Start: 2025-04-06 23:41:09 GMT
[oldstable]
Package: python3-pairtools
Source: pairtools (0.3.0-2)
Version: 0.3.0-2+b2
Installed-Size: 440
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libc6 (>= 2.14), cython3, python3 (<< 3.10), python3 (>= 3.9~), python3-click, python3-nose, python3-numpy, python3:any
Description: Framework to process sequencing data from a Hi-C experiment
Homepage: https://github.com/mirnylab/pairtools
Description-md5: a340132b5467a45fa9b90e04ece3e5c1
Section: python
Priority: optional
Filename: pool/main/p/pairtools/python3-pairtools_0.3.0-2+b2_amd64.deb
Size: 124224
MD5sum: 337f6673fb6f149bb8d615223d70fc87
SHA256: 2167b621603f917130cfa98a7ad01614e70390929a431b90169b40e57c88859c
[stable]
Package: python3-pairtools
Source: pairtools (1.0.2-2)
Version: 1.0.2-2+b1
Installed-Size: 685
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), cython3, python3 (<< 3.12), python3 (>= 3.11~), python3-bioframe, python3-click, python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any
Suggests: python3-pairtools-examples (>= 1.0.2)
Description: Framework to process sequencing data from a Hi-C experiment
Homepage: https://github.com/mirnylab/pairtools
Description-md5: a340132b5467a45fa9b90e04ece3e5c1
Section: python
Priority: optional
Filename: pool/main/p/pairtools/python3-pairtools_1.0.2-2+b1_amd64.deb
Size: 165424
MD5sum: 4c8493139ea6d69ec56236651011bfc2
SHA256: ac685faeb4b2619bca8ae60b81a9a257f6efaf8e5a1f19d97a646e2fa1d51750
[testing]
Package: python3-pairtools
Source: pairtools (1.1.3-1)
Version: 1.1.3-1+b1
Installed-Size: 833
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: python3-standard-pipes, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), python3 (<< 3.14), python3 (>= 3.13~), python3-bioframe, python3-click, python3-numpy, python3-numpy2-abi0 | python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any
Suggests: python3-pairtools-examples (>= 1.0.2)
Description: Framework to process sequencing data from a Hi-C experiment
Homepage: https://github.com/mirnylab/pairtools
Description-md5: a340132b5467a45fa9b90e04ece3e5c1
Section: python
Priority: optional
Filename: pool/main/p/pairtools/python3-pairtools_1.1.3-1+b1_amd64.deb
Size: 207068
MD5sum: 69eb3c6e74046d498e5aef47f8106f33
SHA256: 413bfb5ff113c99270df2798fb8b32782b7627157892fc057e223d414550e9ce
[sid]
Package: python3-pairtools
Source: pairtools (1.1.3-1)
Version: 1.1.3-1+b1
Installed-Size: 833
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: python3-standard-pipes, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), python3 (<< 3.14), python3 (>= 3.13~), python3-bioframe, python3-click, python3-numpy, python3-numpy2-abi0 | python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any
Suggests: python3-pairtools-examples (>= 1.0.2)
Description: Framework to process sequencing data from a Hi-C experiment
Homepage: https://github.com/mirnylab/pairtools
Description-md5: a340132b5467a45fa9b90e04ece3e5c1
Section: python
Priority: optional
Filename: pool/main/p/pairtools/python3-pairtools_1.1.3-1+b1_amd64.deb
Size: 207068
MD5sum: 69eb3c6e74046d498e5aef47f8106f33
SHA256: 413bfb5ff113c99270df2798fb8b32782b7627157892fc057e223d414550e9ce
Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/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/bullseye-merged-usr_amd64.tar.gz -d oldstable -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/oldstable222sid/reference-chroot-metadata.dat --apt python3-pairtools=1.1.3-1+b1
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile.
0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ
0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong.
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: piuparts version 1.5.2~202503162239~1.5.1-10-g345d5865 starting up.
0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/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/bullseye-merged-usr_amd64.tar.gz -d oldstable -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/oldstable222sid/reference-chroot-metadata.dat --apt python3-pairtools=1.1.3-1+b1
0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64
0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpdq6cj8uq
0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpdq6cj8uq
0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz']
0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz']
0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/proc']
0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/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/tmpdq6cj8uq/dev/pts']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/pts']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/ptmx']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/ptmx']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/9', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/console']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/9', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/console']
0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/shm']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/shm']
0m0.4s DEBUG: sources.list:
deb http://deb.debian.org/debian/ bullseye 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/tmpdq6cj8uq/tmp/scripts/
0m0.4s INFO: Running scripts post_chroot_unpack
0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', 'update']
0m1.1s DUMP:
Hit:1 http://deb.debian.org/debian bullseye InRelease
Reading package lists...
0m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', 'update']
0m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-yf', 'dist-upgrade']
0m1.4s DUMP:
Reading package lists...
Building dependency tree...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-yf', 'dist-upgrade']
0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m1.6s DUMP:
f58ca9ba0b3223edf5b7797c101a5448 -
0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m1.6s INFO: Running scripts post_setup
0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_dummy_users']
0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_dummy_users']
0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_forbid_home']
0m2.6s DUMP:
Disabling /home
Adding 'local diversion of /home to /home.distrib'
0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_forbid_home']
0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_force-unsafe-io']
0m2.6s DUMP:
Enabling dpkg --force-unsafe-io.
Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib'
Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged'
'/bin/sync' -> 'true'
0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_force-unsafe-io']
0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_minimize']
0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_minimize']
0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_squeeze-backports']
0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_squeeze-backports']
0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_zz_backports']
0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_setup_zz_backports']
0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m2.7s DUMP:
install ok installed adduser adduser 3.118+deb11u1
install ok installed apt apt 2.2.4
install ok installed base-files base-files 11.1+deb11u11
install ok installed base-passwd base-passwd 3.5.51
install ok installed bash bash 5.1-2+deb11u1
install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u2
install ok installed coreutils coreutils 8.32-4+b1
install ok installed dash dash 0.5.11+git20200708+dd9ef66-5
install ok installed debconf debconf 1.5.77
install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1
install ok installed debianutils debianutils 4.11.2
install ok installed diffutils diffutils 1:3.7-5
install ok installed dpkg dpkg 1.20.13
install ok installed e2fsprogs e2fsprogs 1.46.2-2
install ok installed findutils findutils 4.8.0-1
install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6
install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22
install ok installed gpgv gpgv 2.2.27-2+deb11u2
install ok installed grep grep 3.6-1+deb11u1
install ok installed gzip gzip 1.10-4+deb11u1
install ok installed hostname hostname 3.23
install ok installed init-system-helpers init-system-helpers 1.60
install ok installed libacl1:amd64 libacl1 2.2.53-10
install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4
install ok installed libattr1:amd64 libattr1 1:2.4.48-6
install ok installed libaudit-common libaudit-common 1:3.0-2
install ok installed libaudit1:amd64 libaudit1 1:3.0-2
install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u2
install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4
install ok installed libc-bin libc-bin 2.31-13+deb11u11
install ok installed libc6:amd64 libc6 2.31-13+deb11u11
install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1
install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4
install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260
install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2
install ok installed libffi7:amd64 libffi7 3.3-6
install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6
install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6
install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1
install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u5
install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2
install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u5
install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1
install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5
install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u5
install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2
install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u5
install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u5
install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2
install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1
install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u2
install ok installed libnettle8:amd64 libnettle8 3.7.3-1
install ok installed libnsl2:amd64 libnsl2 1.3.0-2
install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1
install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1
install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1
install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1
install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1
install ok installed libpcre3:amd64 libpcre3 2:8.39-13
install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1
install ok installed libselinux1:amd64 libselinux1 3.1-3
install ok installed libsemanage-common libsemanage-common 3.1-1
install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2
install ok installed libsepol1:amd64 libsepol1 3.1-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u2
install ok installed libss2:amd64 libss2 1.46.2-2
install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1
install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6
install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u5
install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1
install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2
install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1
install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1
install ok installed libudev1:amd64 libudev1 247.3-7+deb11u5
install ok installed libunistring2:amd64 libunistring2 0.9.10-4
install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2
install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2
install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1
install ok installed login login 1:4.8.1-1
install ok installed logsave logsave 1.46.2-2
install ok installed lsb-base lsb-base 11.1.0
install ok installed mawk mawk 1.3.4.20200120-2
install ok installed mount mount 2.36.1-8+deb11u2
install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2
install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2
install ok installed passwd passwd 1:4.8.1-1
install ok installed perl-base perl-base 5.32.1-4+deb11u3
install ok installed sed sed 4.7-1
install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1
install ok installed tar tar 1.34+dfsg-1+deb11u1
install ok installed tzdata tzdata 2024a-0+deb11u1
install ok installed util-linux util-linux 2.36.1-8+deb11u2
install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2
0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m2.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/oldstable222sid/reference-chroot-metadata.dat
0m2.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
0m3.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
0m3.2s INFO: Running scripts is_testable
0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/is_testable_uninstallable']
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/is_testable_uninstallable']
0m3.3s INFO: Running scripts pre_test
0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_test_exceptions']
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_test_exceptions']
0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_test_root_password']
0m3.3s DUMP:
New password: Retype new password: passwd: password updated successfully
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_test_root_password']
0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools']
0m3.6s DUMP:
Package: python3-pairtools
Source: pairtools (0.3.0-2)
Version: 0.3.0-2+b2
Installed-Size: 440
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libc6 (>= 2.14), cython3, python3 (<< 3.10), python3 (>= 3.9~), python3-click, python3-nose, python3-numpy, python3:any
Description-en: Framework to process sequencing data from a Hi-C experiment
Simple and fast command-line framework to process sequencing data from a Hi-C
experiment.
.
Process pair-end sequence alignments and perform the following operations:
.
- Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end
sequences of Hi-C DNA molecules
- Sort .pairs files for downstream analyses
- Detect, tag and remove PCR/optical duplicates
- Generate extensive statistics of Hi-C datasets
- Select Hi-C pairs given flexibly defined criteria
- Restore .sam alignments from Hi-C pairs
Description-md5: a340132b5467a45fa9b90e04ece3e5c1
Homepage: https://github.com/mirnylab/pairtools
Section: python
Priority: optional
Filename: pool/main/p/pairtools/python3-pairtools_0.3.0-2+b2_amd64.deb
Size: 124224
MD5sum: 337f6673fb6f149bb8d615223d70fc87
SHA256: 2167b621603f917130cfa98a7ad01614e70390929a431b90169b40e57c88859c
0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools']
0m3.6s INFO: apt-cache knows about the following packages: python3-pairtools
0m3.6s INFO: Running scripts pre_install
0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
0m3.7s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian bullseye/main amd64 Packages
release v=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
0m3.7s DUMP:
python3-pairtools:
Installed: (none)
Candidate: 0.3.0-2+b2
Version table:
0.3.0-2+b2 500
500 http://deb.debian.org/debian bullseye/main amd64 Packages
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools']
0m11.0s DUMP:
Reading package lists...
Building dependency tree...
The following additional packages will be installed:
cython3 libblas3 libexpat1 libgfortran5 liblapack3 libmpdec3 libncursesw6
libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0
libreadline8 libsqlite3-0 media-types python3 python3-click python3-colorama
python3-minimal python3-nose python3-numpy python3-pkg-resources python3.9
python3.9-minimal readline-common
Suggested packages:
cython-doc python3-doc python3-tk python3-venv python-nose-doc gcc gfortran
python-numpy-doc python3-dev python3-numpy-dbg python3-pytest
python3-setuptools python3.9-venv python3.9-doc binutils binfmt-support
readline-doc
Recommended packages:
python3-dev gcc libgpm2 ca-certificates
The following NEW packages will be installed:
cython3 libblas3 libexpat1 libgfortran5 liblapack3 libmpdec3 libncursesw6
libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0
libreadline8 libsqlite3-0 media-types python3 python3-click python3-colorama
python3-minimal python3-nose python3-numpy python3-pairtools
python3-pkg-resources python3.9 python3.9-minimal readline-common
0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded.
Need to get 14.1 MB of archives.
After this operation, 56.9 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB]
Get:2 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB]
Get:3 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB]
Get:4 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB]
Get:5 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB]
Get:6 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB]
Get:7 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB]
Get:8 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB]
Get:9 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB]
Get:10 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB]
Get:11 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB]
Get:12 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB]
Get:13 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB]
Get:14 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB]
Get:15 http://deb.debian.org/debian bullseye/main amd64 cython3 amd64 0.29.21-3+b1 [1312 kB]
Get:16 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB]
Get:17 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB]
Get:18 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB]
Get:19 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB]
Get:20 http://deb.debian.org/debian bullseye/main amd64 python3-colorama all 0.4.4-1 [28.5 kB]
Get:21 http://deb.debian.org/debian bullseye/main amd64 python3-click all 7.1.2-1 [75.7 kB]
Get:22 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB]
Get:23 http://deb.debian.org/debian bullseye/main amd64 python3-nose all 1.3.7-7 [133 kB]
Get:24 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB]
Get:25 http://deb.debian.org/debian bullseye/main amd64 python3-pairtools amd64 0.3.0-2+b2 [124 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 14.1 MB in 0s (108 MB/s)
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Selecting previously unselected package libexpat1:amd64.
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Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../python3.9-minimal_3.9.2-1_amd64.deb ...
Unpacking python3.9-minimal (3.9.2-1) ...
Setting up libpython3.9-minimal:amd64 (3.9.2-1) ...
Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ...
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Selecting previously unselected package python3-pairtools.
Preparing to unpack .../11-python3-pairtools_0.3.0-2+b2_amd64.deb ...
Unpacking python3-pairtools (0.3.0-2+b2) ...
Setting up media-types (4.0.0) ...
Setting up libsqlite3-0:amd64 (3.34.1-3) ...
Setting up libblas3:amd64 (3.9.0-3+deb11u1) ...
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 libquadmath0:amd64 (10.2.1-6) ...
Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ...
Setting up libgfortran5:amd64 (10.2.1-6) ...
Setting up libmpdec3:amd64 (2.5.1-1) ...
Setting up readline-common (8.1-1) ...
Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up libreadline8:amd64 (8.1-1) ...
Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ...
Setting up libpython3-stdlib:amd64 (3.9.2-3) ...
Setting up python3.9 (3.9.2-1) ...
Setting up python3 (3.9.2-3) ...
Setting up cython3 (0.29.21-3+b1) ...
Setting up python3-pkg-resources (52.0.0-4) ...
Setting up python3-colorama (0.4.4-1) ...
Setting up python3-click (7.1.2-1) ...
Setting up python3-nose (1.3.7-7) ...
Setting up python3-numpy (1:1.19.5-1) ...
Setting up python3-pairtools (0.3.0-2+b2) ...
Processing triggers for libc-bin (2.31-13+deb11u11) ...
0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools']
0m11.0s INFO: Running scripts post_install
0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
0m11.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
0m11.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
0m11.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpdq6cj8uq to stable
0m11.4s DEBUG: sources.list:
deb http://deb.debian.org/debian/ bookworm main
0m11.4s INFO: Running scripts pre_distupgrade
0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_exceptions']
0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_exceptions']
0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', 'update']
0m14.2s DUMP:
Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB]
Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8792 kB]
Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6109 kB]
Fetched 15.1 MB in 2s (8473 kB/s)
Reading package lists...
0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', 'update']
0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-yf', 'dist-upgrade']
1m17.3s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
libmpdec3 libpython3.9-minimal libpython3.9-stdlib python3-nose python3.9
python3.9-minimal
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
libsemanage1
The following NEW packages will be installed:
binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp
cpp-12 fontconfig-config fonts-dejavu-core fonts-lyx g++ g++-12 gcc gcc-12
gcc-12-base libasan8 libatomic1 libbinutils libboost-dev libboost1.74-dev
libbrotli1 libbsd0 libc-dev-bin libc6-dev libcap2 libcc1-0 libcrypt-dev
libctf-nobfd0 libctf0 libcurl3-gnutls libdeflate0 libexpat1-dev libffi8
libfile-find-rule-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev
libgdbm-compat4 libgdbm6 libglib2.0-0 libgomp1 libgprofng0 libgraphite2-3
libharfbuzz0b libhts3 libhtscodecs2 libicu72 libimagequant0 libisl23 libitm1
libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui
libjs-sphinxdoc libjs-underscore liblbfgsb0 liblcms2-2 libldap-2.5-0
liblerc4 liblsan0 libmd0 libmpc3 libmpfr6 libnghttp2-14 libnsl-dev
libnumber-compare-perl libopenblas-dev libopenblas-pthread-dev libopenblas0
libopenblas0-pthread libopenjp2-7 libperl5.36 libpng16-16 libpsl5
libpython3-all-dev libpython3-dev libpython3.11 libpython3.11-dev
libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 librtmp1
libsasl2-2 libsasl2-modules-db libsemanage2 libsepol2 libssh2-1 libssl3
libstdc++-12-dev libtcl8.6 libtext-glob-perl libtiff6 libtirpc-dev libtk8.6
libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data
libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev
libxslt1.1 libxss1 libyaml-0-2 linux-libc-dev openssl perl perl-modules-5.36
python-matplotlib-data python3-all python3-all-dev python3-appdirs
python3-attr python3-beniget python3-bioframe python3-brotli python3-certifi
python3-chardet python3-charset-normalizer python3-contourpy python3-cycler
python3-dateutil python3-decorator python3-dev python3-distutils
python3-fonttools python3-fs python3-gast python3-idna python3-kiwisolver
python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-mpmath
python3-packaging python3-pandas python3-pandas-lib python3-pil
python3-pil.imagetk python3-ply python3-pyparsing python3-pysam
python3-pythran python3-requests python3-scipy python3-six python3-sympy
python3-tk python3-tz python3-ufolib2 python3-urllib3 python3-yaml
python3.11 python3.11-dev python3.11-minimal rpcsvc-proto tk8.6-blt2.5
unicode-data usrmerge util-linux-extra x11-common zlib1g-dev
The following packages will be upgraded:
adduser apt base-files base-passwd bash bsdutils coreutils cython3 dash
debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs
findutils gpgv grep gzip hostname init-system-helpers libacl1 libapt-pkg6.0
libattr1 libaudit-common libaudit1 libblas3 libblkid1 libbz2-1.0 libc-bin
libc6 libcap-ng0 libcom-err2 libcrypt1 libdb5.3 libdebconfclient0 libexpat1
libext2fs2 libgcc-s1 libgcrypt20 libgfortran5 libgmp10 libgnutls30
libgpg-error0 libgssapi-krb5-2 libhogweed6 libidn2-0 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblz4-1 liblzma5
libmount1 libncursesw6 libnettle8 libp11-kit0 libpam-modules
libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3
libpython3-stdlib libquadmath0 libreadline8 libseccomp2 libselinux1
libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++6 libsystemd0
libtasn1-6 libtinfo6 libtirpc-common libtirpc3 libudev1 libunistring2
libuuid1 libxxhash0 libzstd1 login logsave lsb-base mawk media-types mount
ncurses-base ncurses-bin passwd perl-base python3 python3-click
python3-colorama python3-minimal python3-nose python3-numpy
python3-pairtools python3-pkg-resources readline-common sed sysvinit-utils
tar tzdata util-linux zlib1g
109 upgraded, 175 newly installed, 1 to remove and 0 not upgraded.
Need to get 230 MB of archives.
After this operation, 951 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u10 [70.9 kB]
Get:2 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-9+deb12u10 [2757 kB]
Get:3 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u10 [608 kB]
Get:4 http://deb.debian.org/debian bookworm/main amd64 gcc-12-base amd64 12.2.0-14 [37.5 kB]
Get:5 http://deb.debian.org/debian bookworm/main amd64 libgcc-s1 amd64 12.2.0-14 [49.9 kB]
Get:6 http://deb.debian.org/debian bookworm/main amd64 debianutils amd64 5.7-0.5~deb12u1 [103 kB]
Get:7 http://deb.debian.org/debian bookworm/main amd64 bash amd64 5.2.15-2+b7 [1490 kB]
Get:8 http://deb.debian.org/debian bookworm/main amd64 bsdutils amd64 1:2.38.1-5+deb12u3 [94.4 kB]
Get:9 http://deb.debian.org/debian bookworm/main amd64 libgmp10 amd64 2:6.2.1+dfsg1-1.1 [563 kB]
Get:10 http://deb.debian.org/debian bookworm/main amd64 coreutils amd64 9.1-1 [2897 kB]
Get:11 http://deb.debian.org/debian bookworm/main amd64 liblzma5 amd64 5.4.1-0.2 [205 kB]
Get:12 http://deb.debian.org/debian bookworm/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB]
Get:13 http://deb.debian.org/debian bookworm/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [290 kB]
Get:14 http://deb.debian.org/debian bookworm/main amd64 tar amd64 1.34+dfsg-1.2+deb12u1 [836 kB]
Get:15 http://deb.debian.org/debian bookworm/main amd64 dpkg amd64 1.21.22 [1567 kB]
Get:16 http://deb.debian.org/debian bookworm/main amd64 dash amd64 0.5.12-2 [91.8 kB]
Get:17 http://deb.debian.org/debian bookworm/main amd64 diffutils amd64 1:3.8-4 [352 kB]
Get:18 http://deb.debian.org/debian bookworm/main amd64 findutils amd64 4.9.0-4 [636 kB]
Get:19 http://deb.debian.org/debian bookworm/main amd64 grep amd64 3.8-5 [421 kB]
Get:20 http://deb.debian.org/debian bookworm/main amd64 gzip amd64 1.12-1 [140 kB]
Get:21 http://deb.debian.org/debian bookworm/main amd64 hostname amd64 3.23+nmu1 [10.5 kB]
Get:22 http://deb.debian.org/debian bookworm/main amd64 login amd64 1:4.13+dfsg1-1+b1 [616 kB]
Get:23 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB]
Get:24 http://deb.debian.org/debian bookworm/main amd64 libtinfo6 amd64 6.4-4 [331 kB]
Get:25 http://deb.debian.org/debian bookworm/main amd64 ncurses-bin amd64 6.4-4 [421 kB]
Get:26 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.36.0-7+deb12u1 [1608 kB]
Get:27 http://deb.debian.org/debian bookworm/main amd64 sed amd64 4.9-1 [329 kB]
Get:28 http://deb.debian.org/debian bookworm/main amd64 libblkid1 amd64 2.38.1-5+deb12u3 [147 kB]
Get:29 http://deb.debian.org/debian bookworm/main amd64 libpcre2-8-0 amd64 10.42-1 [261 kB]
Get:30 http://deb.debian.org/debian bookworm/main amd64 libselinux1 amd64 3.4-1+b6 [73.7 kB]
Get:31 http://deb.debian.org/debian bookworm/main amd64 libmount1 amd64 2.38.1-5+deb12u3 [166 kB]
Get:32 http://deb.debian.org/debian bookworm/main amd64 libsmartcols1 amd64 2.38.1-5+deb12u3 [107 kB]
Get:33 http://deb.debian.org/debian bookworm/main amd64 libaudit-common all 1:3.0.9-1 [10.4 kB]
Get:34 http://deb.debian.org/debian bookworm/main amd64 libcap-ng0 amd64 0.8.3-1+b3 [17.1 kB]
Get:35 http://deb.debian.org/debian bookworm/main amd64 libaudit1 amd64 1:3.0.9-1 [46.8 kB]
Get:36 http://deb.debian.org/debian bookworm/main amd64 util-linux-extra amd64 2.38.1-5+deb12u3 [111 kB]
Get:37 http://deb.debian.org/debian bookworm/main amd64 util-linux amd64 2.38.1-5+deb12u3 [1177 kB]
Get:38 http://deb.debian.org/debian bookworm/main amd64 libgpg-error0 amd64 1.46-1 [76.9 kB]
Get:39 http://deb.debian.org/debian bookworm/main amd64 libgcrypt20 amd64 1.10.1-3 [696 kB]
Get:40 http://deb.debian.org/debian bookworm/main amd64 libstdc++6 amd64 12.2.0-14 [614 kB]
Get:41 http://deb.debian.org/debian bookworm/main amd64 libbz2-1.0 amd64 1.0.8-5+b1 [47.3 kB]
Get:42 http://deb.debian.org/debian bookworm/main amd64 liblz4-1 amd64 1.9.4-1 [62.9 kB]
Get:43 http://deb.debian.org/debian bookworm/main amd64 libcap2 amd64 1:2.66-4 [27.0 kB]
Get:44 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.36-1~deb12u1 [332 kB]
Get:45 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.36-1~deb12u1 [109 kB]
Get:46 http://deb.debian.org/debian bookworm/main amd64 libxxhash0 amd64 0.8.1-1 [27.6 kB]
Get:47 http://deb.debian.org/debian bookworm/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB]
Get:48 http://deb.debian.org/debian bookworm/main amd64 libapt-pkg6.0 amd64 2.6.1 [907 kB]
Get:49 http://deb.debian.org/debian bookworm/main amd64 libnettle8 amd64 3.8.1-2 [288 kB]
Get:50 http://deb.debian.org/debian bookworm/main amd64 libhogweed6 amd64 3.8.1-2 [328 kB]
Get:51 http://deb.debian.org/debian bookworm/main amd64 libunistring2 amd64 1.0-2 [437 kB]
Get:52 http://deb.debian.org/debian bookworm/main amd64 libidn2-0 amd64 2.3.3-1+b1 [124 kB]
Get:53 http://deb.debian.org/debian bookworm/main amd64 libffi8 amd64 3.4.4-1 [22.9 kB]
Get:54 http://deb.debian.org/debian bookworm/main amd64 libp11-kit0 amd64 0.24.1-2 [345 kB]
Get:55 http://deb.debian.org/debian bookworm/main amd64 libtasn1-6 amd64 4.19.0-2+deb12u1 [48.6 kB]
Get:56 http://deb.debian.org/debian bookworm/main amd64 libgnutls30 amd64 3.7.9-2+deb12u4 [1405 kB]
Get:57 http://deb.debian.org/debian bookworm/main amd64 libsemanage-common all 3.4-1 [21.6 kB]
Get:58 http://deb.debian.org/debian bookworm/main amd64 libsepol2 amd64 3.4-2.1 [276 kB]
Get:59 http://deb.debian.org/debian bookworm/main amd64 libsemanage2 amd64 3.4-1+b5 [89.9 kB]
Get:60 http://deb.debian.org/debian bookworm/main amd64 passwd amd64 1:4.13+dfsg1-1+b1 [972 kB]
Get:61 http://deb.debian.org/debian bookworm/main amd64 debconf all 1.5.82 [121 kB]
Get:62 http://deb.debian.org/debian bookworm/main amd64 libpam0g amd64 1.5.2-6+deb12u1 [92.0 kB]
Get:63 http://deb.debian.org/debian bookworm/main amd64 libcrypt1 amd64 1:4.4.33-2 [89.5 kB]
Get:64 http://deb.debian.org/debian bookworm/main amd64 libpam-modules-bin amd64 1.5.2-6+deb12u1 [75.6 kB]
Get:65 http://deb.debian.org/debian bookworm/main amd64 libpam-modules amd64 1.5.2-6+deb12u1 [291 kB]
Get:66 http://deb.debian.org/debian bookworm/main amd64 adduser all 3.134 [183 kB]
Get:67 http://deb.debian.org/debian bookworm/main amd64 gpgv amd64 2.2.40-1.1 [648 kB]
Get:68 http://deb.debian.org/debian bookworm/main amd64 debian-archive-keyring all 2023.3+deb12u1 [161 kB]
Get:69 http://deb.debian.org/debian bookworm/main amd64 libseccomp2 amd64 2.5.4-1+deb12u1 [46.8 kB]
Get:70 http://deb.debian.org/debian bookworm/main amd64 apt amd64 2.6.1 [1373 kB]
Get:71 http://deb.debian.org/debian bookworm/main amd64 libdebconfclient0 amd64 0.270 [9900 B]
Get:72 http://deb.debian.org/debian bookworm/main amd64 base-passwd amd64 3.6.1 [60.0 kB]
Get:73 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB]
Get:74 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB]
Get:75 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB]
Get:76 http://deb.debian.org/debian bookworm/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [697 kB]
Get:77 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB]
Get:78 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB]
Get:79 http://deb.debian.org/debian bookworm/main amd64 libnumber-compare-perl all 0.03-3 [6332 B]
Get:80 http://deb.debian.org/debian bookworm/main amd64 libtext-glob-perl all 0.11-3 [7676 B]
Get:81 http://deb.debian.org/debian bookworm/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB]
Get:82 http://deb.debian.org/debian bookworm/main amd64 usrmerge all 37~deb12u1 [13.3 kB]
Get:83 http://deb.debian.org/debian bookworm/main amd64 init-system-helpers all 1.65.2 [49.8 kB]
Get:84 http://deb.debian.org/debian bookworm/main amd64 ncurses-base all 6.4-4 [261 kB]
Get:85 http://deb.debian.org/debian bookworm/main amd64 sysvinit-utils amd64 3.06-4 [31.0 kB]
Get:86 http://deb.debian.org/debian bookworm/main amd64 lsb-base all 11.6 [4584 B]
Get:87 http://deb.debian.org/debian bookworm/main amd64 logsave amd64 1.47.0-2 [19.6 kB]
Get:88 http://deb.debian.org/debian bookworm/main amd64 libext2fs2 amd64 1.47.0-2 [205 kB]
Get:89 http://deb.debian.org/debian bookworm/main amd64 e2fsprogs amd64 1.47.0-2 [571 kB]
Get:90 http://deb.debian.org/debian bookworm/main amd64 mount amd64 2.38.1-5+deb12u3 [134 kB]
Get:91 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.15-1~deb12u1 [2025 kB]
Get:92 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6+deb12u5 [816 kB]
Get:93 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1+deb12u1 [98.9 kB]
Get:94 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6+deb12u5 [2067 kB]
Get:95 http://deb.debian.org/debian bookworm/main amd64 python3-pairtools amd64 1.0.2-2+b1 [165 kB]
Get:96 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1+deb12u1 [4960 kB]
Get:97 http://deb.debian.org/debian bookworm/main amd64 cython3 amd64 0.29.32-2+b1 [1302 kB]
Get:98 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get:99 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get:100 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:101 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:102 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB]
Get:103 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB]
Get:104 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB]
Get:105 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB]
Get:106 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2025a-0+deb12u1 [299 kB]
Get:107 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB]
Get:108 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get:109 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB]
Get:110 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5+deb12u3 [398 kB]
Get:111 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB]
Get:112 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB]
Get:113 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB]
Get:114 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB]
Get:115 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2+deb12u1 [189 kB]
Get:116 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB]
Get:117 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u5 [1403 kB]
Get:118 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB]
Get:119 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB]
Get:120 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB]
Get:121 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get:122 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB]
Get:123 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB]
Get:124 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB]
Get:125 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u2 [316 kB]
Get:126 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB]
Get:127 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB]
Get:128 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB]
Get:129 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB]
Get:130 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get:131 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB]
Get:132 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+deb12u1 [472 kB]
Get:133 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB]
Get:134 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB]
Get:135 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB]
Get:136 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB]
Get:137 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB]
Get:138 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB]
Get:139 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB]
Get:140 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get:141 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB]
Get:142 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB]
Get:143 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB]
Get:144 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB]
Get:145 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB]
Get:146 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB]
Get:147 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+deb12u1 [74.2 kB]
Get:148 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB]
Get:149 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1+deb12u1 [296 kB]
Get:150 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get:151 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get:152 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get:153 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2+deb12u1 [839 kB]
Get:154 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB]
Get:155 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB]
Get:156 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB]
Get:157 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB]
Get:158 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB]
Get:159 http://deb.debian.org/debian bookworm/main amd64 libcom-err2 amd64 1.47.0-2 [19.8 kB]
Get:160 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B]
Get:161 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB]
Get:162 http://deb.debian.org/debian bookworm/main amd64 libuuid1 amd64 2.38.1-5+deb12u3 [28.8 kB]
Get:163 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u5 [1797 kB]
Get:164 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u5 [573 kB]
Get:165 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB]
Get:166 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB]
Get:167 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB]
Get:168 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB]
Get:169 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB]
Get:170 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB]
Get:171 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B]
Get:172 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB]
Get:173 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB]
Get:174 http://deb.debian.org/debian bookworm/main amd64 libisl23 amd64 0.25-1.1 [683 kB]
Get:175 http://deb.debian.org/debian bookworm/main amd64 libmpfr6 amd64 4.2.0-1 [701 kB]
Get:176 http://deb.debian.org/debian bookworm/main amd64 libmpc3 amd64 1.3.1-1 [51.5 kB]
Get:177 http://deb.debian.org/debian bookworm/main amd64 cpp-12 amd64 12.2.0-14 [9764 kB]
Get:178 http://deb.debian.org/debian bookworm/main amd64 cpp amd64 4:12.2.0-3 [6836 B]
Get:179 http://deb.debian.org/debian bookworm/main amd64 libcc1-0 amd64 12.2.0-14 [41.7 kB]
Get:180 http://deb.debian.org/debian bookworm/main amd64 binutils-common amd64 2.40-2 [2487 kB]
Get:181 http://deb.debian.org/debian bookworm/main amd64 libbinutils amd64 2.40-2 [572 kB]
Get:182 http://deb.debian.org/debian bookworm/main amd64 libctf-nobfd0 amd64 2.40-2 [153 kB]
Get:183 http://deb.debian.org/debian bookworm/main amd64 libctf0 amd64 2.40-2 [89.8 kB]
Get:184 http://deb.debian.org/debian bookworm/main amd64 libgprofng0 amd64 2.40-2 [812 kB]
Get:185 http://deb.debian.org/debian bookworm/main amd64 libjansson4 amd64 2.14-2 [40.8 kB]
Get:186 http://deb.debian.org/debian bookworm/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2 [2246 kB]
Get:187 http://deb.debian.org/debian bookworm/main amd64 binutils amd64 2.40-2 [65.0 kB]
Get:188 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB]
Get:189 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B]
Get:190 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB]
Get:191 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB]
Get:192 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB]
Get:193 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB]
Get:194 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB]
Get:195 http://deb.debian.org/debian bookworm/main amd64 gcc-12 amd64 12.2.0-14 [19.3 MB]
Get:196 http://deb.debian.org/debian bookworm/main amd64 gcc amd64 4:12.2.0-3 [5216 B]
Get:197 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u10 [47.1 kB]
Get:198 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.129-1 [2115 kB]
Get:199 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB]
Get:200 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB]
Get:201 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB]
Get:202 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB]
Get:203 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u10 [1903 kB]
Get:204 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB]
Get:205 http://deb.debian.org/debian bookworm/main amd64 g++-12 amd64 12.2.0-14 [10.7 MB]
Get:206 http://deb.debian.org/debian bookworm/main amd64 g++ amd64 4:12.2.0-3 [1356 B]
Get:207 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB]
Get:208 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB]
Get:209 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB]
Get:210 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB]
Get:211 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B]
Get:212 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6+deb12u5 [1988 kB]
Get:213 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1+deb12u1 [150 kB]
Get:214 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Get:215 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6+deb12u5 [4739 kB]
Get:216 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B]
Get:217 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B]
Get:218 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get:219 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB]
Get:220 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B]
Get:221 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6+deb12u5 [616 kB]
Get:222 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:223 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get:224 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB]
Get:225 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B]
Get:226 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB]
Get:227 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B]
Get:228 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B]
Get:229 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB]
Get:230 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB]
Get:231 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB]
Get:232 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB]
Get:233 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB]
Get:234 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB]
Get:235 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB]
Get:236 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB]
Get:237 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB]
Get:238 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB]
Get:239 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB]
Get:240 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get:241 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB]
Get:242 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB]
Get:243 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB]
Get:244 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB]
Get:245 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB]
Get:246 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB]
Get:247 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB]
Get:248 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB]
Get:249 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB]
Get:250 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB]
Get:251 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB]
Get:252 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB]
Get:253 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.15-1~deb12u1 [1427 kB]
Get:254 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB]
Get:255 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB]
Get:256 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB]
Get:257 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1+deb12u1 [41.0 kB]
Get:258 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1+deb12u1 [114 kB]
Get:259 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB]
Get:260 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get:261 http://deb.debian.org/debian bookworm/main amd64 python3-bioframe all 0.3.3-2 [69.9 kB]
Get:262 http://deb.debian.org/debian bookworm/main amd64 python3-colorama all 0.4.6-2 [36.8 kB]
Get:263 http://deb.debian.org/debian bookworm/main amd64 python3-click all 8.1.3-2 [92.2 kB]
Get:264 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB]
Get:265 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB]
Get:266 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB]
Get:267 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u2 [73.0 kB]
Get:268 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB]
Get:269 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get:270 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get:271 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u12 [386 kB]
Get:272 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB]
Get:273 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB]
Get:274 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB]
Get:275 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB]
Get:276 http://deb.debian.org/debian bookworm/main amd64 python3-yaml amd64 6.0-3+b2 [119 kB]
Get:277 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get:278 http://deb.debian.org/debian bookworm/main amd64 libpam-runtime all 1.5.2-6+deb12u1 [161 kB]
Get:279 http://deb.debian.org/debian bookworm/main amd64 libacl1 amd64 2.3.1-3 [31.5 kB]
Get:280 http://deb.debian.org/debian bookworm/main amd64 libattr1 amd64 1:2.5.1-4 [22.2 kB]
Get:281 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB]
Get:282 http://deb.debian.org/debian bookworm/main amd64 mawk amd64 1.3.4.20200120-3.1 [119 kB]
Get:283 http://deb.debian.org/debian bookworm/main amd64 libss2 amd64 1.47.0-2 [24.5 kB]
Get:284 http://deb.debian.org/debian bookworm/main amd64 python3-nose all 1.3.7-9 [130 kB]
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Setting up python3-pairtools (1.0.2-2+b1) ...
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0 added, 0 removed; done.
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done.
1m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-yf', 'dist-upgrade']
1m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'sh', '-c', 'apt-cache dumpavail | md5sum']
1m18.1s DUMP:
3b6124cc38d42e60354965f1a19282fe -
1m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'sh', '-c', 'apt-cache dumpavail | md5sum']
1m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools']
1m18.3s DUMP:
Package: python3-pairtools
Source: pairtools (1.0.2-2)
Version: 1.0.2-2+b1
Installed-Size: 685
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), cython3, python3 (<< 3.12), python3 (>= 3.11~), python3-bioframe, python3-click, python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any
Suggests: python3-pairtools-examples (>= 1.0.2)
Description-en: Framework to process sequencing data from a Hi-C experiment
Simple and fast command-line framework to process sequencing data from a Hi-C
experiment.
.
Process pair-end sequence alignments and perform the following operations:
.
- Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end
sequences of Hi-C DNA molecules
- Sort .pairs files for downstream analyses
- Detect, tag and remove PCR/optical duplicates
- Generate extensive statistics of Hi-C datasets
- Select Hi-C pairs given flexibly defined criteria
- Restore .sam alignments from Hi-C pairs
Description-md5: a340132b5467a45fa9b90e04ece3e5c1
Homepage: https://github.com/mirnylab/pairtools
Section: python
Priority: optional
Filename: pool/main/p/pairtools/python3-pairtools_1.0.2-2+b1_amd64.deb
Size: 165424
MD5sum: 4c8493139ea6d69ec56236651011bfc2
SHA256: ac685faeb4b2619bca8ae60b81a9a257f6efaf8e5a1f19d97a646e2fa1d51750
1m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools']
1m18.3s INFO: apt-cache knows about the following packages: python3-pairtools
1m18.3s INFO: Running scripts pre_install
1m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
1m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
1m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
1m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
1m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
1m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
1m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
1m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
1m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
1m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
1m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
1m18.4s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian bookworm/main amd64 Packages
release v=12.10,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
1m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
1m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
1m18.5s DUMP:
python3-pairtools:
Installed: 1.0.2-2+b1
Candidate: 1.0.2-2+b1
Version table:
*** 1.0.2-2+b1 500
500 http://deb.debian.org/debian bookworm/main amd64 Packages
100 /var/lib/dpkg/status
1m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
1m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools']
1m18.9s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
python3-pairtools is already the newest version (1.0.2-2+b1).
The following packages were automatically installed and are no longer required:
libmpdec3 libpython3.9-minimal libpython3.9-stdlib python3-nose python3.9
python3.9-minimal
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools']
1m18.9s INFO: Running scripts post_install
1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
1m18.9s INFO: Running scripts post_distupgrade
1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_base_cleanup']
1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_base_cleanup']
1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_exceptions']
1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_exceptions']
1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_force-unsafe-io']
1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_force-unsafe-io']
1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_squeeze-backports']
1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_squeeze-backports']
1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_zz_backports']
1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_zz_backports']
1m18.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
1m20.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
1m20.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpdq6cj8uq to testing
1m20.8s DEBUG: sources.list:
deb http://deb.debian.org/debian/ trixie main
1m20.8s INFO: Running scripts pre_distupgrade
1m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
1m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
1m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_exceptions']
1m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_exceptions']
1m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
1m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
1m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_database-server']
1m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_database-server']
1m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
1m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
1m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', 'update']
1m23.5s DUMP:
Get:1 http://deb.debian.org/debian trixie InRelease [175 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9624 kB]
Get:3 http://deb.debian.org/debian trixie/main Translation-en [6456 kB]
Fetched 16.3 MB in 2s (9462 kB/s)
Reading package lists...
1m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', 'update']
1m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-yf', 'dist-upgrade']
2m44.4s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
cython3 libboost-dev libboost1.83-dev libfile-find-rule-perl libicu72
liblbfgsb0 libldap-2.5-0 libmpdec3 libnsl-dev libnumber-compare-perl
libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.36
libpython3-all-dev libpython3.11 libpython3.11-dev libpython3.11-minimal
libpython3.11-stdlib libpython3.9-minimal libpython3.9-stdlib
libtext-glob-perl libtirpc-dev libxsimd-dev perl-modules-5.36
python3-all-dev python3-appdirs python3-beniget python3-colorama
python3-gast python3-nose python3-ply python3-pythran python3-six python3.11
python3.11-dev python3.11-minimal python3.9 python3.9-minimal usrmerge
xtl-dev
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
libboost1.74-dev libcurl3-gnutls libdb5.3 libext2fs2 libgdbm-compat4
libgdbm6 libglib2.0-0 libgnutls30 libhogweed6 libhts3 libnettle8 libpng16-16
libpsl5 libreadline8 libssh2-1 libssl3 libtirpc3 python3-distutils
python3-lib2to3
The following NEW packages will be installed:
cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu fonts-dejavu-mono g++-14
g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-14 gcc-14-base
gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libapt-pkg7.0 libboost1.83-dev
libcurl3t64-gnutls libdb5.3t64 libext2fs2t64 libgcc-14-dev
libgdbm-compat4t64 libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libhogweed6t64
libhts3t64 libhwasan0 libldap2 libnettle8t64 libnghttp3-9 libngtcp2-16
libngtcp2-crypto-gnutls8 libperl5.40 libpng16-16t64 libpsl5t64 libpython3.13
libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libreadline8t64
libsframe1 libsharpyuv0 libssh2-1t64 libssl3t64 libstdc++-14-dev
libtirpc3t64 libunistring5 login.defs netbase openssl-provider-legacy
perl-modules-5.40 python3-autocommand python3-inflect python3-jaraco.context
python3-jaraco.functools python3-jaraco.text python3-more-itertools
python3-numpy-dev python3-platformdirs python3-pytz python3-setuptools
python3-standard-pipes python3-typeguard python3-typing-extensions
python3-zipp python3.13 python3.13-dev python3.13-minimal python3.13-tk sqv
xtl-dev
The following packages will be upgraded:
adduser apt base-files base-passwd bash binutils binutils-common
binutils-x86-64-linux-gnu blt bsdutils ca-certificates coreutils cpp cpp-12
cython3 dash debconf debian-archive-keyring debianutils diffutils dpkg
e2fsprogs findutils fontconfig-config fonts-dejavu-core fonts-lyx g++ g++-12
gcc gcc-12 gcc-12-base gpgv grep gzip hostname init-system-helpers libacl1
libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblas3
libblkid1 libboost-dev libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin
libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev
libcrypt1 libctf-nobfd0 libctf0 libdebconfclient0 libdeflate0 libexpat1
libexpat1-dev libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev
libgcc-s1 libgcrypt20 libgfortran5 libgmp10 libgomp1 libgpg-error0
libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhtscodecs2
libicu72 libidn2-0 libimagequant0 libisl23 libitm1 libjansson4 libjbig0
libjpeg62-turbo libjs-sphinxdoc libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblz4-1
liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnghttp2-14
libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0
libopenblas0-pthread libopenjp2-7 libp11-kit0 libpam-modules
libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpython3-all-dev
libpython3-dev libpython3-stdlib libqhull-r8.0 libquadmath0 libraqm0
librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1
libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2
libstdc++-12-dev libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libtiff6
libtinfo6 libtirpc-common libtirpc-dev libtk8.6 libtsan2 libubsan1 libudev1
libuuid1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6
libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev
libxslt1.1 libxss1 libxxhash0 libyaml-0-2 libzstd1 linux-libc-dev login
logsave mawk media-types mount ncurses-base ncurses-bin openssl passwd perl
perl-base python-matplotlib-data python3 python3-all python3-all-dev
python3-attr python3-bioframe python3-brotli python3-certifi python3-chardet
python3-charset-normalizer python3-click python3-colorama python3-contourpy
python3-cycler python3-dateutil python3-decorator python3-dev
python3-fonttools python3-fs python3-gast python3-idna python3-kiwisolver
python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath
python3-numpy python3-packaging python3-pairtools python3-pandas
python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources
python3-ply python3-pyparsing python3-pysam python3-pythran python3-requests
python3-scipy python3-six python3-sympy python3-tk python3-tz
python3-ufolib2 python3-urllib3 python3-yaml readline-common sed
sysvinit-utils tar tk8.6-blt2.5 tzdata unicode-data usrmerge util-linux
util-linux-extra x11-common zlib1g zlib1g-dev
242 upgraded, 68 newly installed, 19 to remove and 0 not upgraded.
Need to get 311 MB of archives.
After this operation, 446 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian trixie/main amd64 base-files amd64 13.7 [73.0 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 libnsl-dev amd64 1.3.0-3+b3 [67.5 kB]
Get:3 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB]
Get:4 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.41-6 [1988 kB]
Get:5 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.41-6 [57.0 kB]
Get:6 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.6+ds-1 [11.0 kB]
Get:7 http://deb.debian.org/debian trixie/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [191 kB]
Get:8 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.6+ds-1 [83.3 kB]
Get:9 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB]
Get:10 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB]
Get:11 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB]
Get:12 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB]
Get:13 http://deb.debian.org/debian trixie/main amd64 libzstd1 amd64 1.5.7+dfsg-1 [304 kB]
Get:14 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB]
Get:15 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.41-6 [2843 kB]
Get:16 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.41-6 [635 kB]
Get:17 http://deb.debian.org/debian trixie/main amd64 libgmp10 amd64 2:6.3.0+dfsg-3 [560 kB]
Get:18 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get:19 http://deb.debian.org/debian trixie/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB]
Get:20 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get:21 http://deb.debian.org/debian trixie/main amd64 gcc-14-base amd64 14.2.0-19 [49.4 kB]
Get:22 http://deb.debian.org/debian trixie/main amd64 libgcc-s1 amd64 14.2.0-19 [72.8 kB]
Get:23 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get:24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB]
Get:25 http://deb.debian.org/debian trixie/main amd64 libnettle8t64 amd64 3.10.1-1 [305 kB]
Get:26 http://deb.debian.org/debian trixie/main amd64 libhogweed6t64 amd64 3.10.1-1 [335 kB]
Get:27 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get:28 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 257.4-3 [451 kB]
Get:29 http://deb.debian.org/debian trixie/main amd64 libpam-modules-bin amd64 1.7.0-3 [48.9 kB]
Get:30 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-9 [704 kB]
Get:31 http://deb.debian.org/debian trixie/main amd64 libpam-modules amd64 1.7.0-3 [177 kB]
Get:32 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get:33 http://deb.debian.org/debian trixie/main amd64 openssl-provider-legacy amd64 3.4.1-1 [302 kB]
Get:34 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.4.1-1 [2304 kB]
Get:35 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get:36 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB]
Get:37 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get:38 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB]
Get:39 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB]
Get:40 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get:41 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get:42 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.13.0-1 [374 kB]
Get:43 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB]
Get:44 http://deb.debian.org/debian trixie/main amd64 sqv amd64 1.2.1-6+b1 [623 kB]
Get:45 http://deb.debian.org/debian trixie/main amd64 libstdc++6 amd64 14.2.0-19 [714 kB]
Get:46 http://deb.debian.org/debian trixie/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB]
Get:47 http://deb.debian.org/debian trixie/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB]
Get:48 http://deb.debian.org/debian trixie/main amd64 liblz4-1 amd64 1.10.0-4 [63.9 kB]
Get:49 http://deb.debian.org/debian trixie/main amd64 liblzma5 amd64 5.6.4-1 [280 kB]
Get:50 http://deb.debian.org/debian trixie/main amd64 libcap2 amd64 1:2.75-4 [27.9 kB]
Get:51 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 257.4-3 [149 kB]
Get:52 http://deb.debian.org/debian trixie/main amd64 libapt-pkg7.0 amd64 2.9.35 [1112 kB]
Get:53 http://deb.debian.org/debian trixie/main amd64 libdebconfclient0 amd64 0.277 [10.4 kB]
Get:54 http://deb.debian.org/debian trixie/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB]
Get:55 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.8.1-1 [84.7 kB]
Get:56 http://deb.debian.org/debian trixie/main amd64 base-passwd amd64 3.6.7 [53.7 kB]
Get:57 http://deb.debian.org/debian trixie/main amd64 login.defs all 1:4.17.3-3 [186 kB]
Get:58 http://deb.debian.org/debian trixie/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB]
Get:59 http://deb.debian.org/debian trixie/main amd64 libcap-ng0 amd64 0.8.5-4+b1 [17.6 kB]
Get:60 http://deb.debian.org/debian trixie/main amd64 libaudit1 amd64 1:4.0.2-2+b2 [55.1 kB]
Get:61 http://deb.debian.org/debian trixie/main amd64 libcrypt1 amd64 1:4.4.38-1 [90.1 kB]
Get:62 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.1-2 [3017 kB]
Get:63 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB]
Get:64 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB]
Get:65 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.1-2 [4315 kB]
Get:66 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.1-2 [267 kB]
Get:67 http://deb.debian.org/debian trixie/main amd64 perl-base amd64 5.40.1-2 [1665 kB]
Get:68 http://deb.debian.org/debian trixie/main amd64 debconf all 1.5.91 [121 kB]
Get:69 http://deb.debian.org/debian trixie/main amd64 libpam0g amd64 1.7.0-3 [69.7 kB]
Get:70 http://deb.debian.org/debian trixie/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB]
Get:71 http://deb.debian.org/debian trixie/main amd64 libattr1 amd64 1:2.5.2-3 [22.9 kB]
Get:72 http://deb.debian.org/debian trixie/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB]
Get:73 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-2 [131 kB]
Get:74 http://deb.debian.org/debian trixie/main amd64 libsemanage-common all 3.8.1-1 [7812 B]
Get:75 http://deb.debian.org/debian trixie/main amd64 libsepol2 amd64 3.8.1-1 [296 kB]
Get:76 http://deb.debian.org/debian trixie/main amd64 libsemanage2 amd64 3.8.1-1 [95.3 kB]
Get:77 http://deb.debian.org/debian trixie/main amd64 passwd amd64 1:4.17.3-3 [1228 kB]
Get:78 http://deb.debian.org/debian trixie/main amd64 adduser all 3.149 [187 kB]
Get:79 http://deb.debian.org/debian trixie/main amd64 debian-archive-keyring all 2023.4 [161 kB]
Get:80 http://deb.debian.org/debian trixie/main amd64 libseccomp2 amd64 2.6.0-2 [51.7 kB]
Get:81 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.35 [1449 kB]
Get:82 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get:83 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB]
Get:84 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get:85 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get:86 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get:87 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get:88 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB]
Get:89 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB]
Get:90 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get:91 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB]
Get:92 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.12.21-1 [2542 kB]
Get:93 http://deb.debian.org/debian trixie/main amd64 debianutils amd64 5.21 [92.1 kB]
Get:94 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.37-1.1+b2 [1500 kB]
Get:95 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.4-5 [106 kB]
Get:96 http://deb.debian.org/debian trixie/main amd64 usrmerge all 39+nmu2 [13.3 kB]
Get:97 http://deb.debian.org/debian trixie/main amd64 coreutils amd64 9.5-1+b1 [2922 kB]
Get:98 http://deb.debian.org/debian trixie/main amd64 dash amd64 0.5.12-12 [98.5 kB]
Get:99 http://deb.debian.org/debian trixie/main amd64 diffutils amd64 1:3.10-3 [385 kB]
Get:100 http://deb.debian.org/debian trixie/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB]
Get:101 http://deb.debian.org/debian trixie/main amd64 dpkg amd64 1.22.18 [1545 kB]
Get:102 http://deb.debian.org/debian trixie/main amd64 findutils amd64 4.10.0-3 [700 kB]
Get:103 http://deb.debian.org/debian trixie/main amd64 grep amd64 3.11-4 [431 kB]
Get:104 http://deb.debian.org/debian trixie/main amd64 gzip amd64 1.13-1 [138 kB]
Get:105 http://deb.debian.org/debian trixie/main amd64 hostname amd64 3.25 [11.0 kB]
Get:106 http://deb.debian.org/debian trixie/main amd64 libpam-runtime all 1.7.0-3 [248 kB]
Get:107 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.4-5 [88.7 kB]
Get:108 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB]
Get:109 http://deb.debian.org/debian trixie/main amd64 libtinfo6 amd64 6.5+20250216-2 [348 kB]
Get:110 http://deb.debian.org/debian trixie/main amd64 ncurses-bin amd64 6.5+20250216-2 [438 kB]
Get:111 http://deb.debian.org/debian trixie/main amd64 sed amd64 4.9-2 [329 kB]
Get:112 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.4-5 [169 kB]
Get:113 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.4-5 [200 kB]
Get:114 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.4-5 [140 kB]
Get:115 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.4-5 [36.5 kB]
Get:116 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.4-5 [1205 kB]
Get:117 http://deb.debian.org/debian trixie/main amd64 util-linux-extra amd64 2.40.4-5 [276 kB]
Get:118 http://deb.debian.org/debian trixie/main amd64 init-system-helpers all 1.68 [38.7 kB]
Get:119 http://deb.debian.org/debian trixie/main amd64 ncurses-base all 6.5+20250216-2 [273 kB]
Get:120 http://deb.debian.org/debian trixie/main amd64 sysvinit-utils amd64 3.14-4 [34.1 kB]
Get:121 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB]
Get:122 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14.2.0-19 [26.0 kB]
Get:123 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-19 [9308 B]
Get:124 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14.2.0-19 [2725 kB]
Get:125 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14.2.0-19 [1204 kB]
Get:126 http://deb.debian.org/debian trixie/main amd64 libisl23 amd64 0.27-1 [659 kB]
Get:127 http://deb.debian.org/debian trixie/main amd64 libmpfr6 amd64 4.2.2-1 [729 kB]
Get:128 http://deb.debian.org/debian trixie/main amd64 libmpc3 amd64 1.3.1-1+b3 [52.2 kB]
Get:129 http://deb.debian.org/debian trixie/main amd64 g++-12 amd64 12.4.0-5 [10.8 MB]
Get:130 http://deb.debian.org/debian trixie/main amd64 gcc-12 amd64 12.4.0-5 [19.6 MB]
Get:131 http://deb.debian.org/debian trixie/main amd64 cpp-12 amd64 12.4.0-5 [9887 kB]
Get:132 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14.2.0-19 [1074 kB]
Get:133 http://deb.debian.org/debian trixie/main amd64 libstdc++-12-dev amd64 12.4.0-5 [2081 kB]
Get:134 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-19 [145 kB]
Get:135 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB]
Get:136 http://deb.debian.org/debian trixie/main amd64 libcc1-0 amd64 14.2.0-19 [42.8 kB]
Get:137 http://deb.debian.org/debian trixie/main amd64 libgcc-12-dev amd64 12.4.0-5 [2434 kB]
Get:138 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14.2.0-19 [2460 kB]
Get:139 http://deb.debian.org/debian trixie/main amd64 gcc-12-base amd64 12.4.0-5 [43.9 kB]
Get:140 http://deb.debian.org/debian trixie/main amd64 libgprofng0 amd64 2.44-3 [808 kB]
Get:141 http://deb.debian.org/debian trixie/main amd64 libctf0 amd64 2.44-3 [88.6 kB]
Get:142 http://deb.debian.org/debian trixie/main amd64 libctf-nobfd0 amd64 2.44-3 [156 kB]
Get:143 http://deb.debian.org/debian trixie/main amd64 libsframe1 amd64 2.44-3 [78.4 kB]
Get:144 http://deb.debian.org/debian trixie/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3 [1014 kB]
Get:145 http://deb.debian.org/debian trixie/main amd64 binutils-common amd64 2.44-3 [2509 kB]
Get:146 http://deb.debian.org/debian trixie/main amd64 binutils amd64 2.44-3 [265 kB]
Get:147 http://deb.debian.org/debian trixie/main amd64 libbinutils amd64 2.44-3 [534 kB]
Get:148 http://deb.debian.org/debian trixie/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB]
Get:149 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14.2.0-19 [1488 kB]
Get:150 http://deb.debian.org/debian trixie/main amd64 libgcc-14-dev amd64 14.2.0-19 [2672 kB]
Get:151 http://deb.debian.org/debian trixie/main amd64 libstdc++-14-dev amd64 14.2.0-19 [2376 kB]
Get:152 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B]
Get:153 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB]
Get:154 http://deb.debian.org/debian trixie/main amd64 logsave amd64 1.47.2-1+b1 [24.2 kB]
Get:155 http://deb.debian.org/debian trixie/main amd64 libext2fs2t64 amd64 1.47.2-1+b1 [212 kB]
Get:156 http://deb.debian.org/debian trixie/main amd64 e2fsprogs amd64 1.47.2-1+b1 [590 kB]
Get:157 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB]
Get:158 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.0-2 [1513 kB]
Get:159 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get:160 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB]
Get:161 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB]
Get:162 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get:163 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-3 [861 kB]
Get:164 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.7.1-1 [161 kB]
Get:165 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB]
Get:166 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-3 [2212 kB]
Get:167 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.13.2-2 [1064 B]
Get:168 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.2-2 [1044 B]
Get:169 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.13.2-2 [1068 B]
Get:170 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.2-2 [10.3 kB]
Get:171 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.2-2 [26.1 kB]
Get:172 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB]
Get:173 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB]
Get:174 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B]
Get:175 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.13.2-1 [9516 B]
Get:176 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.15.2-7 [16.3 MB]
Get:177 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB]
Get:178 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 11.1.0-5+b1 [81.6 kB]
Get:179 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB]
Get:180 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-8+b1 [4517 kB]
Get:181 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.2.3+dfsg-8 [3097 kB]
Get:182 http://deb.debian.org/debian trixie/main amd64 python3-pairtools amd64 1.1.3-1+b1 [207 kB]
Get:183 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-7+b1 [23.0 MB]
Get:184 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5084 kB]
Get:185 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.4.0+dfsg-2 [25.3 kB]
Get:186 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.1-1+b1 [1288 kB]
Get:187 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB]
Get:188 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.55.3-2+b1 [1448 kB]
Get:189 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.1-1+b1 [216 kB]
Get:190 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB]
Get:191 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB]
Get:192 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get:193 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get:194 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB]
Get:195 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-1 [259 kB]
Get:196 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB]
Get:197 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:198 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:199 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.2 [318 kB]
Get:200 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.2 [391 kB]
Get:201 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get:202 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get:203 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get:204 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB]
Get:205 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB]
Get:206 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB]
Get:207 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB]
Get:208 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get:209 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB]
Get:210 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB]
Get:211 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB]
Get:212 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.2-3 [107 kB]
Get:213 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:214 http://deb.debian.org/debian trixie/main amd64 python3-standard-pipes all 3.13.0-5 [7376 B]
Get:215 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:216 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get:217 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.0-1 [90.1 kB]
Get:218 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB]
Get:219 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:220 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:221 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get:222 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get:223 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.8.0-1 [724 kB]
Get:224 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B]
Get:225 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB]
Get:226 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.3-1 [190 kB]
Get:227 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-7 [2735 kB]
Get:228 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB]
Get:229 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB]
Get:230 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB]
Get:231 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB]
Get:232 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get:233 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB]
Get:234 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get:235 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get:236 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB]
Get:237 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get:238 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get:239 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get:240 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get:241 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-2 [345 kB]
Get:242 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB]
Get:243 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB]
Get:244 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:245 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B]
Get:246 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.7-1 [16.6 kB]
Get:247 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-7 [95.2 kB]
Get:248 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB]
Get:249 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-4 [82.1 kB]
Get:250 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB]
Get:251 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.2 [233 kB]
Get:252 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB]
Get:253 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-5 [4148 kB]
Get:254 http://deb.debian.org/debian trixie/main amd64 python3-attr all 25.3.0-1 [69.5 kB]
Get:255 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB]
Get:256 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB]
Get:257 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get:258 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB]
Get:259 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2025.1-3 [4004 B]
Get:260 http://deb.debian.org/debian trixie/main amd64 python3-pytz all 2025.1-3 [150 kB]
Get:261 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB]
Get:262 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B]
Get:263 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB]
Get:264 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB]
Get:265 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-2 [114 kB]
Get:266 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get:267 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB]
Get:268 http://deb.debian.org/debian trixie/main amd64 python3-bioframe all 0.4.1-2 [71.9 kB]
Get:269 http://deb.debian.org/debian trixie/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [95.4 kB]
Get:270 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [138 kB]
Get:271 http://deb.debian.org/debian trixie/main amd64 libopenblas-pthread-dev amd64 0.3.29+ds-3 [5063 kB]
Get:272 http://deb.debian.org/debian trixie/main amd64 libopenblas0-pthread amd64 0.3.29+ds-3 [6740 kB]
Get:273 http://deb.debian.org/debian trixie/main amd64 libopenblas0 amd64 0.3.29+ds-3 [42.7 kB]
Get:274 http://deb.debian.org/debian trixie/main amd64 libopenblas-dev amd64 0.3.29+ds-3 [57.0 kB]
Get:275 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get:276 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get:277 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB]
Get:278 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-2 [913 kB]
Get:279 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-3 [1952 kB]
Get:280 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.2-3 [2158 kB]
Get:281 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.2-3 [5015 kB]
Get:282 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-3 [746 kB]
Get:283 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.2-3 [506 kB]
Get:284 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get:285 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get:286 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.4-5 [156 kB]
Get:287 http://deb.debian.org/debian trixie/main amd64 gpgv amd64 2.2.46-6 [221 kB]
Get:288 http://deb.debian.org/debian trixie/main amd64 mawk amd64 1.3.4.20250131-1 [141 kB]
Get:289 http://deb.debian.org/debian trixie/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19 [11.0 MB]
Get:290 http://deb.debian.org/debian trixie/main amd64 g++ amd64 4:14.2.0-1 [1344 B]
Get:291 http://deb.debian.org/debian trixie/main amd64 gcc amd64 4:14.2.0-1 [5136 B]
Get:292 http://deb.debian.org/debian trixie/main amd64 cpp amd64 4:14.2.0-1 [1568 B]
Get:293 http://deb.debian.org/debian trixie/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1 [4840 B]
Get:294 http://deb.debian.org/debian trixie/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19 [21.4 MB]
Get:295 http://deb.debian.org/debian trixie/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19 [12.1 MB]
Get:296 http://deb.debian.org/debian trixie/main amd64 cpp-14 amd64 14.2.0-19 [1280 B]
Get:297 http://deb.debian.org/debian trixie/main amd64 gcc-14 amd64 14.2.0-19 [540 kB]
Get:298 http://deb.debian.org/debian trixie/main amd64 g++-14 amd64 14.2.0-19 [22.5 kB]
Get:299 http://deb.debian.org/debian trixie/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1 [1436 B]
Get:300 http://deb.debian.org/debian trixie/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1 [1200 B]
Get:301 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get:302 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB]
Get:303 http://deb.debian.org/debian trixie/main amd64 libss2 amd64 1.47.2-1+b1 [29.0 kB]
Get:304 http://deb.debian.org/debian trixie/main amd64 xtl-dev all 0.7.7-1 [90.3 kB]
Get:305 http://deb.debian.org/debian trixie/main amd64 libxsimd-dev amd64 13.2.0-1 [133 kB]
Get:306 http://deb.debian.org/debian trixie/main amd64 python3-colorama all 0.4.6-4 [36.2 kB]
Get:307 http://deb.debian.org/debian trixie/main amd64 python3-gast all 0.6.0-1 [18.7 kB]
Get:308 http://deb.debian.org/debian trixie/main amd64 python3-ply all 3.11-9 [62.9 kB]
Get:309 http://deb.debian.org/debian trixie/main amd64 python3-pythran amd64 0.17.0+ds-1 [456 kB]
Get:310 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.17.0-1 [16.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
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dpkg: libtirpc3:amd64: dependency problems, but removing anyway as you requested:
libpython3.9-stdlib:amd64 depends on libtirpc3 (>= 1.0.2).
libpython3.11-stdlib:amd64 depends on libtirpc3 (>= 1.0.2).
libnsl2:amd64 depends on libtirpc3 (>= 1.0.2).
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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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Selecting previously unselected package gcc-14-base:amd64.
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dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested:
libhogweed6:amd64 depends on libnettle8.
libgnutls30:amd64 depends on libnettle8 (>= 3.7~).
libcurl3-gnutls:amd64 depends on libnettle8.
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dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested:
libgnutls30:amd64 depends on libhogweed6 (>= 3.6).
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dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested:
libldap-2.5-0:amd64 depends on libgnutls30 (>= 3.7.5).
libcurl3-gnutls:amd64 depends on libgnutls30 (>= 3.7.5).
apt depends on libgnutls30 (>= 3.7.5).
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dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested:
libsasl2-modules-db:amd64 depends on libdb5.3.
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invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of restart.
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Current default time zone: 'Etc/UTC'
Local time is now: Sun Apr 6 23:43:20 UTC 2025.
Universal Time is now: Sun Apr 6 23:43:20 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
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Setting up fontconfig-config (2.15.0-2.2) ...
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Installing new version of config file /etc/cron.d/e2scrub_all ...
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Setting up ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
rehash: warning: skipping ca-certificates.crt, it does not contain exactly one certificate or CRL
21 added, 9 removed; done.
Setting up libxsimd-dev:amd64 (13.2.0-1) ...
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No schema files found: doing nothing.
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Setting up libgcc-12-dev:amd64 (12.4.0-5) ...
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Setting up cpp-14 (14.2.0-19) ...
Setting up libreadline8t64:amd64 (8.2-6) ...
Setting up libopenblas0:amd64 (0.3.29+ds-3) ...
Setting up libxslt1.1:amd64 (1.1.35-1.2) ...
Setting up libc6-dev:amd64 (2.41-6) ...
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Setting up libxss1:amd64 (1:1.2.3-1+b3) ...
Setting up libfontconfig1:amd64 (2.15.0-2.2) ...
Setting up libgcc-14-dev:amd64 (14.2.0-19) ...
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Setting up binutils-x86-64-linux-gnu (2.44-3) ...
Setting up libpython3.13:amd64 (3.13.2-3) ...
Setting up cpp-x86-64-linux-gnu (4:14.2.0-1) ...
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Setting up libtirpc3t64:amd64 (1.3.6+ds-1) ...
Setting up python3.13 (3.13.2-3) ...
Setting up libtk8.6:amd64 (8.6.16-1) ...
Setting up libcurl3t64-gnutls:amd64 (8.13.0-1) ...
Setting up python3 (3.13.2-2) ...
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Setting up python3-zipp (3.21.0-1) ...
Setting up python3-click (8.2.0+0.really.8.1.8-1) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up python3.13-tk (3.13.2-3) ...
Setting up python3-platformdirs (4.3.7-1) ...
Setting up python3-fs (2.4.16-7) ...
Setting up python3-six (1.17.0-1) ...
Setting up libopenblas-dev:amd64 (0.3.29+ds-3) ...
Setting up python3-decorator (5.1.1-5) ...
Setting up python3-packaging (24.2-1) ...
Setting up libtirpc-dev:amd64 (1.3.6+ds-1) ...
Setting up python3-chardet (5.2.0+dfsg-2) ...
Setting up libexpat1-dev:amd64 (2.7.1-1) ...
Setting up python3-pyparsing (3.1.2-1) ...
Setting up python3-certifi (2025.1.31+ds-1) ...
Setting up gcc-12 (12.4.0-5) ...
Setting up python3-brotli (1.1.0-2+b7) ...
Setting up libraqm0:amd64 (0.10.2-1) ...
Setting up python3-cycler (0.12.1-1) ...
Setting up python3-kiwisolver (1.4.7-3+b1) ...
Setting up python3-idna (3.10-1) ...
Setting up cython3 (3.0.11+dfsg-2+b1) ...
Setting up python3-typing-extensions (4.13.0-1) ...
Setting up python3-numpy (1:2.2.3+ds-5) ...
Setting up python3-urllib3 (2.3.0-2) ...
Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up python3-lxml:amd64 (5.3.1-1+b1) ...
Setting up cpp (4:14.2.0-1) ...
Setting up libnsl2:amd64 (1.3.0-3+b3) ...
Setting up libhts3t64:amd64 (1.21+ds-1) ...
Setting up python3-dateutil (2.9.0-4) ...
Setting up python3-contourpy (1.3.1-1+b1) ...
Setting up libboost-dev:amd64 (1.83.0.2+b2) ...
Setting up gcc-14-x86-64-linux-gnu (14.2.0-19) ...
Setting up python3-mpmath (1.3.0-1) ...
Setting up g++-12 (12.4.0-5) ...
Setting up python3-more-itertools (10.6.0-1) ...
Setting up python3-sympy (1.13.3-5) ...
Setting up python3-attr (25.3.0-1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ...
Setting up python3-pysam (0.23.0+ds-1+b1) ...
Setting up python3-scipy (1.15.2-7) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up gcc-x86-64-linux-gnu (4:14.2.0-1) ...
Setting up python3-jaraco.context (6.0.1-1) ...
Setting up python3-standard-pipes (3.13.0-5) ...
Setting up python3-colorama (0.4.6-4) ...
Setting up python3-lz4 (4.4.0+dfsg-2) ...
Setting up python3-charset-normalizer (3.4.1-1+b1) ...
Setting up blt (2.5.3+dfsg-8) ...
Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8+b1) ...
Setting up python3-ply (3.11-9) ...
Setting up python3-typeguard (4.4.2-1) ...
Setting up python3-gast (0.6.0-1) ...
Setting up python3-all (3.13.2-2) ...
Setting up python3-yaml (6.0.2-1+b2) ...
Setting up python3-tk:amd64 (3.13.2-1) ...
Setting up python3-pytz (2025.1-3) ...
Setting up python3-tz (2025.1-3) ...
Setting up gcc-14 (14.2.0-19) ...
Setting up python3-pil:amd64 (11.1.0-5+b1) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-pandas (2.2.3+dfsg-8) ...
Setting up python3-pil.imagetk:amd64 (11.1.0-5+b1) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up libpython3.13-dev:amd64 (3.13.2-3) ...
Setting up python3-requests (2.32.3+dfsg-4) ...
Setting up g++-14-x86-64-linux-gnu (14.2.0-19) ...
Setting up libnsl-dev:amd64 (1.3.0-3+b3) ...
Setting up g++-x86-64-linux-gnu (4:14.2.0-1) ...
Setting up g++-14 (14.2.0-19) ...
Setting up python3-pkg-resources (75.8.0-1) ...
Setting up libpython3-dev:amd64 (3.13.2-2) ...
Setting up python3-setuptools (75.8.0-1) ...
Setting up python3.13-dev (3.13.2-3) ...
Setting up gcc (4:14.2.0-1) ...
Setting up libpython3-all-dev:amd64 (3.13.2-2) ...
Setting up python3-dev (3.13.2-2) ...
Setting up g++ (4:14.2.0-1) ...
Setting up python3-all-dev (3.13.2-2) ...
Setting up python3-pythran (0.17.0+ds-1) ...
Setting up python3-fonttools (4.55.3-2+b1) ...
Setting up python3-ufolib2 (0.17.0+dfsg1-1) ...
Setting up python3-matplotlib (3.8.3-7+b1) ...
Setting up python3-bioframe (0.4.1-2) ...
Setting up python3-pairtools (1.1.3-1+b1) ...
Processing triggers for libc-bin (2.41-6) ...
Processing triggers for debianutils (5.21) ...
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.
2m44.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-yf', 'dist-upgrade']
2m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'sh', '-c', 'apt-cache dumpavail | md5sum']
2m45.7s DUMP:
5b72cc3ff1f8bc636cbb926d0a8f661e -
2m45.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'sh', '-c', 'apt-cache dumpavail | md5sum']
2m45.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools']
2m46.0s DUMP:
Package: python3-pairtools
Source: pairtools (1.1.3-1)
Version: 1.1.3-1+b1
Installed-Size: 833
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: python3-standard-pipes, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), python3 (<< 3.14), python3 (>= 3.13~), python3-bioframe, python3-click, python3-numpy, python3-numpy2-abi0 | python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any
Suggests: python3-pairtools-examples (>= 1.0.2)
Description-en: Framework to process sequencing data from a Hi-C experiment
Simple and fast command-line framework to process sequencing data from a Hi-C
experiment.
.
Process pair-end sequence alignments and perform the following operations:
.
- Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end
sequences of Hi-C DNA molecules
- Sort .pairs files for downstream analyses
- Detect, tag and remove PCR/optical duplicates
- Generate extensive statistics of Hi-C datasets
- Select Hi-C pairs given flexibly defined criteria
- Restore .sam alignments from Hi-C pairs
Description-md5: a340132b5467a45fa9b90e04ece3e5c1
Homepage: https://github.com/mirnylab/pairtools
Section: python
Priority: optional
Filename: pool/main/p/pairtools/python3-pairtools_1.1.3-1+b1_amd64.deb
Size: 207068
MD5sum: 69eb3c6e74046d498e5aef47f8106f33
SHA256: 413bfb5ff113c99270df2798fb8b32782b7627157892fc057e223d414550e9ce
2m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools']
2m46.0s INFO: apt-cache knows about the following packages: python3-pairtools
2m46.0s INFO: Running scripts pre_install
2m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
2m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
2m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
2m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
2m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
2m46.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
2m46.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
2m46.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
2m46.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
2m46.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
2m46.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
2m46.2s 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:
2m46.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
2m46.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
2m46.2s DUMP:
python3-pairtools:
Installed: 1.1.3-1+b1
Candidate: 1.1.3-1+b1
Version table:
*** 1.1.3-1+b1 500
500 http://deb.debian.org/debian trixie/main amd64 Packages
100 /var/lib/dpkg/status
2m46.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
2m46.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools']
2m46.8s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
python3-pairtools is already the newest version (1.1.3-1+b1).
The following packages were automatically installed and are no longer required:
cython3 libboost-dev libboost1.83-dev libfile-find-rule-perl libicu72
liblbfgsb0 libldap-2.5-0 libmpdec3 libnsl-dev libnumber-compare-perl
libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.36
libpython3-all-dev libpython3.11 libpython3.11-dev libpython3.11-minimal
libpython3.11-stdlib libpython3.9-minimal libpython3.9-stdlib
libtext-glob-perl libtirpc-dev libxsimd-dev perl-modules-5.36
python3-all-dev python3-appdirs python3-beniget python3-colorama
python3-gast python3-nose python3-ply python3-pythran python3-six python3.11
python3.11-dev python3.11-minimal python3.9 python3.9-minimal usrmerge
xtl-dev
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
2m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools']
2m46.8s INFO: Running scripts post_install
2m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
2m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
2m46.8s INFO: Running scripts post_distupgrade
2m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_base_cleanup']
2m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_base_cleanup']
2m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_exceptions']
2m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_exceptions']
2m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_force-unsafe-io']
2m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_force-unsafe-io']
2m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_squeeze-backports']
2m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_squeeze-backports']
2m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_zz_backports']
2m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_zz_backports']
2m46.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
2m50.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
2m50.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpdq6cj8uq to sid
2m50.5s DEBUG: sources.list:
deb http://deb.debian.org/debian/ sid main
2m50.5s INFO: Running scripts pre_distupgrade
2m50.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
2m50.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
2m50.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_exceptions']
2m50.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_exceptions']
2m50.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
2m50.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
2m50.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_database-server']
2m50.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_database-server']
2m50.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
2m50.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
2m50.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', 'update']
2m53.6s DUMP:
Get:1 http://deb.debian.org/debian sid InRelease [205 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7413 kB]
Fetched 17.8 MB in 2s (8220 kB/s)
Reading package lists...
2m53.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', 'update']
2m53.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-yf', 'dist-upgrade']
3m11.4s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
cython3 libboost-dev libboost1.83-dev libfile-find-rule-perl libicu72
liblbfgsb0 libldap-2.5-0 libmpdec3 libnsl-dev libnumber-compare-perl
libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.36
libpython3-all-dev libpython3.11 libpython3.11-dev libpython3.11-minimal
libpython3.11-stdlib libpython3.9-minimal libpython3.9-stdlib
libtext-glob-perl libtirpc-dev libxsimd-dev perl-modules-5.36
python3-all-dev python3-appdirs python3-beniget python3-colorama
python3-gast python3-nose python3-ply python3-pythran python3-six python3.11
python3.11-dev python3.11-minimal python3.9 python3.9-minimal usrmerge
xtl-dev
Use 'sudo apt autoremove' to remove them.
The following NEW packages will be installed:
liblastlog2-2 libzopfli1 python3-zopfli
The following packages will be upgraded:
adduser apt bsdutils coreutils libapt-pkg7.0 libblkid1 libdebconfclient0
libglib2.0-0t64 libkeyutils1 libldap-2.5-0 liblzma5 libmount1 libsmartcols1
libsystemd0 libtiff6 libudev1 libuuid1 login login.defs mount passwd
python-matplotlib-data python3-appdirs python3-decorator python3-fonttools
python3-matplotlib python3-numpy python3-numpy-dev python3-pandas
python3-pandas-lib python3-pytz python3-requests python3-tz python3-ufolib2
sqv util-linux util-linux-extra
37 upgraded, 3 newly installed, 0 to remove and 0 not upgraded.
Need to get 54.6 MB of archives.
After this operation, 3896 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.41-3 [110 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.6-2 [2993 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.41-3 [300 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 liblastlog2-2 amd64 2.41-3 [28.3 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.41-3 [37.5 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.41-3 [171 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.41-3 [208 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.41-3 [142 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.41-3 [1231 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 mount amd64 2.41-3 [162 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.8.1-1 [309 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257.4-9 [452 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257.4-9 [151 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 libapt-pkg7.0 amd64 3.0.0 [1112 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.17.4-1 [186 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.17.4-1 [1226 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 adduser all 3.150 [187 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 sqv amd64 1.3.0-1 [661 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 apt amd64 3.0.0 [1450 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.41-3 [112 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.278 [10.5 kB]
Get:24 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.84.1-1 [1514 kB]
Get:25 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-5 [9316 B]
Get:26 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.19+dfsg-1 [187 kB]
Get:27 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.7.0-3 [346 kB]
Get:28 http://deb.debian.org/debian sid/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB]
Get:29 http://deb.debian.org/debian sid/main amd64 python-matplotlib-data all 3.10.1+dfsg1-2 [2736 kB]
Get:30 http://deb.debian.org/debian sid/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB]
Get:31 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.2.1-1 [32.9 kB]
Get:32 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB]
Get:33 http://deb.debian.org/debian sid/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB]
Get:34 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.57.0-1 [1438 kB]
Get:35 http://deb.debian.org/debian sid/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-2 [23.8 MB]
Get:36 http://deb.debian.org/debian sid/main amd64 python3-pytz all 2025.2-1 [151 kB]
Get:37 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB]
Get:38 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB]
Get:39 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.32.3+dfsg-5 [72.2 kB]
Get:40 http://deb.debian.org/debian sid/main amd64 python3-tz all 2025.2-1 [4072 B]
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(Reading database ... 52783 files and directories currently installed.)
Preparing to unpack .../00-libglib2.0-0t64_2.84.1-1_amd64.deb ...
Unpacking libglib2.0-0t64:amd64 (2.84.1-1) over (2.84.0-2) ...
Preparing to unpack .../01-libkeyutils1_1.6.3-5_amd64.deb ...
Unpacking libkeyutils1:amd64 (1.6.3-5) over (1.6.3-4) ...
Preparing to unpack .../02-libldap-2.5-0_2.5.19+dfsg-1_amd64.deb ...
Unpacking libldap-2.5-0:amd64 (2.5.19+dfsg-1) over (2.5.13+dfsg-5) ...
Preparing to unpack .../03-libtiff6_4.7.0-3_amd64.deb ...
Unpacking libtiff6:amd64 (4.7.0-3) over (4.7.0-2) ...
Selecting previously unselected package libzopfli1.
Preparing to unpack .../04-libzopfli1_1.0.3-3_amd64.deb ...
Unpacking libzopfli1 (1.0.3-3) ...
Preparing to unpack .../05-python-matplotlib-data_3.10.1+dfsg1-2_all.deb ...
Unpacking python-matplotlib-data (3.10.1+dfsg1-2) over (3.8.3-7) ...
Preparing to unpack .../06-python3-appdirs_1.4.4-4_all.deb ...
Unpacking python3-appdirs (1.4.4-4) over (1.4.4-3) ...
Preparing to unpack .../07-python3-decorator_5.2.1-1_all.deb ...
Unpacking python3-decorator (5.2.1-1) over (5.1.1-5) ...
Preparing to unpack .../08-python3-ufolib2_0.17.1+dfsg1-1_all.deb ...
Unpacking python3-ufolib2 (0.17.1+dfsg1-1) over (0.17.0+dfsg1-1) ...
Selecting previously unselected package python3-zopfli.
Preparing to unpack .../09-python3-zopfli_0.2.3.post1-1+b1_amd64.deb ...
Unpacking python3-zopfli (0.2.3.post1-1+b1) ...
Preparing to unpack .../10-python3-fonttools_4.57.0-1_amd64.deb ...
Unpacking python3-fonttools (4.57.0-1) over (4.55.3-2+b1) ...
Preparing to unpack .../11-python3-matplotlib_3.10.1+dfsg1-2_amd64.deb ...
Unpacking python3-matplotlib (3.10.1+dfsg1-2) over (3.8.3-7+b1) ...
Preparing to unpack .../12-python3-pytz_2025.2-1_all.deb ...
Unpacking python3-pytz (2025.2-1) over (2025.1-3) ...
Preparing to unpack .../13-python3-pandas-lib_2.2.3+dfsg-9_amd64.deb ...
Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-9) over (2.2.3+dfsg-8+b1) ...
Preparing to unpack .../14-python3-pandas_2.2.3+dfsg-9_all.deb ...
Unpacking python3-pandas (2.2.3+dfsg-9) over (2.2.3+dfsg-8) ...
Preparing to unpack .../15-python3-requests_2.32.3+dfsg-5_all.deb ...
Unpacking python3-requests (2.32.3+dfsg-5) over (2.32.3+dfsg-4) ...
Preparing to unpack .../16-python3-tz_2025.2-1_all.deb ...
Unpacking python3-tz (2025.2-1) over (2025.1-3) ...
Setting up libkeyutils1:amd64 (1.6.3-5) ...
Setting up python3-pytz (2025.2-1) ...
Setting up libldap-2.5-0:amd64 (2.5.19+dfsg-1) ...
Setting up python3-tz (2025.2-1) ...
Setting up python3-decorator (5.2.1-1) ...
Setting up libglib2.0-0t64:amd64 (2.84.1-1) ...
No schema files found: doing nothing.
Setting up libzopfli1 (1.0.3-3) ...
Setting up python3-requests (2.32.3+dfsg-5) ...
Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ...
Setting up python3-numpy (1:2.2.4+ds-1) ...
Setting up mount (2.41-3) ...
Setting up libtiff6:amd64 (4.7.0-3) ...
Setting up python-matplotlib-data (3.10.1+dfsg1-2) ...
Installing new version of config file /etc/matplotlibrc ...
Setting up python3-appdirs (1.4.4-4) ...
Setting up util-linux-extra (2.41-3) ...
Setting up login (1:4.16.0-2+really2.41-3) ...
Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-9) ...
Setting up python3-zopfli (0.2.3.post1-1+b1) ...
Setting up python3-pandas (2.2.3+dfsg-9) ...
Setting up python3-fonttools (4.57.0-1) ...
Setting up python3-ufolib2 (0.17.1+dfsg1-1) ...
Setting up python3-matplotlib (3.10.1+dfsg1-2) ...
Processing triggers for libc-bin (2.41-6) ...
3m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-yf', 'dist-upgrade']
3m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'sh', '-c', 'apt-cache dumpavail | md5sum']
3m12.6s DUMP:
d5f772eeb8e92a17191412f612b8f6fe -
3m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'sh', '-c', 'apt-cache dumpavail | md5sum']
3m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools']
3m12.9s DUMP:
Package: python3-pairtools
Source: pairtools (1.1.3-1)
Version: 1.1.3-1+b1
Installed-Size: 833
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: python3-standard-pipes, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), python3 (<< 3.14), python3 (>= 3.13~), python3-bioframe, python3-click, python3-numpy, python3-numpy2-abi0 | python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any
Suggests: python3-pairtools-examples (>= 1.0.2)
Description-en: Framework to process sequencing data from a Hi-C experiment
Simple and fast command-line framework to process sequencing data from a Hi-C
experiment.
.
Process pair-end sequence alignments and perform the following operations:
.
- Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end
sequences of Hi-C DNA molecules
- Sort .pairs files for downstream analyses
- Detect, tag and remove PCR/optical duplicates
- Generate extensive statistics of Hi-C datasets
- Select Hi-C pairs given flexibly defined criteria
- Restore .sam alignments from Hi-C pairs
Description-md5: a340132b5467a45fa9b90e04ece3e5c1
Homepage: https://github.com/mirnylab/pairtools
Section: python
Priority: optional
Filename: pool/main/p/pairtools/python3-pairtools_1.1.3-1+b1_amd64.deb
Size: 207068
MD5sum: 69eb3c6e74046d498e5aef47f8106f33
SHA256: 413bfb5ff113c99270df2798fb8b32782b7627157892fc057e223d414550e9ce
3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools']
3m12.9s INFO: apt-cache knows about the following packages: python3-pairtools
3m12.9s INFO: Running scripts pre_install
3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
3m13.0s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian sid/main amd64 Packages
release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
3m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
3m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
3m13.1s DUMP:
python3-pairtools:
Installed: 1.1.3-1+b1
Candidate: 1.1.3-1+b1
Version table:
*** 1.1.3-1+b1 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
3m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
3m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools']
3m13.6s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
python3-pairtools is already the newest version (1.1.3-1+b1).
The following packages were automatically installed and are no longer required:
cython3 libboost-dev libboost1.83-dev libfile-find-rule-perl libicu72
liblbfgsb0 libldap-2.5-0 libmpdec3 libnsl-dev libnumber-compare-perl
libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.36
libpython3-all-dev libpython3.11 libpython3.11-dev libpython3.11-minimal
libpython3.11-stdlib libpython3.9-minimal libpython3.9-stdlib
libtext-glob-perl libtirpc-dev libxsimd-dev perl-modules-5.36
python3-all-dev python3-appdirs python3-beniget python3-colorama
python3-gast python3-nose python3-ply python3-pythran python3-six python3.11
python3.11-dev python3.11-minimal python3.9 python3.9-minimal usrmerge
xtl-dev
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
3m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools']
3m13.6s INFO: Running scripts post_install
3m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
3m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
3m13.6s INFO: Running scripts post_distupgrade
3m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_base_cleanup']
3m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_base_cleanup']
3m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_exceptions']
3m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_exceptions']
3m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_force-unsafe-io']
3m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_force-unsafe-io']
3m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_squeeze-backports']
3m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_squeeze-backports']
3m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_zz_backports']
3m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_distupgrade_zz_backports']
3m13.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
3m16.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
3m16.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
3m18.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
3m18.4s INFO: Running scripts pre_install
3m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
3m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_database-server']
3m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
3m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_exceptions']
3m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
3m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_extras']
3m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
3m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture']
3m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
3m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_install_foreign_architecture_i386']
3m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
3m18.6s 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:
3m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy']
3m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
3m18.6s DUMP:
python3-pairtools:
Installed: 1.1.3-1+b1
Candidate: 1.1.3-1+b1
Version table:
*** 1.1.3-1+b1 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
3m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-cache', 'policy', 'python3-pairtools']
3m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools=1.1.3-1+b1']
3m19.2s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
python3-pairtools is already the newest version (1.1.3-1+b1).
The following packages were automatically installed and are no longer required:
cython3 libboost-dev libboost1.83-dev libfile-find-rule-perl libicu72
liblbfgsb0 libldap-2.5-0 libmpdec3 libnsl-dev libnumber-compare-perl
libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.36
libpython3-all-dev libpython3.11 libpython3.11-dev libpython3.11-minimal
libpython3.11-stdlib libpython3.9-minimal libpython3.9-stdlib
libtext-glob-perl libtirpc-dev libxsimd-dev perl-modules-5.36
python3-all-dev python3-appdirs python3-beniget python3-colorama
python3-gast python3-nose python3-ply python3-pythran python3-six python3.11
python3.11-dev python3.11-minimal python3.9 python3.9-minimal usrmerge
xtl-dev
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
3m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', 'install', 'python3-pairtools=1.1.3-1+b1']
3m19.2s INFO: Running scripts post_install
3m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
3m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/post_install_exceptions']
3m19.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
3m22.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
3m22.1s INFO: /lib converted to /usr/lib by /usr merge
3m22.1s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge
3m25.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', '-ac', '--ignore-obsolete']
3m31.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', '-ac', '--ignore-obsolete']
3m31.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
3m31.4s DUMP:
0.15.6
3m31.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
3m31.4s INFO: Running adequate version 0.15.6 now.
3m31.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'python3-pairtools']
3m31.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'python3-pairtools']
3m31.6s INFO: Running scripts pre_remove
3m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
3m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
3m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
3m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
3m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
3m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
3m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_50_find_bad_permissions']
3m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_50_find_bad_permissions']
3m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_50_find_missing_copyright']
3m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_50_find_missing_copyright']
3m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_exceptions']
3m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'tmp/scripts/pre_remove_exceptions']
3m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
3m39.7s DUMP:
install ok installed adduser adduser 3.150
install ok installed apt apt 3.0.0
install ok installed base-files base-files 13.7
install ok installed base-passwd base-passwd 3.6.7
install ok installed bash bash 5.2.37-1.1+b2
install ok installed binutils binutils 2.44-3
install ok installed binutils-common:amd64 binutils-common 2.44-3
install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.44-3
install ok installed blt blt 2.5.3+dfsg-8
install ok installed bsdutils bsdutils 1:2.41-3
install ok installed ca-certificates ca-certificates 20241223
install ok installed coreutils coreutils 9.6-2
install ok installed cpp cpp 4:14.2.0-1
install ok installed cpp-12 cpp-12 12.4.0-5
install ok installed cpp-14 cpp-14 14.2.0-19
install ok installed cpp-14-x86-64-linux-gnu cpp-14-x86-64-linux-gnu 14.2.0-19
install ok installed cpp-x86-64-linux-gnu cpp-x86-64-linux-gnu 4:14.2.0-1
install ok installed cython3 cython3 3.0.11+dfsg-2+b1
install ok installed dash dash 0.5.12-12
install ok installed debconf debconf 1.5.91
install ok installed debian-archive-keyring debian-archive-keyring 2023.4
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-3
install ok installed dpkg dpkg 1.22.18
install ok installed e2fsprogs e2fsprogs 1.47.2-1+b1
install ok installed findutils findutils 4.10.0-3
install ok installed fontconfig-config fontconfig-config 2.15.0-2.2
install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8
install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8
install ok installed fonts-lyx fonts-lyx 2.4.3-1
install ok installed g++ g++ 4:14.2.0-1
install ok installed g++-12 g++-12 12.4.0-5
install ok installed g++-14 g++-14 14.2.0-19
install ok installed g++-14-x86-64-linux-gnu g++-14-x86-64-linux-gnu 14.2.0-19
install ok installed g++-x86-64-linux-gnu g++-x86-64-linux-gnu 4:14.2.0-1
install ok installed gcc gcc 4:14.2.0-1
install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6
install ok installed gcc-12 gcc-12 12.4.0-5
install ok installed gcc-12-base:amd64 gcc-12-base 12.4.0-5
install ok installed gcc-14 gcc-14 14.2.0-19
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19
install ok installed gcc-14-x86-64-linux-gnu gcc-14-x86-64-linux-gnu 14.2.0-19
install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22
install ok installed gcc-x86-64-linux-gnu gcc-x86-64-linux-gnu 4:14.2.0-1
install ok installed gpgv gpgv 2.2.46-6
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-pkg6.0:amd64 libapt-pkg6.0 2.6.1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0
install ok installed libasan8:amd64 libasan8 14.2.0-19
install ok installed libatomic1:amd64 libatomic1 14.2.0-19
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+b2
install ok installed libbinutils:amd64 libbinutils 2.44-3
install ok installed libblas3:amd64 libblas3 3.12.1-2
install ok installed libblkid1:amd64 libblkid1 2.41-3
install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2
install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-4.2
install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7
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 2.41-6
install ok installed libc-dev-bin libc-dev-bin 2.41-6
install ok installed libc6:amd64 libc6 2.41-6
install ok installed libc6-dev:amd64 libc6-dev 2.41-6
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.75-4
install ok installed libcc1-0:amd64 libcc1-0 14.2.0-19
install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1+b1
install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.38-1
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1
install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.44-3
install ok installed libctf0:amd64 libctf0 2.44-3
install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.13.0-1
install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278
install ok installed libdeflate0:amd64 libdeflate0 1.23-1+b1
install ok installed libexpat1:amd64 libexpat1 2.7.1-1
install ok installed libexpat1-dev:amd64 libexpat1-dev 2.7.1-1
install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1+b1
install ok installed libffi7:amd64 libffi7 3.3-6
install ok installed libffi8:amd64 libffi8 3.4.7-1
install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3
install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2.2
install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1
install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1
install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.4.0-5
install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-19
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19
install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-7
install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2
install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2
install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19
deinstall ok config-files libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u5
install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.1-1
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 14.2.0-19
install ok installed libgpg-error0:amd64 libgpg-error0 1.51-4
install ok installed libgprofng0:amd64 libgprofng0 2.44-3
install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1
install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5
install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1+b1
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed libhts3t64:amd64 libhts3t64 1.21+ds-1
install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-2
install ok installed libhwasan0:amd64 libhwasan0 14.2.0-19
install ok installed libicu72:amd64 libicu72 72.1-6
install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2
install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2
install ok installed libisl23:amd64 libisl23 0.27-1
install ok installed libitm1:amd64 libitm1 14.2.0-19
install ok installed libjansson4:amd64 libjansson4 2.14-2+b3
install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2
install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3.1
install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1
install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1
install ok installed libjs-sphinxdoc libjs-sphinxdoc 8.1.3-5
install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3
install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-5
install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-5
install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-5
install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-5
install ok installed liblapack3:amd64 liblapack3 3.12.1-2
install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-3
install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b2
install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2
install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.19+dfsg-1
install ok installed libldap2:amd64 libldap2 2.6.9+dfsg-2
install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5
install ok installed liblsan0:amd64 liblsan0 14.2.0-19
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4
install ok installed liblzma5:amd64 liblzma5 5.8.1-1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.41-3
install ok installed libmpc3:amd64 libmpc3 1.3.1-1+b3
install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1
install ok installed libmpfr6:amd64 libmpfr6 4.2.2-1
install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2
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 1.8.0-1
install ok installed libngtcp2-16:amd64 libngtcp2-16 1.11.0-1
install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.11.0-1
install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3+b3
install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3
install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3
install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.29+ds-3
install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.29+ds-3
install ok installed libopenblas0:amd64 libopenblas0 0.3.29+ds-3
install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.29+ds-3
install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.3-2
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 libpcre3:amd64 libpcre3 2:8.39-15
install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1
install ok installed libperl5.40:amd64 libperl5.40 5.40.1-2
install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.47-1.1
install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1
install ok installed libpython3-all-dev:amd64 libpython3-all-dev 3.13.2-2
install ok installed libpython3-dev:amd64 libpython3-dev 3.13.2-2
install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.2-2
install ok installed libpython3.11:amd64 libpython3.11 3.11.2-6+deb12u5
install ok installed libpython3.11-dev:amd64 libpython3.11-dev 3.11.2-6+deb12u5
install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.2-6+deb12u5
install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6+deb12u5
install ok installed libpython3.13:amd64 libpython3.13 3.13.2-3
install ok installed libpython3.13-dev:amd64 libpython3.13-dev 3.13.2-3
install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.2-3
install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.2-3
install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1
install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1
install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2
install ok installed libquadmath0:amd64 libquadmath0 14.2.0-19
install ok installed libraqm0:amd64 libraqm0 0.10.2-1
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+dfsg1-9
install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-9
install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2
install ok installed libselinux1:amd64 libselinux1 3.8.1-1
install ok installed libsemanage-common libsemanage-common 3.8.1-1
install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1
install ok installed libsepol1:amd64 libsepol1 3.1-1
install ok installed libsepol2:amd64 libsepol2 3.8.1-1
install ok installed libsframe1:amd64 libsframe1 2.44-3
install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1
install ok installed libsmartcols1:amd64 libsmartcols1 2.41-3
install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2
install ok installed libss2:amd64 libss2 1.47.2-1+b1
install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1
install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1
install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1
install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.4.0-5
install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-19
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19
install ok installed libsystemd0:amd64 libsystemd0 257.4-9
install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2
install ok installed libtcl8.6:amd64 libtcl8.6 8.6.16+dfsg-1
install ok installed libtext-glob-perl libtext-glob-perl 0.11-3
install ok installed libtiff6:amd64 libtiff6 4.7.0-3
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2
install ok installed libtirpc-common libtirpc-common 1.3.6+ds-1
install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.6+ds-1
install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.6+ds-1
install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1
install ok installed libtsan2:amd64 libtsan2 14.2.0-19
install ok installed libubsan1:amd64 libubsan1 14.2.0-19
install ok installed libudev1:amd64 libudev1 257.4-9
install ok installed libunistring2:amd64 libunistring2 1.0-2
install ok installed libunistring5:amd64 libunistring5 1.3-2
install ok installed libuuid1:amd64 libuuid1 2.41-3
install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1
install ok installed libwebpdemux2:amd64 libwebpdemux2 1.5.0-0.1
install ok installed libwebpmux3:amd64 libwebpmux3 1.5.0-0.1
install ok installed libx11-6:amd64 libx11-6 2:1.8.12-1
install ok installed libx11-data libx11-data 2:1.8.12-1
install ok installed libxau6:amd64 libxau6 1:1.0.11-1
install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1
install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1
install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3
install ok installed libxft2:amd64 libxft2 2.3.6-1+b4
install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.4
install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1
install ok installed libxsimd-dev:amd64 libxsimd-dev 13.2.0-1
install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.2
install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b3
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-2
install ok installed libzopfli1 libzopfli1 1.0.3-3
install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1
install ok installed linux-libc-dev linux-libc-dev 6.12.21-1
install ok installed login login 1:4.16.0-2+really2.41-3
install ok installed login.defs login.defs 1:4.17.4-1
install ok installed logsave logsave 1.47.2-1+b1
install ok installed lsb-base lsb-base 11.6
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed media-types media-types 13.0.0
install ok installed mount mount 2.41-3
install ok installed ncurses-base ncurses-base 6.5+20250216-2
install ok installed ncurses-bin ncurses-bin 6.5+20250216-2
install ok installed netbase netbase 6.5
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 1:4.17.4-1
install ok installed perl perl 5.40.1-2
install ok installed perl-base perl-base 5.40.1-2
install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1
install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-2
install ok installed python-matplotlib-data python-matplotlib-data 3.10.1+dfsg1-2
install ok installed python3 python3 3.13.2-2
install ok installed python3-all python3-all 3.13.2-2
install ok installed python3-all-dev python3-all-dev 3.13.2-2
install ok installed python3-appdirs python3-appdirs 1.4.4-4
install ok installed python3-attr python3-attr 25.3.0-1
install ok installed python3-autocommand python3-autocommand 2.2.2-3
install ok installed python3-beniget python3-beniget 0.4.1-3
install ok installed python3-bioframe python3-bioframe 0.4.1-2
install ok installed python3-brotli python3-brotli 1.1.0-2+b7
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+b1
install ok installed python3-click python3-click 8.2.0+0.really.8.1.8-1
install ok installed python3-colorama python3-colorama 0.4.6-4
install ok installed python3-contourpy python3-contourpy 1.3.1-1+b1
install ok installed python3-cycler python3-cycler 0.12.1-1
install ok installed python3-dateutil python3-dateutil 2.9.0-4
install ok installed python3-decorator python3-decorator 5.2.1-1
install ok installed python3-dev python3-dev 3.13.2-2
install ok installed python3-fonttools python3-fonttools 4.57.0-1
install ok installed python3-fs python3-fs 2.4.16-7
install ok installed python3-gast python3-gast 0.6.0-1
install ok installed python3-idna python3-idna 3.10-1
install ok installed python3-inflect python3-inflect 7.3.1-2
install ok installed python3-jaraco.context python3-jaraco.context 6.0.1-1
install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1
install ok installed python3-jaraco.text python3-jaraco.text 4.0.0-1
install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-3+b1
install ok installed python3-lxml:amd64 python3-lxml 5.3.1-1+b1
install ok installed python3-lz4 python3-lz4 4.4.0+dfsg-2
install ok installed python3-matplotlib python3-matplotlib 3.10.1+dfsg1-2
install ok installed python3-minimal python3-minimal 3.13.2-2
install ok installed python3-more-itertools python3-more-itertools 10.6.0-1
install ok installed python3-mpmath python3-mpmath 1.3.0-1
install ok installed python3-nose python3-nose 1.3.7-9
install ok installed python3-numpy python3-numpy 1:2.2.4+ds-1
install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.4+ds-1
install ok installed python3-packaging python3-packaging 24.2-1
install ok installed python3-pairtools python3-pairtools 1.1.3-1+b1
install ok installed python3-pandas python3-pandas 2.2.3+dfsg-9
install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.2.3+dfsg-9
install ok installed python3-pil:amd64 python3-pil 11.1.0-5+b1
install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 11.1.0-5+b1
install ok installed python3-pkg-resources python3-pkg-resources 75.8.0-1
install ok installed python3-platformdirs python3-platformdirs 4.3.7-1
install ok installed python3-ply python3-ply 3.11-9
install ok installed python3-pyparsing python3-pyparsing 3.1.2-1
install ok installed python3-pysam python3-pysam 0.23.0+ds-1+b1
install ok installed python3-pythran python3-pythran 0.17.0+ds-1
install ok installed python3-pytz python3-pytz 2025.2-1
install ok installed python3-requests python3-requests 2.32.3+dfsg-5
install ok installed python3-scipy python3-scipy 1.15.2-7
install ok installed python3-setuptools python3-setuptools 75.8.0-1
install ok installed python3-six python3-six 1.17.0-1
install ok installed python3-standard-pipes python3-standard-pipes 3.13.0-5
install ok installed python3-sympy python3-sympy 1.13.3-5
install ok installed python3-tk:amd64 python3-tk 3.13.2-1
install ok installed python3-typeguard python3-typeguard 4.4.2-1
install ok installed python3-typing-extensions python3-typing-extensions 4.13.0-1
install ok installed python3-tz python3-tz 2025.2-1
install ok installed python3-ufolib2 python3-ufolib2 0.17.1+dfsg1-1
install ok installed python3-urllib3 python3-urllib3 2.3.0-2
install ok installed python3-yaml python3-yaml 6.0.2-1+b2
install ok installed python3-zipp python3-zipp 3.21.0-1
install ok installed python3-zopfli python3-zopfli 0.2.3.post1-1+b1
install ok installed python3.11 python3.11 3.11.2-6+deb12u5
install ok installed python3.11-dev python3.11-dev 3.11.2-6+deb12u5
install ok installed python3.11-minimal python3.11-minimal 3.11.2-6+deb12u5
install ok installed python3.13 python3.13 3.13.2-3
install ok installed python3.13-dev python3.13-dev 3.13.2-3
install ok installed python3.13-minimal python3.13-minimal 3.13.2-3
install ok installed python3.13-tk python3.13-tk 3.13.2-3
install ok installed python3.9 python3.9 3.9.2-1
install ok installed python3.9-minimal python3.9-minimal 3.9.2-1
install ok installed readline-common readline-common 8.2-6
install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1
install ok installed sed sed 4.9-2
install ok installed sqv sqv 1.3.0-1
install ok installed sysvinit-utils sysvinit-utils 3.14-4
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-8
install ok installed tzdata tzdata 2025b-1
install ok installed unicode-data unicode-data 15.1.0-1
install ok installed usrmerge usrmerge 39+nmu2
install ok installed util-linux util-linux 2.41-3
install ok installed util-linux-extra util-linux-extra 2.41-3
install ok installed x11-common x11-common 1:7.7+24
install ok installed xtl-dev xtl-dev 0.7.7-1
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1+b1
3m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
3m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libgnutls30:amd64=3.7.9-2+deb12u4', 'binutils-', 'binutils-common:amd64-', 'binutils-x86-64-linux-gnu-', 'blt-', 'ca-certificates-', 'cpp-', 'cpp-12-', 'cpp-14-', 'cpp-14-x86-64-linux-gnu-', 'cpp-x86-64-linux-gnu-', 'cython3-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'fonts-lyx-', 'g++-', 'g++-12-', 'g++-14-', 'g++-14-x86-64-linux-gnu-', 'g++-x86-64-linux-gnu-', 'gcc-', 'gcc-12-', 'gcc-14-', 'gcc-14-x86-64-linux-gnu-', 'gcc-x86-64-linux-gnu-', 'libasan8:amd64-', 'libatomic1:amd64-', 'libbinutils:amd64-', 'libblas3:amd64-', 'libboost-dev:amd64-', 'libboost1.83-dev:amd64-', 'libbrotli1:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcc1-0:amd64-', 'libcrypt-dev:amd64-', 'libctf-nobfd0:amd64-', 'libctf0:amd64-', 'libcurl3t64-gnutls:amd64-', 'libdeflate0:amd64-', 'libexpat1:amd64-', 'libexpat1-dev:amd64-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgcc-12-dev:amd64-', 'libgcc-14-dev:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgnutls30t64:amd64-', 'libgomp1:amd64-', 'libgprofng0:amd64-', 'libgraphite2-3:amd64-', 'libharfbuzz0b:amd64-', 'libhts3t64:amd64-', 'libhtscodecs2:amd64-', 'libhwasan0:amd64-', 'libicu72:amd64-', 'libimagequant0:amd64-', 'libisl23:amd64-', 'libitm1:amd64-', 'libjansson4:amd64-', 'libjbig0:amd64-', 'libjpeg62-turbo:amd64-', 'libjs-jquery-', 'libjs-jquery-ui-', 'libjs-sphinxdoc-', 'libjs-underscore-', 'liblapack3:amd64-', 'liblbfgsb0:amd64-', 'liblcms2-2:amd64-', 'libldap-2.5-0:amd64-', 'libldap2:amd64-', 'liblerc4:amd64-', 'liblsan0:amd64-', 'libmpc3:amd64-', 'libmpdec3:amd64-', 'libmpfr6:amd64-', 'libncursesw6:amd64-', 'libnghttp2-14:amd64-', 'libnghttp3-9:amd64-', 'libngtcp2-16:amd64-', 'libngtcp2-crypto-gnutls8:amd64-', 'libnsl-dev:amd64-', 'libopenblas-dev:amd64-', 'libopenblas-pthread-dev:amd64-', 'libopenblas0:amd64-', 'libopenblas0-pthread:amd64-', 'libopenjp2-7:amd64-', 'libpng16-16t64:amd64-', 'libpsl5t64:amd64-', 'libpython3-all-dev:amd64-', 'libpython3-dev:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11:amd64-', 'libpython3.11-dev:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.13:amd64-', 'libpython3.13-dev:amd64-', 'libpython3.13-minimal:amd64-', 'libpython3.13-stdlib:amd64-', 'libpython3.9-minimal:amd64-', 'libpython3.9-stdlib:amd64-', 'libqhull-r8.0:amd64-', 'libquadmath0:amd64-', 'libraqm0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsframe1:amd64-', 'libsharpyuv0:amd64-', 'libssh2-1t64:amd64-', 'libstdc++-12-dev:amd64-', 'libstdc++-14-dev:amd64-', 'libtcl8.6:amd64-', 'libtiff6:amd64-', 'libtirpc-dev:amd64-', 'libtk8.6:amd64-', 'libtsan2:amd64-', 'libubsan1:amd64-', 'libwebp7:amd64-', 'libwebpdemux2:amd64-', 'libwebpmux3:amd64-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxml2:amd64-', 'libxrender1:amd64-', 'libxsimd-dev:amd64-', 'libxslt1.1:amd64-', 'libxss1:amd64-', 'libyaml-0-2:amd64-', 'libzopfli1-', 'linux-libc-dev-', 'media-types-', 'netbase-', 'openssl-', 'python-matplotlib-data-', 'python3-', 'python3-all-', 'python3-all-dev-', 'python3-appdirs-', 'python3-attr-', 'python3-autocommand-', 'python3-beniget-', 'python3-bioframe-', 'python3-brotli-', 'python3-certifi-', 'python3-chardet-', 'python3-charset-normalizer-', 'python3-click-', 'python3-colorama-', 'python3-contourpy-', 'python3-cycler-', 'python3-dateutil-', 'python3-decorator-', 'python3-dev-', 'python3-fonttools-', 'python3-fs-', 'python3-gast-', 'python3-idna-', 'python3-inflect-', 'python3-jaraco.context-', 'python3-jaraco.functools-', 'python3-jaraco.text-', 'python3-kiwisolver-', 'python3-lxml:amd64-', 'python3-lz4-', 'python3-matplotlib-', 'python3-minimal-', 'python3-more-itertools-', 'python3-mpmath-', 'python3-nose-', 'python3-numpy-', 'python3-numpy-dev:amd64-', 'python3-packaging-', 'python3-pandas-', 'python3-pandas-lib:amd64-', 'python3-pil:amd64-', 'python3-pil.imagetk:amd64-', 'python3-pkg-resources-', 'python3-platformdirs-', 'python3-ply-', 'python3-pyparsing-', 'python3-pysam-', 'python3-pythran-', 'python3-pytz-', 'python3-requests-', 'python3-scipy-', 'python3-setuptools-', 'python3-six-', 'python3-standard-pipes-', 'python3-sympy-', 'python3-tk:amd64-', 'python3-typeguard-', 'python3-typing-extensions-', 'python3-tz-', 'python3-ufolib2-', 'python3-urllib3-', 'python3-yaml-', 'python3-zipp-', 'python3-zopfli-', 'python3.11-', 'python3.11-dev-', 'python3.11-minimal-', 'python3.13-', 'python3.13-dev-', 'python3.13-minimal-', 'python3.13-tk-', 'python3.9-', 'python3.9-minimal-', 'readline-common-', 'rpcsvc-proto-', 'tk8.6-blt2.5-', 'unicode-data-', 'x11-common-', 'xtl-dev-', 'zlib1g-dev:amd64-', 'python3-pairtools-']
3m39.9s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Package libgnutls30 is a virtual package provided by:
libgnutls30t64 3.8.9-2 (= 3.8.9-2)
W: --force-yes is deprecated, use one of the options starting with --allow instead.
E: Version '3.7.9-2+deb12u4' for 'libgnutls30' was not found
3m39.9s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libgnutls30:amd64=3.7.9-2+deb12u4', 'binutils-', 'binutils-common:amd64-', 'binutils-x86-64-linux-gnu-', 'blt-', 'ca-certificates-', 'cpp-', 'cpp-12-', 'cpp-14-', 'cpp-14-x86-64-linux-gnu-', 'cpp-x86-64-linux-gnu-', 'cython3-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'fonts-lyx-', 'g++-', 'g++-12-', 'g++-14-', 'g++-14-x86-64-linux-gnu-', 'g++-x86-64-linux-gnu-', 'gcc-', 'gcc-12-', 'gcc-14-', 'gcc-14-x86-64-linux-gnu-', 'gcc-x86-64-linux-gnu-', 'libasan8:amd64-', 'libatomic1:amd64-', 'libbinutils:amd64-', 'libblas3:amd64-', 'libboost-dev:amd64-', 'libboost1.83-dev:amd64-', 'libbrotli1:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcc1-0:amd64-', 'libcrypt-dev:amd64-', 'libctf-nobfd0:amd64-', 'libctf0:amd64-', 'libcurl3t64-gnutls:amd64-', 'libdeflate0:amd64-', 'libexpat1:amd64-', 'libexpat1-dev:amd64-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgcc-12-dev:amd64-', 'libgcc-14-dev:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgnutls30t64:amd64-', 'libgomp1:amd64-', 'libgprofng0:amd64-', 'libgraphite2-3:amd64-', 'libharfbuzz0b:amd64-', 'libhts3t64:amd64-', 'libhtscodecs2:amd64-', 'libhwasan0:amd64-', 'libicu72:amd64-', 'libimagequant0:amd64-', 'libisl23:amd64-', 'libitm1:amd64-', 'libjansson4:amd64-', 'libjbig0:amd64-', 'libjpeg62-turbo:amd64-', 'libjs-jquery-', 'libjs-jquery-ui-', 'libjs-sphinxdoc-', 'libjs-underscore-', 'liblapack3:amd64-', 'liblbfgsb0:amd64-', 'liblcms2-2:amd64-', 'libldap-2.5-0:amd64-', 'libldap2:amd64-', 'liblerc4:amd64-', 'liblsan0:amd64-', 'libmpc3:amd64-', 'libmpdec3:amd64-', 'libmpfr6:amd64-', 'libncursesw6:amd64-', 'libnghttp2-14:amd64-', 'libnghttp3-9:amd64-', 'libngtcp2-16:amd64-', 'libngtcp2-crypto-gnutls8:amd64-', 'libnsl-dev:amd64-', 'libopenblas-dev:amd64-', 'libopenblas-pthread-dev:amd64-', 'libopenblas0:amd64-', 'libopenblas0-pthread:amd64-', 'libopenjp2-7:amd64-', 'libpng16-16t64:amd64-', 'libpsl5t64:amd64-', 'libpython3-all-dev:amd64-', 'libpython3-dev:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11:amd64-', 'libpython3.11-dev:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.13:amd64-', 'libpython3.13-dev:amd64-', 'libpython3.13-minimal:amd64-', 'libpython3.13-stdlib:amd64-', 'libpython3.9-minimal:amd64-', 'libpython3.9-stdlib:amd64-', 'libqhull-r8.0:amd64-', 'libquadmath0:amd64-', 'libraqm0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsframe1:amd64-', 'libsharpyuv0:amd64-', 'libssh2-1t64:amd64-', 'libstdc++-12-dev:amd64-', 'libstdc++-14-dev:amd64-', 'libtcl8.6:amd64-', 'libtiff6:amd64-', 'libtirpc-dev:amd64-', 'libtk8.6:amd64-', 'libtsan2:amd64-', 'libubsan1:amd64-', 'libwebp7:amd64-', 'libwebpdemux2:amd64-', 'libwebpmux3:amd64-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxml2:amd64-', 'libxrender1:amd64-', 'libxsimd-dev:amd64-', 'libxslt1.1:amd64-', 'libxss1:amd64-', 'libyaml-0-2:amd64-', 'libzopfli1-', 'linux-libc-dev-', 'media-types-', 'netbase-', 'openssl-', 'python-matplotlib-data-', 'python3-', 'python3-all-', 'python3-all-dev-', 'python3-appdirs-', 'python3-attr-', 'python3-autocommand-', 'python3-beniget-', 'python3-bioframe-', 'python3-brotli-', 'python3-certifi-', 'python3-chardet-', 'python3-charset-normalizer-', 'python3-click-', 'python3-colorama-', 'python3-contourpy-', 'python3-cycler-', 'python3-dateutil-', 'python3-decorator-', 'python3-dev-', 'python3-fonttools-', 'python3-fs-', 'python3-gast-', 'python3-idna-', 'python3-inflect-', 'python3-jaraco.context-', 'python3-jaraco.functools-', 'python3-jaraco.text-', 'python3-kiwisolver-', 'python3-lxml:amd64-', 'python3-lz4-', 'python3-matplotlib-', 'python3-minimal-', 'python3-more-itertools-', 'python3-mpmath-', 'python3-nose-', 'python3-numpy-', 'python3-numpy-dev:amd64-', 'python3-packaging-', 'python3-pandas-', 'python3-pandas-lib:amd64-', 'python3-pil:amd64-', 'python3-pil.imagetk:amd64-', 'python3-pkg-resources-', 'python3-platformdirs-', 'python3-ply-', 'python3-pyparsing-', 'python3-pysam-', 'python3-pythran-', 'python3-pytz-', 'python3-requests-', 'python3-scipy-', 'python3-setuptools-', 'python3-six-', 'python3-standard-pipes-', 'python3-sympy-', 'python3-tk:amd64-', 'python3-typeguard-', 'python3-typing-extensions-', 'python3-tz-', 'python3-ufolib2-', 'python3-urllib3-', 'python3-yaml-', 'python3-zipp-', 'python3-zopfli-', 'python3.11-', 'python3.11-dev-', 'python3.11-minimal-', 'python3.13-', 'python3.13-dev-', 'python3.13-minimal-', 'python3.13-tk-', 'python3.9-', 'python3.9-minimal-', 'readline-common-', 'rpcsvc-proto-', 'tk8.6-blt2.5-', 'unicode-data-', 'x11-common-', 'xtl-dev-', 'zlib1g-dev:amd64-', 'python3-pairtools-']
Reading package lists...
Building dependency tree...
Reading state information...
Package libgnutls30 is a virtual package provided by:
libgnutls30t64 3.8.9-2 (= 3.8.9-2)
W: --force-yes is deprecated, use one of the options starting with --allow instead.
E: Version '3.7.9-2+deb12u4' for 'libgnutls30' was not found
3m42.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/shm']
3m42.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/shm']
3m42.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/console']
3m42.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/console']
3m42.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/ptmx']
3m42.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/ptmx']
3m42.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/pts']
3m42.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/dev/pts']
3m42.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/proc']
3m42.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq/proc']
3m42.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
3m44.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpdq6cj8uq']
3m44.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpdq6cj8uq
3m44.0s ERROR: piuparts run ends.
ret=1
End: 2025-04-06 23:44:53 GMT