in huge files; optimized
for use over network filesystems)
* Data structures for working with intervals on sequences
* "Binned bitsets" which act just like chromosome sized bit arrays, but
lazily allocate regions and allow large blocks of all set or all unset
bits to be stored compactly
* "Intersecter" for performing fast intersection tests that preserve both
query and target intervals and associated annotation
Description-md5: 67d503eba4b89cb2b658656d4c7560a1
Homepage: https://github.com/bxlab/bx-python
Section: python
Priority: optional
Filename: pool/main/p/python-bx/python3-bx_0.13.0-1+b3_amd64.deb
Size: 711784
MD5sum: 284408d35921b0c2c9f1aab85db3b857
SHA256: 071ef6247463988193bfc5b46e0eb342d2bf142bccba902d07926960df429444
0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'show', '--no-all-versions', 'python3-bx']
0m13.2s INFO: apt-cache knows about the following packages: python3-bx
0m13.2s INFO: Running scripts pre_install
0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_database-server']
0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_database-server']
0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_exceptions']
0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_exceptions']
0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_extras']
0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_extras']
0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture']
0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture']
0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy']
0m13.3s 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:
0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy']
0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy', 'python3-bx']
0m13.3s DUMP:
python3-bx:
Installed: 0.13.0-1+b3
Candidate: 0.13.0-1+b3
Version table:
*** 0.13.0-1+b3 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy', 'python3-bx']
0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-y', 'install', 'python3-bx']
0m13.5s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
python3-bx is already the newest version (0.13.0-1+b3).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-y', 'install', 'python3-bx']
0m13.5s INFO: Running scripts post_install
0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_install_exceptions']
0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_install_exceptions']
0m13.5s INFO: Running scripts post_distupgrade
0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_base_cleanup']
0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_base_cleanup']
0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_exceptions']
0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_exceptions']
0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_zz_backports']
0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_distupgrade_zz_backports']
0m13.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m13.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m13.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m14.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m14.1s INFO: Running scripts pre_install
0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_database-server']
0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_database-server']
0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_exceptions']
0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_exceptions']
0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_extras']
0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_extras']
0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture']
0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture']
0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy']
0m14.2s 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:
0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy']
0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy', 'python3-bx']
0m14.2s DUMP:
python3-bx:
Installed: 0.13.0-1+b3
Candidate: 0.13.0-1+b3
Version table:
*** 0.13.0-1+b3 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-cache', 'policy', 'python3-bx']
0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-y', 'install', 'python3-bx=0.13.0-1+b3']
0m14.4s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
python3-bx is already the newest version (0.13.0-1+b3).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', '-y', 'install', 'python3-bx=0.13.0-1+b3']
0m14.4s INFO: Running scripts post_install
0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_install_exceptions']
0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_install_exceptions']
0m14.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m14.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m15.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', '-ac', '--ignore-obsolete']
0m15.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', '-ac', '--ignore-obsolete']
0m15.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m15.5s DUMP:
0.15.6
0m15.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m15.5s INFO: Running adequate version 0.15.6 now.
0m15.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'python3-bx']
0m15.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'python3-bx']
0m15.9s INFO: Running scripts pre_remove
0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_exceptions']
0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/pre_remove_exceptions']
0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m16.3s 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 1:2.40.4-5
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 14.2.0-17
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 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 2.40.4-5
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 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 libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed liblapack3:amd64 liblapack3 3.12.1-2
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 liblzo2-2:amd64 liblzo2-2 2.10-3+b1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.40.4-5
install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-1
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
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 libpython3-stdlib:amd64 libpython3-stdlib 3.13.2-1
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 libseccomp2:amd64 libseccomp2 2.5.5-2+b1
install ok installed libselinux1:amd64 libselinux1 3.8-4
install ok installed libsemanage-common libsemanage-common 3.8-1
install ok installed libsemanage2:amd64 libsemanage2 3.8-1+b1
install ok installed libsepol2:amd64 libsepol2 3.8-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-5
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 libssl3t64:amd64 libssl3t64 3.4.1-1
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-17
install ok installed libsystemd0:amd64 libsystemd0 257.3-1
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-1
install ok installed libudev1:amd64 libudev1 257.3-1
install ok installed libuuid1:amd64 libuuid1 2.40.4-5
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+really2.40.4-5
install ok installed login.defs login.defs 1:4.17.3-1
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 12.0.0
install ok installed mount mount 2.40.4-5
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-provider-legacy openssl-provider-legacy 3.4.1-1
install ok installed passwd passwd 1:4.17.3-1
install ok installed perl-base perl-base 5.40.1-2
install ok installed python3 python3 3.13.2-1
install ok installed python3-bx python3-bx 0.13.0-1+b3
install ok installed python3-lzo:amd64 python3-lzo 1.15-2+b1
install ok installed python3-minimal python3-minimal 3.13.2-1
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-pyparsing python3-pyparsing 3.1.2-1
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 3.14-3
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 2.40.4-5
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', 'remove', 'libblas3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'liblapack3:amd64', 'liblzo2-2:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-lzo:amd64', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pyparsing', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-bx']
0m17.1s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
libblas3 libexpat1 libffi8 libgfortran5 liblapack3 liblzo2-2 libncursesw6
libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64
libsqlite3-0 media-types netbase python3 python3-bx python3-lzo
python3-minimal python3-numpy python3-numpy-dev python3-pyparsing python3.13
python3.13-minimal readline-common
0 upgraded, 0 newly installed, 24 to remove and 0 not upgraded.
After this operation, 87.9 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 ... 7239 files and directories currently installed.)
Removing python3-bx (0.13.0-1+b3) ...
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-lzo:amd64 (1.15-2+b1) ...
Removing python3-pyparsing (3.1.2-1) ...
Removing python3 (3.13.2-1) ...
Removing python3-minimal (3.13.2-1) ...
Removing python3.13 (3.13.2-1) ...
Removing python3.13-minimal (3.13.2-1) ...
Removing libexpat1:amd64 (2.6.4-1) ...
Removing libpython3-stdlib:amd64 (3.13.2-1) ...
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 liblzo2-2:amd64 (2.10-3+b1) ...
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 (12.0.0) ...
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) ...
0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', 'remove', 'libblas3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'liblapack3:amd64', 'liblzo2-2:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-lzo:amd64', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pyparsing', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-bx']
0m17.1s INFO: Running scripts post_remove
0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_remove_exceptions']
0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_remove_exceptions']
0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg', '--purge', 'libblas3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'liblapack3:amd64', 'liblzo2-2:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-lzo:amd64', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pyparsing', 'python3.13', 'python3.13-minimal', 'readline-common']
0m17.2s DUMP:
dpkg: warning: ignoring request to remove libblas3 which isn't installed
dpkg: warning: ignoring request to remove libexpat1 which isn't installed
dpkg: warning: ignoring request to remove libffi8 which isn't installed
dpkg: warning: ignoring request to remove libgfortran5 which isn't installed
dpkg: warning: ignoring request to remove liblapack3 which isn't installed
dpkg: warning: ignoring request to remove liblzo2-2 which isn't installed
dpkg: warning: ignoring request to remove libncursesw6 which isn't installed
dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed
(Reading database ... 5078 files and directories currently 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 libsqlite3-0 which isn't installed
Purging configuration files for media-types (12.0.0) ...
Purging configuration files for netbase (6.4) ...
Purging configuration files for python3 (3.13.2-1) ...
dpkg: warning: ignoring request to remove python3-lzo which isn't installed
dpkg: warning: ignoring request to remove python3-minimal 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-pyparsing 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) ...
0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg', '--purge', 'libblas3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'liblapack3:amd64', 'liblzo2-2:amd64', 'libncursesw6:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'python3', 'python3-lzo:amd64', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pyparsing', 'python3.13', 'python3.13-minimal', 'readline-common']
0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg', '--purge', 'python3-bx']
0m17.2s DUMP:
dpkg: warning: ignoring request to remove python3-bx which isn't installed
0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg', '--purge', 'python3-bx']
0m17.2s INFO: Running scripts post_purge
0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_purge_exceptions']
0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_purge_exceptions']
0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg', '--purge', '--pending']
0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg', '--purge', '--pending']
0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg', '--remove', '--pending']
0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg', '--remove', '--pending']
0m17.2s INFO: Running scripts post_test
0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_test_exceptions']
0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'tmp/scripts/post_test_exceptions']
0m17.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m17.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg-divert', '--list']
0m17.4s 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
0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'dpkg-divert', '--list']
0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', 'clean']
0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_', 'apt-get', 'clean']
0m17.5s DEBUG: Recording chroot state
0m18.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/shm']
0m18.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/shm']
0m18.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/console']
0m18.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/console']
0m18.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/ptmx']
0m18.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/ptmx']
0m18.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/pts']
0m18.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/dev/pts']
0m18.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/proc']
0m18.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_/proc']
0m18.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m18.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvbvq_vp_']
0m18.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpvbvq_vp_
0m18.1s INFO: PASS: Upgrading between Debian distributions.
0m18.1s INFO: PASS: All tests.
0m18.1s INFO: piuparts run ends.
ret=0
End: 2025-02-26 22:35:40 GMT